RCSB PDB: Search

6P1M \| pdb_00006p1m	Download File View File

Binary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCP(8OG)PTPAPCPG)-3') (nucleic acid) DNA (5'-D(CPGPTPA)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	BR, CL, CO2, EDO, K

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6P1N \| pdb_00006p1n	Download File View File

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming dAMPNPP

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCP(8OG)PTPAPCPG)-3') (nucleic acid) DNA (5'-D(CPGPTPA)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	CL, DZ4, EDO, EPE, MG, NA

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6P1O \| pdb_00006p1o	Download File View File

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated dAMP

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCP(8OG)PTPAPCPG)-3') (nucleic acid) DNA (5'-D(CPGPTPAPA)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid)
Unique Ligands	ATP, CL, EDO, EPE, MG, MN, NA, PPV

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6P1P \| pdb_00006p1p	Download File View File

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming dCMPNPP

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCP(8OG)PTPAPCPG)-3') (nucleic acid) DNA (5'-D(CPGPTPA)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	0KX, CL, EDO, EPE, MG, NA

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6P1Q \| pdb_00006p1q	Download File View File

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated dCMP

Pedersen, L.C., Kaminski, A.M., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCP(8OG)PTPAPCPG)-3') (nucleic acid) DNA (5'-D(CPGPTPAPC)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid)
Unique Ligands	CL, EPE, MG, NA, PPV

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6P1R \| pdb_00006p1r	Download File View File

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming AMPNPP

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.701 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCP(8OG)PTPAPCPG)-3') (nucleic acid) DNA (5'-D(CPGPTPA)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	CL, EPE, MG, NA, ZAN

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6P1S \| pdb_00006p1s	Download File View File

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated AMP

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCP(8OG)PTPAPCPG)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid) DNA/RNA (5'-D(CPGPTPA)-R(PA)-3') (hybrid)
Unique Ligands	ATP, CL, EDO, EPE, MN, NA

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6P1T \| pdb_00006p1t	Download File View File

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound CMPCPP

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCP(8OG)PTPAPCPG)-3') (nucleic acid) DNA (5'-D(CPGPTPA)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	2TM, CL, EDO, EPE, MG, NA

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6P1U \| pdb_00006p1u	Download File View File

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated CMP

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCP(8OG)PTPAPCPG)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid) DNA/RNA (5'-D(CPGPTPA)-R(PC)-3') (hybrid)
Unique Ligands	CL, CTP, EDO, EPE, MN, NA, PPV

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6P1V \| pdb_00006p1v	Download File View File

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing undamaged template dG and bound incoming dCMPNPP

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCPGPTPAPCPG)-3') (nucleic acid) DNA (5'-D(CPGPTPA)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	0KX, CL, EDO, EPE, MG, NA

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6P1W \| pdb_00006p1w	Download File View File

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing undamaged template dG and bound incoming CMPCPP

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Chiruvella, K.K., Ramsden, D.A., Kunkel, T.A.

(2019) Nucleic Acids Res 47: 9410-9422

Released	2019-09-04
Method	X-RAY DIFFRACTION 1.751 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(CPGPGPCPGPTPAPCPG)-3') (nucleic acid) DNA (5'-D(CPGPTPA)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	2TM, CL, EDO, EPE, MG, NA

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6WIC \| pdb_00006wic	Download File View File

Pre-catalytic quaternary complex of human Polymerase Mu on a complementary DNA double-strand break substrate

Kaminski, A.M., Kunkel, T.A., Pedersen, L.C., Bebenek, K.

(2020) Nat Commun 11: 4784-4784

Released	2020-10-07
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(APCPG)-3') (nucleic acid) DNA (5'-D(CPGPGPCPAPT)-3') (nucleic acid) DNA (5'-D(CPGPTPA)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	1PE, CL, DUP, GOL, K, MG, NA, PEG

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6WID \| pdb_00006wid	Download File View File

Nucleotide incorporation intermediate into quaternary complex of human Polymerase Mu on a complementary DNA double-strand break substrate

Kaminski, A.M., Kunkel, T.A., Pedersen, L.C., Bebenek, K.

(2020) Nat Commun 11: 4784-4784

Released	2020-10-07
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(APCPG)-3') (nucleic acid) DNA (5'-D(CPGPGPCPAPT)-3') (nucleic acid) DNA (5'-D(CPGPTPAPT)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid)
Unique Ligands	1PE, CL, DUP, GOL, MG, NA, PEG, PPV

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6WIE \| pdb_00006wie	Download File View File

Post-catalytic nicked complex of human Polymerase Mu on a complementary DNA double-strand break substrate

Kaminski, A.M., Kunkel, T.A., Pedersen, L.C., Bebenek, K.

(2020) Nat Commun 11: 4784-4784

Released	2020-10-07
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-directed DNA/RNA polymerase mu (protein) DNA (5'-D(APCPG)-3') (nucleic acid) DNA (5'-D(CPGPGPCPAPT)-3') (nucleic acid) DNA (5'-D(CPGPTPAPT)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid)
Unique Ligands	1PE, CL, GOL, MG, NA, PEG, PPV, SO4

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7M07 \| pdb_00007m07	Download File View File

Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP

Kaminski, A.M., Bebenek, K., Pedersen, L.C., Kunkel, T.A.

(2022) Nat Commun 13: 3806-3806

Released	2022-03-16
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(CPAPGPTPAPC)-3') (nucleic acid) DNA (5'-D(CPGPGPCPAPGPTPAPCPTPG)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	CL, DUP, EDO, MG, NA

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7M08 \| pdb_00007m08	Download File View File

Post-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP

Kaminski, A.M., Bebenek, K., Pedersen, L.C., Kunkel, T.A.

Not Published

Released	2022-03-16
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(CPAPGPTPAPCPT)-3') (nucleic acid) DNA (5'-D(CPGPGPCPAPGPTPAPCPTPG)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid)
Unique Ligands	ACT, CL, EDO, MG, NA

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7M09 \| pdb_00007m09	Download File View File

Pre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate and incoming dUMPNPP

Kaminski, A.M., Bebenek, K., Pedersen, L.C., Kunkel, T.A.

(2022) Nat Commun 13: 3806-3806

Released	2022-03-16
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(CPAPGPTPGPC)-3') (nucleic acid) DNA (5'-D(CPGPGPCPA)-3') (nucleic acid) DNA (5'-D(GPCPAPCPTPG)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	CA, CL, DUP, GOL, MG, NA

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7M0A \| pdb_00007m0a	Download File View File

Incomplete in crystallo incorporation by DNA Polymerase Lambda bound to blunt-ended DSB substrate and incoming dTTP

Kaminski, A.M., Bebenek, K., Pedersen, L.C., Kunkel, T.A.

(2022) Nat Commun 13: 3806-3806

Released	2022-03-16
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(CPAPGPTPGPCPT)-3') (nucleic acid) DNA (5'-D(CPGPGPCPA)-3') (nucleic acid) DNA (5'-D(GPCPAPCPTPG)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid)
Unique Ligands	CA, CL, GOL, MG, NA, PPV, TTP

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7M0B \| pdb_00007m0b	Download File View File

Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound mismatched DSB and incoming dUMPNPP

Kaminski, A.M., Bebenek, K., Pedersen, L.C., Kunkel, T.A.

(2022) Nat Commun 13: 3806-3806

Released	2022-03-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(CPAPGPTPGPC)-3') (nucleic acid) DNA (5'-D(CPGPGPCPAPG)-3') (nucleic acid) DNA (5'-D(TPAPCPTPG)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	CL, DUP, EDO, MG, NA, SO4

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7M0C \| pdb_00007m0c	Download File View File

Post-catalytic nicked complex of DNA Polymerase Lambda with bound mismatched DSB substrate

Kaminski, A.M., Bebenek, K., Pedersen, L.C., Kunkel, T.A.

Not Published

Released	2022-03-16
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(CPAPGPTPGPCPT)-3') (nucleic acid) DNA (5'-D(CPGPGPCPAPG)-3') (nucleic acid) DNA (5'-D(TPAPCPTPG)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid)
Unique Ligands	CL, EDO, MG, NA, PPV, SO4

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7M0D \| pdb_00007m0d	Download File View File

Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound complementary DSB substrate and incoming dUMPNPP

Kaminski, A.M., Bebenek, K., Pedersen, L.C., Kunkel, T.A.

(2022) Nat Commun 13: 3806-3806

Released	2022-03-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(APCPTPG)-3') (nucleic acid) DNA (5'-D(CPAPGPTPGPC)-3') (nucleic acid) DNA (5'-D(CPGPGPCPAPGPC)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	CIT, CL, DUP, EDO, FMT, K, MG, NA, TRS

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7M0E \| pdb_00007m0e	Download File View File

Pre-catalytic synaptic complex of DNA Polymerase Lambda with gapped DSB substrate and incoming dUMPNPP

Kaminski, A.M., Bebenek, K., Pedersen, L.C., Kunkel, T.A.

(2022) Nat Commun 13: 3806-3806

Released	2022-03-16
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(CPAPGPTPGPC)-3') (nucleic acid) DNA (5'-D(CPGPGPCPAPGPC)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	DUP, EDO, MG, NA, SO4

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7SCD \| pdb_00007scd	Download File View File

Ternary complex of fixed-arm Trx-3ost5 (I299E) with 8mer-1 octasaccharide substrate and co-factor product PAP

Wander, R., Kaminski, A.M., Krahn, J.M., Liu, J., Pedersen, L.C.

(2021) ACS Catal 11: 14956-14966

Released	2022-01-19
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia coli K-12 Homo sapiens
Macromolecule	Thioredoxin 1,Heparan sulfate glucosamine 3-O-sulfotransferase 5 (protein)
Unique Ligands	A3P
Unique branched monosaccharides	BDP, SGN

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7SCE \| pdb_00007sce	Download File View File

Ternary complex of fixed-arm Trx-3ost5 (I299E) with 8mer-2 octasaccharide substrate and co-factor product PAP

Wander, R., Kaminski, A.M., Krahn, J.M., Liu, J., Pedersen, L.C.

(2021) ACS Catal 11: 14956-14966

Released	2022-01-19
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Escherichia coli K-12 Homo sapiens
Macromolecule	Thioredoxin 1,Heparan sulfate glucosamine 3-O-sulfotransferase 5 (protein)
Unique Ligands	A3P
Unique branched monosaccharides	BDP, IDS, SGN

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8U0O \| pdb_00008u0o	Download File View File

Synaptic complex of human DNA polymerase Lambda DL variant engaged on a DNA double-strand break containing an unpaired 3' primer terminus

Kaminski, A.M., Pedersen, L.C., Bebenek, K., Kunkel, T.A., Chiruvella, K.K., Ramsden, D.A.

(2024) DNA Repair (Amst) 136: 103645-103645

Released	2024-03-13
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(APCPGPCPGPGPCPA)-3') (nucleic acid) DNA (5'-D(PGPCPCPGPCPGPTPA)-3') (nucleic acid)
Unique Ligands	CL, EDO, NA, PO4

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

6P1M | pdb_00006p1m

6P1N | pdb_00006p1n

6P1O | pdb_00006p1o

6P1P | pdb_00006p1p

6P1Q | pdb_00006p1q

6P1R | pdb_00006p1r

6P1S | pdb_00006p1s

6P1T | pdb_00006p1t

6P1U | pdb_00006p1u

6P1V | pdb_00006p1v

6P1W | pdb_00006p1w

6WIC | pdb_00006wic

6WID | pdb_00006wid

6WIE | pdb_00006wie

7M07 | pdb_00007m07

7M08 | pdb_00007m08

7M09 | pdb_00007m09

7M0A | pdb_00007m0a

7M0B | pdb_00007m0b

7M0C | pdb_00007m0c

7M0D | pdb_00007m0d

7M0E | pdb_00007m0e

7SCD | pdb_00007scd

7SCE | pdb_00007sce

8U0O | pdb_00008u0o