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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Koerber, J.T."

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Search Summary

This query matches 25 Structures.

Refinements

Structure Determination Methodology

experimental (25)

Scientific Name of Source Organism

	Homo sapiens (25)
	Oryctolagus cuniculus (3)
	Aequorea victoria (1)
	Glycine max (1)
	Human adenovirus 2 (1)
	Lama glama (1)
	Mus musculus (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (25)
	Varidnaviria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (21)
	ELECTRON MICROSCOPY (4)

Polymer Entity Type

Protein (25)

Refinement Resolution (Å)

	1.5 - 2.0 (8)
	2.0 - 2.5 (8)
	2.5 - 3.0 (4)
	3.0 - 3.5 (5)

Release Date

	2010 - 2014 (10)
	2015 - 2019 (1)
	2020 - 2024 (14)

Enzyme Classification Name

	Hydrolases (13)
	Oxidoreductases (1)

Membrane Protein Annotation

	PDBTM (4)
	MemProtMD (2)
	OPM (2)
	mpstruc (2)

Symmetry Type

	Asymmetric (17)
	Cyclic (7)
	Dihedral (1)

SCOP Classification

	All beta proteins (7)
	Alpha and beta proteins (a/b) (5)
	Artifacts (5)

AllSelected

1 to 25 of 25 Structures

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4JFX \| pdb_00004jfx	Download File View File

Structure of phosphotyrosine (pTyr) scaffold bound to pTyr peptide

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-09-25
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) Phosphopeptide (protein)
Unique Ligands	PG4

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4JFY \| pdb_00004jfy	Download File View File

Apo structure of phosphotyrosine (pYAb) scaffold

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-08-28
Method	X-RAY DIFFRACTION 2.63 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein)
Unique Ligands	PG4

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4JFZ \| pdb_00004jfz	Download File View File

Structure of phosphoserine (pSAb) scaffold bound to pSer peptide

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-08-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) Phosphopeptide (protein)
Unique Ligands	PPI

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4JG0 \| pdb_00004jg0	Download File View File

Structure of phosphoserine/threonine (pSTAb) scaffold bound to pSer peptide

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-08-28
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) Phosphopeptide (protein)
Unique Ligands	PPI

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4JG1 \| pdb_00004jg1	Download File View File

Structure of phosphoserine/threonine (pSTAb) scaffold bound to pThr peptide

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-08-28
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) Phosphopeptide (protein)
Unique Ligands	PPI

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4JQY \| pdb_00004jqy	Download File View File

Human procaspase-3, crystal form 1

Thomsen, N.D., Wells, J.A.

(2013) Proc Natl Acad Sci U S A 110: 8477-8482

Released	2013-05-08
Method	X-RAY DIFFRACTION 2.495 Å
Organisms	Homo sapiens
Macromolecule	Procaspase-3 (protein)

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4JQZ \| pdb_00004jqz	Download File View File

Human procaspase-3, crystal form 2

Thomsen, N.D., Wells, J.A.

(2013) Proc Natl Acad Sci U S A 110: 8477-8482

Released	2013-05-08
Method	X-RAY DIFFRACTION 2.889 Å
Organisms	Homo sapiens
Macromolecule	Procaspase-3 (protein)

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4JR0 \| pdb_00004jr0	Download File View File

Human procaspase-3 bound to Ac-DEVD-CMK

Thomsen, N.D., Wells, J.A.

(2013) Proc Natl Acad Sci U S A 110: 8477-8482

Released	2013-05-08
Method	X-RAY DIFFRACTION 1.796 Å
Organisms	Homo sapiens
Macromolecule	Ac-DEVD-CMK (protein) Procaspase-3 (protein)
Unique Ligands	CL

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4JR1 \| pdb_00004jr1	Download File View File

Human procaspase-7 bound to Ac-DEVD-CMK

Thomsen, N.D., Wells, J.A.

(2013) Proc Natl Acad Sci U S A 110: 8477-8482

Released	2013-05-08
Method	X-RAY DIFFRACTION 2.149 Å
Organisms	Homo sapiens
Macromolecule	Ac-DEVD-CMK (protein) Procaspase-7 (protein)
Unique Ligands	CL

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4JR2 \| pdb_00004jr2	Download File View File

Human procaspase-7/caspase-7 heterodimer bound to Ac-DEVD-CMK

Thomsen, N.D., Wells, J.A.

(2013) Proc Natl Acad Sci U S A 110: 8477-8482

Released	2013-05-08
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Ac-DEVD-CMK (protein) Procaspase-7 (protein)
Unique Ligands	CL

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6O1F \| pdb_00006o1f	Download File View File

Complex between soybean trypsin inhibitor beta1-tryptase and a humanized fab

Ultsch, M.H., Yi, T.

(2019) Cell 179: 417-431.e19

Released	2019-10-16
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Glycine max Homo sapiens
Macromolecule	Heavy Chain hu31A.v11 (protein) Light Chain hu31A.v11 (protein) Trypsin inhibitor A (protein) Tryptase alpha/beta-1 (protein)
Unique Ligands	EDO

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6VJA \| pdb_00006vja	Download File View File

Structure of CD20 in complex with rituximab Fab

Rohou, A., Croll, T.I.

(2020) Science 367: 1224-1230

Released	2020-02-26
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens
Macromolecule	B-lymphocyte antigen CD20 (protein) Rituximab Fab heavy chain (protein) Rituximab Fab light chain (protein)
Unique Ligands	Y01

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6VVU \| pdb_00006vvu	Download File View File

Anti-Tryptase fab E104.v1 bound to tryptase

Ultsch, M., Koerber, J.T.

(2020) Nat Commun 11: 6435-6435

Released	2020-12-30
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Fab E104.v1 heavy chain (protein) Fab E104.v1 light chain (protein) Tryptase alpha/beta-1 (protein)
Unique Ligands	0GJ, CA

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7JWP \| pdb_00007jwp	Download File View File

Fab CJ11 in complex IL-18 peptide liberated by Caspase cleavage

Payandeh, J., Ho, H.

(2021) Proc Natl Acad Sci U S A 118:

Released	2021-03-24
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Fab CJ11 Heavy chain (protein) Fab CJ11 Light chain (protein) IL-18 peptide (protein)

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7JWQ \| pdb_00007jwq	Download File View File

Fab CJ11 in complex IL-1beta peptide liberated by Caspase cleavage

Payandeh, J., Ho, H.

(2021) Proc Natl Acad Sci U S A 118:

Released	2021-03-24
Method	X-RAY DIFFRACTION 2.001 Å
Organisms	Homo sapiens
Macromolecule	Fab CJ11 Heavy chain (protein) Fab CJ11 Light chain (protein) IL-1beta peptide (protein)

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7MDP \| pdb_00007mdp	Download File View File

KRas G12C in complex with G-2897

Oh, A., Frank, Y., Wang, W.

(2022) Nat Biotechnol 40: 769-778

Released	2022-03-16
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Homo sapiens
Macromolecule	IgG heavy chain (protein) IgG light chain (protein) Isoform 2B of GTPase KRas (protein)
Unique Ligands	ACT, CAD, DMS, EDO, GDP, MG, P15, Z07

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7MFR \| pdb_00007mfr	Download File View File

Crystal Structure of a Fab fragment bound to peptide GGM

Sudhamsu, J.

(2021) Nat Commun 12: 4608-4608

Released	2021-06-16
Method	X-RAY DIFFRACTION 2.848 Å
Organisms	Homo sapiens Oryctolagus cuniculus
Macromolecule	Antibody fragment - Heavy Chain of fab (protein) Antibody fragment - Light Chain of fab (protein) GLY-GLY-MET (protein)
Unique Ligands	SO4

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7RP2 \| pdb_00007rp2	Download File View File

Crystal structure of Kas G12C in complex with 2H11 CLAMP

Oh, A., Tam, C., Wang, W.

(2022) Nat Biotechnol 40: 769-778

Released	2022-03-16
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	GTPase KRas (protein) immunoglobulin IgG heavy chain (protein) immunoglobulin IgG light chain (protein)
Unique Ligands	CAC, EDO, GDP, MG

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7RP3 \| pdb_00007rp3	Download File View File

Crystal structure of GNE-1952 alkylated KRAS G12C in complex with 2H11 CLAMP

Oh, A., Tam, C., Wang, W.

(2022) Nat Biotechnol 40: 769-778

Released	2022-03-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Isoform 2B of GTPase KRas (protein) immunoglobulin IgG heavy chain (protein) immunoglobulin IgG light chain (protein)
Unique Ligands	EDO, GDP, GOL, MG, MKZ, SO4

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7RP4 \| pdb_00007rp4	Download File View File

Crystal structure of KRAS G12C in complex with GNE-1952

Oh, A., Tam, C., Wang, W.

(2022) Nat Biotechnol 40: 769-778

Released	2022-03-16
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	Isoform 2B of GTPase KRas (protein)
Unique Ligands	GDP, GOL, MG, MKZ

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7U5B \| pdb_00007u5b	Download File View File

Structure of Human KLK5 bound to anti-KLK5 Fab

Yin, J., Sudhamsu, J.

(2022) Sci Transl Med 14: eabp9159-eabp9159

Released	2022-12-14
Method	X-RAY DIFFRACTION 2.371 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Kallikrein-5 (protein) anti-KLK5 Fab Heavy Chain (protein) anti-KLK5 Fab Light Chain (protein)
Unique Ligands	SO4

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7U8G \| pdb_00007u8g	Download File View File

Cryo-EM structure of the core human NADPH oxidase NOX2

Noreng, S., Ota, N., Sun, Y., Masureel, M., Payandeh, J., Yi, T., Koerber, J.T.

(2022) Nat Commun 13: 6079-6079

Released	2022-10-26
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens Oryctolagus cuniculus
Macromolecule	7G5 - heavy chain (protein) 7G5 - light chain (protein) Cytochrome b-245 light chain (protein) EGFP, Cytochrome b-245 heavy chain chimera (protein)
Unique Ligands	HEM, NAG, POV

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8EW6 \| pdb_00008ew6	Download File View File

Anti-human CD8 VHH complex with CD8 alpha

Kiefer, J.R., Williams, S., Davies, C.W., Koerber, J.T., Sriraman, S.K., Yin, Y.P.

(2023) Eur J Nucl Med Mol Imaging 50: 679-691

Released	2022-11-23
Method	X-RAY DIFFRACTION 1.904 Å
Organisms	Homo sapiens Lama glama
Macromolecule	Anti-CD8 alpha VHH (protein) T-cell surface glycoprotein CD8 alpha chain (protein)

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8TLM \| pdb_00008tlm	Download File View File

Structure of a class A GPCR/Fab complex

Sun, D., Johnson, M., Masureel, M.

(2023) Nat Commun 14: 7940-7940

Released	2023-12-20
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Aequorea victoria Homo sapiens Oryctolagus cuniculus
Macromolecule	C-C chemokine receptor type 8, Green fluorescent protein fusion (protein) Fab heavy chain (protein) Fab light chain (protein)

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8U1U \| pdb_00008u1u	Download File View File

Structure of a class A GPCR/agonist complex

Sun, D., Johnson, M., Masureel, M.

(2023) Nat Commun 14: 7940-7940

Released	2023-12-20
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens Human adenovirus 2 Mus musculus
Macromolecule	C-C motif chemokine 1,C-C chemokine receptor type 8,EGFP fusion protein (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(i) subunit alpha-1 (protein) scFv fragment (protein)
Unique Ligands	NAG

1 to 25 of 25 Structures

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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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

4JFX | pdb_00004jfx

4JFY | pdb_00004jfy

4JFZ | pdb_00004jfz

4JG0 | pdb_00004jg0

4JG1 | pdb_00004jg1

4JQY | pdb_00004jqy

4JQZ | pdb_00004jqz

4JR0 | pdb_00004jr0

4JR1 | pdb_00004jr1

4JR2 | pdb_00004jr2

6O1F | pdb_00006o1f

6VJA | pdb_00006vja

6VVU | pdb_00006vvu

7JWP | pdb_00007jwp

7JWQ | pdb_00007jwq

7MDP | pdb_00007mdp

7MFR | pdb_00007mfr

7RP2 | pdb_00007rp2

7RP3 | pdb_00007rp3

7RP4 | pdb_00007rp4

7U5B | pdb_00007u5b

7U8G | pdb_00007u8g

8EW6 | pdb_00008ew6

8TLM | pdb_00008tlm

8U1U | pdb_00008u1u