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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 3.1

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Search Summary

This query matches 13,076 Structures.

Refinements

Structure Determination Methodology

experimental (13,076)

Scientific Name of Source Organism

	Homo sapiens (4,405)
	synthetic construct (785)
	Mus musculus (602)
	Escherichia coli (471)
	Bos taurus (443)
	Staphylococcus aureus (403)
	Rattus norvegicus (345)
	Escherichia coli K-12 (284)
	Saccharomyces cerevisiae (183)
	Severe acute respiratory syndrome coronavirus 2 (180)

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Taxonomy

	Eukaryota (7,604)
	Bacteria (3,866)
	Riboviria (1,111)
	other sequences (796)
	Archaea (411)
	Duplodnaviria (356)
	Eukaryota (eukaryotes) (56)
	Varidnaviria (40)
	unclassified sequences (39)
	Monodnaviria (35)

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Experimental Method

	X-RAY DIFFRACTION (11,572)
	ELECTRON MICROSCOPY (1,192)
	SOLUTION NMR (309)
	NEUTRON DIFFRACTION (7)

Polymer Entity Type

	Protein (13,075)
	DNA (1,454)
	RNA (1,059)
	NA-hybrid (49)

Refinement Resolution (Å)

	0.5 - 1.0 (30)
	1.0 - 1.5 (959)
	1.5 - 2.0 (3,989)
	2.0 - 2.5 (3,886)
	2.5 - 3.0 (2,236)
	3.0 - 3.5 (1,031)
	3.5 - 4.0 (369)
	4.0 - 4.5 (124)
	> 4.5 (144)

Release Date

	1980 - 1984 (5)
	1985 - 1989 (9)
	1990 - 1994 (187)
	1995 - 1999 (498)
	2000 - 2004 (1,023)
	2005 - 2009 (1,987)
	2010 - 2014 (2,396)
	2015 - 2019 (2,981)
	2020 - 2024 (3,835)
	2025 - 2029 (155)

Enzyme Classification Name

	Hydrolases (13,076)
	Transferases (1,589)
	Lyases (762)
	Oxidoreductases (126)
	Isomerases (112)
	Translocases (39)
	Ligases (28)

Membrane Protein Annotation

	OPM (250)
	mpstruc (87)
	PDBTM (83)
	MemProtMD (58)

Symmetry Type

	Asymmetric (9,341)
	Cyclic (3,468)
	Dihedral (737)
	Helical (12)
	Octahedral (7)
	Icosahedral (5)
	Tetrahedral (3)

SCOP Classification

	Alpha and beta proteins (a/b) (3,274)
	Alpha and beta proteins (a+b) (1,656)
	All alpha proteins (958)
	Artifacts (1,065)
	All beta proteins (741)
	Multi-domain proteins (alpha and beta) (474)
	Low resolution protein structures (2)
	Small proteins (34)
	Membrane and cell surface proteins and peptides (14)
	Coiled coil proteins (8)

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AllSelected

1 to 25 of 13,076 Structures

Page 1 of 524

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11BA \| pdb_000011ba	Download File View File

BINDING OF A SUBSTRATE ANALOGUE TO A DOMAIN SWAPPING PROTEIN IN THE COMPLEX OF BOVINE SEMINAL RIBONUCLEASE WITH URIDYLYL-2',5'-ADENOSINE

Vitagliano, L., Adinolfi, S., Riccio, A., Sica, F., Zagari, A., Mazzarella, L.

(1998) Protein Sci 7: 1691-1699

Released	1999-03-26
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Bos taurus
Macromolecule	PROTEIN (RIBONUCLEASE, SEMINAL) (protein)
Unique Ligands	SO4, UPA

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11BG \| pdb_000011bg	Download File View File

A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BOVINE SEMINAL RIBONUCLEASE

Vitagliano, L., Adinolfi, S., Sica, F., Merlino, A., Zagari, A., Mazzarella, L.

(1999) J Mol Biology 293: 569-577

Released	1999-11-05
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	PROTEIN (BOVINE SEMINAL RIBONUCLEASE) (protein)
Unique Ligands	SO4, U2G

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1A17 \| pdb_00001a17	Download File View File

TETRATRICOPEPTIDE REPEATS OF PROTEIN PHOSPHATASE 5

Das, A.K., Cohen, P.T.W., Barford, D.

(1998) EMBO J 17: 1192-1199

Released	1998-04-29
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE PROTEIN PHOSPHATASE 5 (protein)
Unique Ligands	SO4

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1A2A \| pdb_00001a2a	Download File View File

AGKISTROTOXIN, A PHOSPHOLIPASE A2-TYPE PRESYNAPTIC NEUROTOXIN FROM AGKISTRODON HALYS PALLAS

Tang, L., Zhou, Y., Lin, Z.

(1998) J Mol Biology 282: 1-11

Released	1999-01-13
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Gloydius halys
Macromolecule	PHOSPHOLIPASE A2 (protein)
Unique Ligands	CL

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1A2O \| pdb_00001a2o	Download File View File

STRUCTURAL BASIS FOR METHYLESTERASE CHEB REGULATION BY A PHOSPHORYLATION-ACTIVATED DOMAIN

Djordjevic, S., Goudreau, P.N., Xu, Q., Stock, A.M., West, A.H.

(1998) Proc Natl Acad Sci U S A 95: 1381-1386

Released	1998-04-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	CHEB METHYLESTERASE (protein)

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1A2P \| pdb_00001a2p	Download File View File

BARNASE WILDTYPE STRUCTURE AT 1.5 ANGSTROMS RESOLUTION

Martin, C., Richard, V., Salem, M., Hartley, R.W., Mauguen, Y.

(1999) Acta Crystallogr D Biol Crystallogr 55: 386-398

Released	1998-04-29
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Bacillus amyloliquefaciens
Macromolecule	BARNASE (protein)
Unique Ligands	ZN

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1A2T \| pdb_00001a2t	Download File View File

STAPHYLOCOCCAL NUCLEASE, B-MERCAPTOETHANOL DISULFIDE TO V23C VARIANT

Wynn, R., Harkins, P.C., Richards, F.M., Fox, R.O.

(1996) Protein Sci 5: 1026-1031

Released	1998-04-29
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Staphylococcus aureus
Macromolecule	STAPHYLOCOCCAL NUCLEASE (protein)
Unique Ligands	CA, THP

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1A2U \| pdb_00001a2u	Download File View File

STAPHYLOCOCCAL NUCLEASE, V23C VARIANT, COMPLEX WITH 1-N-BUTANE THIOL AND 3',5'-THYMIDINE DIPHOSPHATE

Wynn, R., Harkins, P.C., Richards, F.M., Fox, R.O.

(1996) Protein Sci 5: 1026-1031

Released	1998-04-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Staphylococcus aureus
Macromolecule	STAPHYLOCOCCAL NUCLEASE (protein)
Unique Ligands	CA, THP

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1A2W \| pdb_00001a2w	Download File View File

CRYSTAL STRUCTURE OF A 3D DOMAIN-SWAPPED DIMER OF BOVINE PANCREATIC RIBONUCLEASE A

Liu, Y., Hart, P.J., Schlunegger, M.P., Eisenberg, D.S.

(1998) Proc Natl Acad Sci U S A 95: 3437-3442

Released	1998-04-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bos taurus
Macromolecule	RIBONUCLEASE A (protein)
Unique Ligands	CL, SO4

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1A3D \| pdb_00001a3d	Download File View File

PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM

Segelke, B.W., Nguyen, D., Chee, R., Xuong, H.N., Dennis, E.A.

(1998) J Mol Biology 279: 223-232

Released	1998-04-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Naja naja
Macromolecule	PHOSPHOLIPASE A2 (protein)
Unique Ligands	NA

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1A3F \| pdb_00001a3f	Download File View File

PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM

Segelke, B.W., Nguyen, D., Chee, R., Xuong, H.N., Dennis, E.A.

(1998) J Mol Biology 279: 223-232

Released	1998-04-29
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Naja naja
Macromolecule	PHOSPHOLIPASE A2 (protein)

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1A3T \| pdb_00001a3t	Download File View File

STAPHYLOCOCCAL NUCLEASE, V23C VARIANT, COMPLEX WITH 2-FLUOROETHANE THIOL AND 3',5'-THYMIDINE DIPHOSPHATE

Wynn, R., Harkins, P.C., Richards, F.M., Fox, R.O.

(1997) Protein Sci 6: 1621-1626

Released	1998-04-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Staphylococcus aureus
Macromolecule	STAPHYLOCOCCAL NUCLEASE (protein)
Unique Ligands	CA, THP

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1A3U \| pdb_00001a3u	Download File View File

STAPHYLOCOCCAL NUCLEASE, CYCLOHEXANE THIOL DISULFIDE TO V23C VARIANT

Wynn, R., Harkins, P.C., Richards, F.M., Fox, R.O.

(1997) Protein Sci 6: 1621-1626

Released	1998-04-29
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Staphylococcus aureus
Macromolecule	STAPHYLOCOCCAL NUCLEASE (protein)
Unique Ligands	CA, THP

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1A3V \| pdb_00001a3v	Download File View File

STAPHYLOCOCCAL NUCLEASE, CYCLOPENTANE THIOL DISULFIDE TO V23C VARIANT

Wynn, R., Harkins, P.C., Richards, F.M., Fox, R.O.

(1997) Protein Sci 6: 1621-1626

Released	1998-04-29
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Staphylococcus aureus
Macromolecule	STAPHYLOCOCCAL NUCLEASE (protein)
Unique Ligands	CA, THP

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1A4Y \| pdb_00001a4y	Download File View File

RIBONUCLEASE INHIBITOR-ANGIOGENIN COMPLEX

Papageorgiou, A.C., Acharya, K.R.

(1997) EMBO J 16: 5162-5177

Released	1998-10-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	ANGIOGENIN (protein) RIBONUCLEASE INHIBITOR (protein)

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1A5P \| pdb_00001a5p	Download File View File

C[40,95]A VARIANT OF BOVINE PANCREATIC RIBONUCLEASE A

Pearson, M.A., Karplus, P.A., Dodge, R.W., Laity, J.H., Scheraga, H.A.

(1998) Protein Sci 7: 1255-1258

Released	1998-05-27
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Bos taurus
Macromolecule	RIBONUCLEASE A (protein)
Unique Ligands	SO4

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1A5Q \| pdb_00001a5q	Download File View File

P93A VARIANT OF BOVINE PANCREATIC RIBONUCLEASE A

Pearson, M.A., Karplus, P.A., Dodge, R.W., Laity, J.H., Scheraga, H.A.

(1998) Protein Sci 7: 1255-1258

Released	1998-05-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bos taurus
Macromolecule	RIBONUCLEASE A (protein)
Unique Ligands	SO4

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1A5Y \| pdb_00001a5y	Download File View File

PROTEIN TYROSINE PHOSPHATASE 1B CYSTEINYL-PHOSPHATE INTERMEDIATE

Pannifer, A.D.P., Flint, A.J., Tonks, N.K., Barford, D.

(1998) J Biological Chem 273: 10454-10462

Released	1998-06-17
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN TYROSINE PHOSPHATASE 1B (protein)

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1A6F \| pdb_00001a6f	Download File View File

RNASE P PROTEIN FROM BACILLUS SUBTILIS

Stams, T., Christianson, D.W.

(1998) Science 280: 752-755

Released	1999-03-23
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bacillus subtilis
Macromolecule	RIBONUCLEASE P PROTEIN (protein)
Unique Ligands	SO4, ZN

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1A6Q \| pdb_00001a6q	Download File View File

CRYSTAL STRUCTURE OF THE PROTEIN SERINE/THREONINE PHOSPHATASE 2C AT 2 A RESOLUTION

Das, A.K., Helps, N.R., Cohen, P.T.W., Barford, D.

(1996) EMBO J 15: 6798-6809

Released	1998-05-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	PHOSPHATASE 2C (protein)
Unique Ligands	MN, PO4

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1A73 \| pdb_00001a73	Download File View File

INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA

Flick, K.E., Monnat Junior, R.J., Stoddard, B.L.

(1998) Nature 394: 96-101

Released	1998-10-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Physarum polycephalum
Macromolecule	INTRON 3 (I-PPO) ENCODED ENDONUCLEASE (protein) DNA (5'-D(TPTPGPAPCPTPCPTPCPTPTPAPA)-3') (nucleic acid) DNA (5'-D(PGPAPGPAPGPTPCP*A)-3') (nucleic acid)
Unique Ligands	MG, ZN

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1A74 \| pdb_00001a74	Download File View File

I-PPOL HOMING ENDONUCLEASE/DNA COMPLEX

Jurica, B.L., Flick, K.E., Monnat Junior, R.J., Stoddard, M.S.

(1998) Nature 394: 96-101

Released	1998-06-22
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Physarum polycephalum
Macromolecule	INTRON-ENCODED ENDONUCLEASE I-PPOI (protein) DNA (5'-D(TPTPGPAPCPTPCPTPCPTPTPAPAPGPAPGPA PGPTPCP*A)-3') (nucleic acid)
Unique Ligands	ZN

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1A76 \| pdb_00001a76	Download File View File

FLAP ENDONUCLEASE-1 FROM METHANOCOCCUS JANNASCHII

Hwang, K.Y., Baek, K., Kim, H., Cho, Y.

(1998) Nat Struct Biol 5: 707-713

Released	1999-08-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	FLAP ENDONUCLEASE-1 PROTEIN (protein)
Unique Ligands	MN

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1A77 \| pdb_00001a77	Download File View File

FLAP ENDONUCLEASE-1 FROM METHANOCOCCUS JANNASCHII

Hwang, K.Y., Baek, K., Kim, H., Cho, Y.

(1998) Nat Struct Biol 5: 707-713

Released	1999-08-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	FLAP ENDONUCLEASE-1 PROTEIN (protein)
Unique Ligands	MG