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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 = 3.6.1

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Search Summary

This query matches 2,366 Structures.

Refinements

Structure Determination Methodology

experimental (2,366)

Scientific Name of Source Organism

	Homo sapiens (713)
	Zika virus (197)
	Escherichia coli (122)
	Mus musculus (95)
	Saccharomyces cerevisiae (68)
	Escherichia coli K-12 (59)
	synthetic construct (55)
	Drosophila melanogaster (36)
	Arabidopsis thaliana (33)
	Klebsiella pneumoniae (33)

More...

Taxonomy

	Eukaryota (1,127)
	Bacteria (615)
	Riboviria (585)
	other sequences (55)
	Archaea (51)
	Varidnaviria (36)
	Duplodnaviria (31)
	Monodnaviria (7)
	Viruses incertae sedis (3)
	Eukaryota (eukaryotes) (2)

More...

Experimental Method

	X-RAY DIFFRACTION (2,045)
	ELECTRON MICROSCOPY (256)
	SOLUTION NMR (63)
	NEUTRON DIFFRACTION (2)

Polymer Entity Type

	Protein (2,366)
	RNA (99)
	DNA (64)
	NA-hybrid (8)

Refinement Resolution (Å)

	0.5 - 1.0 (5)
	1.0 - 1.5 (246)
	1.5 - 2.0 (903)
	2.0 - 2.5 (564)
	2.5 - 3.0 (278)
	3.0 - 3.5 (173)
	3.5 - 4.0 (76)
	4.0 - 4.5 (24)
	> 4.5 (34)

Release Date

	1980 - 1984 (1)
	1990 - 1994 (14)
	1995 - 1999 (52)
	2000 - 2004 (141)
	2005 - 2009 (351)
	2010 - 2014 (358)
	2015 - 2019 (594)
	2020 - 2024 (781)
	2025 - 2029 (74)

Enzyme Classification Name

	Hydrolases (2,366)
	Transferases (427)
	Isomerases (45)
	Translocases (12)
	Ligases (3)
	Lyases (2)

Membrane Protein Annotation

	OPM (26)
	PDBTM (27)
	mpstruc (26)
	MemProtMD (24)

Symmetry Type

	Asymmetric (1,471)
	Cyclic (750)
	Dihedral (129)
	Icosahedral (103)
	Helical (6)
	Tetrahedral (3)

SCOP Classification

	All beta proteins (344)
	Alpha and beta proteins (a+b) (350)
	Alpha and beta proteins (a/b) (231)
	Artifacts (198)
	All alpha proteins (79)
	Multi-domain proteins (alpha and beta) (25)
	Small proteins (12)
	Membrane and cell surface proteins and peptides (3)
	Coiled coil proteins (1)

AllSelected

1 to 25 of 2,366 Structures

Page 1 of 95

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Explore in 3D

117E \| pdb_0000117e	Download File View File

THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS

Tuominen, V., Heikinheimo, P., Kajander, T., Torkkel, T., Hyytia, T., Kapyla, J., Lahti, R., Cooperman, B.S., Goldman, A.

(1998) J Mol Biology 284: 1565-1580

Released	1998-12-23
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PROTEIN (INORGANIC PYROPHOSPHATASE) (protein)
Unique Ligands	MN, PO4

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1APS \| pdb_00001aps	Download File View File

THREE-DIMENSIONAL STRUCTURE OF ACYLPHOSPHATASE. REFINEMENT AND STRUCTURE ANALYSIS

Saudek, V., Pastore, A., Ramponi, G., Williams, R.J.P.

(1992) J Mol Biology 224: 427-440

Released	1992-07-15
Method	SOLUTION NMR
Organisms	Equus caballus
Macromolecule	ACYLPHOSPHATASE (protein)

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1ATR \| pdb_00001atr	Download File View File

THREONINE 204 OF THE CHAPERONE PROTEIN HSC70 INFLUENCES THE STRUCTURE OF THE ACTIVE SITE BUT IS NOT ESSENTIAL FOR ATP HYDROLYSIS

O'Brien, M.C., Mckay, D.B.

(1993) J Biological Chem 268: 24323-24329

Released	1993-10-31
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Bos taurus
Macromolecule	HEAT-SHOCK COGNATE 70 KD PROTEIN (protein)
Unique Ligands	ADP, MG, PO4

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1ATS \| pdb_00001ats	Download File View File

THREONINE 204 OF THE CHAPERONE PROTEIN HSC70 INFLUENCES THE STRUCTURE OF THE ACTIVE SITE BUT IS NOT ESSENTIAL FOR ATP HYDROLYSIS

O'Brien, M.C., Mckay, D.B.

(1993) J Biological Chem 268: 24323-24329

Released	1993-10-31
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Bos taurus
Macromolecule	HEAT-SHOCK COGNATE 70 KD PROTEIN (protein)
Unique Ligands	ADP, MG

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1B78 \| pdb_00001b78	Download File View File

STRUCTURE-BASED IDENTIFICATION OF THE BIOCHEMICAL FUNCTION OF A HYPOTHETICAL PROTEIN FROM METHANOCOCCUS JANNASCHII:MJ0226

Hwang, K.Y., Chung, J.H., Han, Y.S., Kim, S.H., Cho, Y.

(1999) Nat Struct Biol 6: 691-696

Released	2000-01-28
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	PYROPHOSPHATASE (protein)

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1B79 \| pdb_00001b79	Download File View File

N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB

Fass, D., Bogden, C.E., Berger, J.M.

(1999) Structure 7: 691-698

Released	1999-06-30
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli
Macromolecule	DnaB Helicase (protein)

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1BA0 \| pdb_00001ba0	Download File View File

HEAT-SHOCK COGNATE 70KD PROTEIN 44KD ATPASE N-TERMINAL 1NGE 3

Wilbanks, S.M., Mckay, D.B.

(1998) Biochemistry 37: 7456-7462

Released	1998-07-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	HEAT-SHOCK COGNATE 70KD PROTEIN (protein)
Unique Ligands	ADP, CL, MG, NA, PO4

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1BA1 \| pdb_00001ba1	Download File View File

HEAT-SHOCK COGNATE 70KD PROTEIN 44KD ATPASE N-TERMINAL MUTANT WITH CYS 17 REPLACED BY LYS

Wilbanks, S.M., Mckay, D.B.

(1998) Biochemistry 37: 7456-7462

Released	1998-07-15
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Bos taurus
Macromolecule	HEAT-SHOCK COGNATE 70KD PROTEIN (protein)
Unique Ligands	ADP, CL, MG, NA

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1D8H \| pdb_00001d8h	Download File View File

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS.

Lima, C.D., Wang, L.K., Shuman, S.

(1999) Cell 99: 533-543

Released	1999-11-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	mRNA TRIPHOSPHATASE CET1 (protein)
Unique Ligands	MN, SO4

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1D8I \| pdb_00001d8i	Download File View File

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION.

Lima, C.D., Wang, L.K., Shuman, S.

(1999) Cell 99: 533-543

Released	1999-11-29
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	MRNA TRIPHOSPHATASE CET1 (protein)
Unique Ligands	SO4

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1DG3 \| pdb_00001dg3	Download File View File

STRUCTURE OF HUMAN GUANYLATE BINDING PROTEIN-1 IN NUCLEOTIDE FREE FORM

Prakash, B., Praefcke, G.J.K., Renault, L., Wittinghofer, A., Herrmann, C.

(2000) Nature 403: 567-571

Released	2000-10-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN (INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1) (protein)

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1DKL \| pdb_00001dkl	Download File View File

CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 4.5 (NO LIGAND BOUND)

Lim, D., Golovan, S., Forsberg, C.W., Jia, Z.

(2000) Nat Struct Biol 7: 108-113

Released	2000-08-03
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli
Macromolecule	PHYTASE (protein)

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1DKM \| pdb_00001dkm	Download File View File

CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 6.6 WITH HG2+ CATION ACTING AS AN INTERMOLECULAR BRIDGE

Lim, D., Golovan, S., Forsberg, C.W., Jia, Z.

(2000) Nat Struct Biol 7: 108-113

Released	2000-08-02
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Escherichia coli
Macromolecule	PHYTASE (protein)
Unique Ligands	HG

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1DKN \| pdb_00001dkn	Download File View File

CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 5.0 WITH HG2+ CATION ACTING AS AN INTERMOLECULAR BRIDGE

Lim, D., Golovan, S., Forsberg, C.W., Jia, Z.

(2000) Nat Struct Biol 7: 108-113

Released	2000-08-03
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli
Macromolecule	PHYTASE (protein)
Unique Ligands	HG

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1DKO \| pdb_00001dko	Download File View File

CRYSTAL STRUCTURE OF TUNGSTATE COMPLEX OF ESCHERICHIA COLI PHYTASE AT PH 6.6 WITH TUNGSTATE BOUND AT THE ACTIVE SITE AND WITH HG2+ CATION ACTING AS AN INTERMOLECULAR BRIDGE

Lim, D., Golovan, S., Forsberg, C.W., Jia, Z.

(2000) Nat Struct Biol 7: 108-113

Released	2000-08-03
Method	X-RAY DIFFRACTION 2.38 Å
Organisms	Escherichia coli
Macromolecule	PHYTASE (protein)
Unique Ligands	HG, WO4

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1DKP \| pdb_00001dkp	Download File View File

CRYSTAL STRUCTURE OF PHYTATE COMPLEX OF ESCHERICHIA COLI PHYTASE AT PH 6.6. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR BRIDGE

Lim, D., Golovan, S., Forsberg, C.W., Jia, Z.

(2000) Nat Struct Biol 7: 108-113

Released	2000-08-03
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Escherichia coli
Macromolecule	PHYTASE (protein)
Unique Ligands	HG, IHP

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1DKQ \| pdb_00001dkq	Download File View File

CRYSTAL STRUCTURE OF PHYTATE COMPLEX ESCHERICHIA COLI PHYTASE AT PH 5.0. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR BRIDGE

Lim, D., Golovan, S., Forsberg, C.W., Jia, Z.

(2000) Nat Struct Biol 7: 108-113

Released	2000-08-03
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Escherichia coli
Macromolecule	PHYTASE (protein)
Unique Ligands	HG, IHP

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1DUC \| pdb_00001duc	Download File View File

EIAV DUTPASE DUDP/STRONTIUM COMPLEX

Dauter, Z., Persson, R., Rosengren, A.M., Nyman, P.O., Wilson, K.S., Cedergren-Zeppezauer, E.S.

(1999) J Mol Biology 285: 655-673

Released	1998-06-03
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Equine infectious anemia virus
Macromolecule	DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE (protein)
Unique Ligands	DUD, SR

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1DUD \| pdb_00001dud	Download File View File

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE (D-UTPASE) COMPLEXED WITH THE SUBSTRATE ANALOGUE DEOXYURIDINE 5'-DIPHOSPHATE (D-UDP)

Larsson, G., Svensson, L.A., Nyman, P.O.

(1996) Nat Struct Biol 3: 532-538

Released	1996-11-08
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli
Macromolecule	DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE (protein)
Unique Ligands	DUD

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1DUN \| pdb_00001dun	Download File View File

EIAV DUTPASE NATIVE

Dauter, Z., Persson, R., Rosengren, A.M., Nyman, P.O., Wilson, K.S., Cedergren-Zeppezauer, E.S.

(1999) J Mol Biology 285: 655-673

Released	1998-05-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Equine infectious anemia virus
Macromolecule	DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE (protein)

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1DUP \| pdb_00001dup	Download File View File

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE (D-UTPASE)

Dauter, Z., Wilson, K.S., Larsson, G., Nyman, P.O., Cedergren, E.

(1992) Nature 355: 740-743

Released	1995-11-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE (protein)

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1DUT \| pdb_00001dut	Download File View File

FIV DUTP PYROPHOSPHATASE

Prasad, G.S., Stura, E.A., Mcree, D.E., Laco, G.S., Hasselkus-Light, C., Elder, J.H., Stout, C.D.

(1996) Protein Sci 5: 2429-2437

Released	1997-01-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Feline immunodeficiency virus (isolate Petaluma)
Macromolecule	DUTP PYROPHOSPHATASE (protein)
Unique Ligands	MG

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1E6A \| pdb_00001e6a	Download File View File

Fluoride-inhibited substrate complex of Saccharomyces cerevisiae inorganic pyrophosphatase

Heikinheimo, P., Tuominen, V., Ahonen, A.-K., Teplyakov, A., Cooperman, B.S., Baykov, A.A., Lahti, R., Goldman, A.

(2001) Proc Natl Acad Sci U S A 98: 3121-3126

Released	2001-03-19
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	INORGANIC PYROPHOSPHATASE (protein)
Unique Ligands	F, MN, NA, PO4, POP

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1E9G \| pdb_00001e9g	Download File View File

STRUCTURE OF INORGANIC PYROPHOSPHATASE

Heikinheimo, P., Tuominen, V., Ahonen, A.-K., Teplyakov, A., Cooperman, B.S., Baykov, A.A., Lahti, R., Goldman, A.

(2001) Proc Natl Acad Sci U S A 98: 3121

Released	2001-03-19
Method	X-RAY DIFFRACTION 1.15 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	INORGANIC PYROPHOSPHATASE (protein)
Unique Ligands	MN, PO4

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1EMS \| pdb_00001ems	Download File View File

CRYSTAL STRUCTURE OF THE C. ELEGANS NITFHIT PROTEIN

Pace, H.C., Hodawadekar, S.C., Draganescu, A., Huang, J., Bieganowski, P., Pekarsky, Y., Croce, C.M., Brenner, C.

(2000) Curr Biol 10: 907-917

Released	2000-07-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Caenorhabditis elegans
Macromolecule	NIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN (protein)
Unique Ligands	EMC, MPD, NA

1 to 25 of 2,366 Structures

Page 1 of 95

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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

117E | pdb_0000117e

1APS | pdb_00001aps

1ATR | pdb_00001atr

1ATS | pdb_00001ats

1B78 | pdb_00001b78

1B79 | pdb_00001b79

1BA0 | pdb_00001ba0

1BA1 | pdb_00001ba1

1D8H | pdb_00001d8h

1D8I | pdb_00001d8i

1DG3 | pdb_00001dg3

1DKL | pdb_00001dkl

1DKM | pdb_00001dkm

1DKN | pdb_00001dkn

1DKO | pdb_00001dko

1DKP | pdb_00001dkp

1DKQ | pdb_00001dkq

1DUC | pdb_00001duc

1DUD | pdb_00001dud

1DUN | pdb_00001dun

1DUP | pdb_00001dup

1DUT | pdb_00001dut

1E6A | pdb_00001e6a

1E9G | pdb_00001e9g

1EMS | pdb_00001ems