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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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Search Summary

This query matches 66 Structures.

Refinements

Structure Determination Methodology

experimental (66)

Scientific Name of Source Organism

	Homo sapiens (11)
	Thermus thermophilus HB8 (7)
	Lactococcus lactis subsp. lactis Il1403 (6)
	Moorella thermoacetica ATCC 39073 (6)
	Pseudomonas aeruginosa PAO1 (4)
	Acetivibrio cellulolyticus (3)
	Thermochaetoides thermophila (3)
	Arabidopsis thaliana (2)
	Bacillus cereus ATCC 14579 (2)
	Sphingomonas paucimobilis (2)

More...

Taxonomy

	Bacteria (41)
	Eukaryota (21)
	Varidnaviria (3)
	other sequences (2)
	Archaea (1)
	Duplodnaviria (1)
	unclassified sequences (1)

Experimental Method

X-RAY DIFFRACTION (66)

Polymer Entity Type

	Protein (65)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (34)
	2.0 - 2.5 (23)
	2.5 - 3.0 (1)
	3.0 - 3.5 (2)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (3)
	2005 - 2009 (3)
	2010 - 2014 (7)
	2015 - 2019 (17)
	2020 - 2024 (35)

Enzyme Classification Name

	Hydrolases (16)
	Isomerases (8)
	Oxidoreductases (5)
	Transferases (6)
	Lyases (1)

Symmetry Type

	Asymmetric (46)
	Dihedral (12)
	Cyclic (8)

SCOP Classification

	Artifacts (16)
	Alpha and beta proteins (a/b) (20)
	Alpha and beta proteins (a+b) (8)
	All beta proteins (8)
	All alpha proteins (1)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 66 Structures

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1D07 \| pdb_00001d07	Download File View File

Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution

Marek, J., Vevodova, J., Damborsky, J., Smatanova, I., Svensson, L.A., Newman, J., Nagata, Y., Takagi, M.

(2000) Biochemistry 39: 14082-14086

Released	2000-09-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sphingomonas paucimobilis
Macromolecule	HALOALKANE DEHALOGENASE (protein)
Unique Ligands	BR, PDO

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1IZ8 \| pdb_00001iz8	Download File View File

Re-refinement of the structure of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution

Streltsov, V.A.

(2003) Biochemistry 42: 10104-10112

Released	2002-10-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sphingomonas paucimobilis
Macromolecule	HALOALKANE DEHALOGENASE, LINB (protein)
Unique Ligands	BR, CA, PDO

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1MR3 \| pdb_00001mr3	Download File View File

Saccharomyces cerevisiae ADP-ribosylation Factor 2 (ScArf2) complexed with GDP-3'P at 1.6A resolution

Amor, J.-C., Horton, J.R., Zhu, X., Wang, Y., Sullards, C., Ringe, D., Cheng, X., Kahn, R.A.

(2001) J Biological Chem 276: 42477-42484

Released	2002-11-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ADP-ribosylation factor 2 (protein)
Unique Ligands	EDO, EOH, G3D, GOL, MG, PDO

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1NAI \| pdb_00001nai	Download File View File

UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED

Thoden, J.B., Frey, P.A., Holden, H.M.

(1996) Biochemistry 35: 2557-2566

Released	1996-12-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	UDP-GALACTOSE 4-EPIMERASE (protein)
Unique Ligands	NA, NAD, PDO, PEG, UDP

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1ZV9 \| pdb_00001zv9	Download File View File

Crystal structure analysis of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus- SeMet derivative

Noach, I., Rosenheck, S., Lamed, R., Shimon, L., Bayer, E., Frolow, F.

(2009) J Mol Biology 391: 86-97

Released	2006-06-13
Method	X-RAY DIFFRACTION 1.28 Å
Organisms	Acetivibrio cellulolyticus
Macromolecule	Cellulosomal scaffoldin adaptor protein B (protein)
Unique Ligands	ACY, EDO, FMT, NO3, PDO

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2O2I \| pdb_00002o2i	Download File View File

Crystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,3-propandiol

Mazumdar, P.A., Hulecki, J., Cherney, M.M., Garen, C.R., James, M.N.G., TB Structural Genomics Consortium (TBSGC)

To be published

Released	2007-11-13
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Haloalkane dehalogenase 3 (protein)
Unique Ligands	BR, PDO

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2YMT \| pdb_00002ymt	Download File View File

gamma 2 adaptin EAR domain crystal structure with phage peptide GEEWGPWV

Juergens, M.C., Voros, J., Rautureau, G., Shepherd, D., Pye, V.E., Muldoon, J., Johnson, C.M., Ashcroft, A., Freund, S.M.V., Ferguson, N.

(2013) Nat Chem Biol 9: 540

Released	2013-07-10
Method	X-RAY DIFFRACTION 1.802 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2 (protein) PHAGE DISPLAY DERIVED GAMMA 2 ADAPTIN EAR DOMAIN BINDING PEPTIDE (protein)
Unique Ligands	PDO

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3FNK \| pdb_00003fnk	Download File View File

Crystal structure of the second type II cohesin module from the cellulosomal adaptor ScaA scaffoldin of Acetivibrio cellulolyticus

Noach, I., Frolow, F., Bayer, E.A.

(2009) J Mol Biology 391: 86-97

Released	2009-06-23
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Acetivibrio cellulolyticus
Macromolecule	Cellulosomal scaffoldin adaptor protein B (protein)
Unique Ligands	ACT, BU1, EDO, PDO

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3L8Q \| pdb_00003l8q	Download File View File

Structure analysis of the type II cohesin dyad from the adaptor ScaA scaffoldin of Acetivibrio cellulolyticus

Noach, I., Frolow, F., Bayer, E.A.

(2010) J Mol Biology 399: 294-305

Released	2010-05-05
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Acetivibrio cellulolyticus
Macromolecule	Cellulosomal scaffoldin adaptor protein B (protein)
Unique Ligands	EDO, HEZ, PDO

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4BCX \| pdb_00004bcx	Download File View File

gamma 2 adaptin EAR domain crystal structure

Juergens, M.C., Voros, J., Rautureau, G., Shepherd, D., Pye, V.E., Muldoon, J., Johnson, C.M., Ashcroft, A., Freund, S.M.V., Ferguson, N.

(2013) Nat Chem Biol 9: 540

Released	2013-07-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2 (protein)
Unique Ligands	IMD, PDO

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4HON \| pdb_00004hon	Download File View File

Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate

Krishnan, S., Trievel, R.C.

(2013) Structure 21: 98-108

Released	2012-11-21
Method	X-RAY DIFFRACTION 1.799 Å
Organisms	Homo sapiens
Macromolecule	Histone H3 Peptide (protein) Lysine-specific demethylase 4D (protein)
Unique Ligands	AKG, NI, NO3, PDO, SCN, ZN

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4K1W \| pdb_00004k1w	Download File View File

Crystal structure of the A314P mutant of mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and d-mannonate

Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

To be published

Released	2014-04-09
Method	X-RAY DIFFRACTION 1.646 Å
Organisms	Novosphingobium aromaticivorans DSM 12444
Macromolecule	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein (protein)
Unique Ligands	CO2, CO3, CS2, MG, PDO, PGE

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4L1F \| pdb_00004l1f	Download File View File

Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a mechanism of flavin-based electron bifurcation

Mowafy, A.M., Chowdhury, N.P., Demmer, J., Upadhyay, V., Kolzer, S., Jayamani, E., Kahnt, J., Demmer, U., Ermler, U., Buckel, W.

(2014) J Biological Chem 289: 5145-5157

Released	2014-01-15
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Acidaminococcus fermentans DSM 20731
Macromolecule	Acyl-CoA dehydrogenase domain protein (protein)
Unique Ligands	COS, FAD, NA, PDO, PO4

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4L68 \| pdb_00004l68	Download File View File

Structure of the psedudokinase domain of BIR2, an immune regulator of the RLK/Pelle family

Blaum, B.S., Stehle, T.

(2014) J Struct Biol 186: 112-121

Released	2014-03-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Arabidopsis thaliana
Macromolecule	Leucine-rich repeat protein kinase-like protein (protein)
Unique Ligands	PDO

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4QVB \| pdb_00004qvb	Download File View File

Mycobacterium tuberculosis protein Rv1155 in complex with co-enzyme F420

Mashalidis, E.H., Gittis, A.G., Tomczak, A., Abell, C., Barry III, C.E., Garboczi, D.N.

(2015) Protein Sci 24: 729-740

Released	2015-02-25
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Mycobacterium tuberculosis 7199-99
Macromolecule	Rv1155 protein (protein)
Unique Ligands	EDO, F42, FMT, NA, PDO, PGO

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4XZ9 \| pdb_00004xz9	Download File View File

Transaldolase variant E60Q/F132Y from T. acidophilum in complex with DHA Schiff base and G3P

Sautner, V., Tittmann, K.

(2015) Biochemistry 54: 4475-4486

Released	2015-09-30
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermoplasma acidophilum DSM 1728
Macromolecule	Probable transaldolase (protein)
Unique Ligands	ACT, G3P, GOL, PDO

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4Y88 \| pdb_00004y88	Download File View File

Crystal structure of the N-terminal domain of CEACAM8

Bonsor, D.A., Sundberg, E.J.

(2015) Proc Natl Acad Sci U S A 112: 13561-13566

Released	2015-10-07
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Carcinoembryonic antigen-related cell adhesion molecule 8 (protein)
Unique Ligands	CL, GOL, PDO, SO4

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5EJ0 \| pdb_00005ej0	Download File View File

The vaccinia virus H3 envelope protein, a major target of neutralizing antibodies, exhibits a glycosyltransferase fold and binds UDP-Glucose

Singh, K., Gittis, A.G., Gitti, R.K., Ostazesky, S.A., Su, H.P., Garboczi, D.N.

(2016) J Virol 90: 5020-5030

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Vaccinia virus WR
Macromolecule	Envelope protein H3 (protein)
Unique Ligands	DHL, EDO, EOH, GOL, MG, MOH, PDO, PG0, POL

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5JA8 \| pdb_00005ja8	Download File View File

Crystal structure of the HigB2 toxin in complex with Nb2

Hadzi, S., Loris, R.

(2017) Nucleic Acids Res 45: 4972-4983

Released	2017-04-05
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Lama glama Vibrio cholerae O1 biovar El Tor str. N16961
Macromolecule	Nanobody 2 (protein) Toxin HigB-2 (protein)
Unique Ligands	ACT, EDO, EPE, PDO, PO4

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5MED \| pdb_00005med	Download File View File

Cyanothece lipoxygenase 2 (CspLOX2)

Newie, J., Neumann, P., Werner, M., Mata, R.A., Ficner, R., Feussner, I.

(2017) Sci Rep 7: 2069-2069

Released	2017-05-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Rippkaea orientalis PCC 8801
Macromolecule	Arachidonate 15-lipoxygenase (protein)
Unique Ligands	1BO, BU1, FE, GOL, HEZ, PDO, PGR, POL

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5OK0 \| pdb_00005ok0	Download File View File

Structure of the D10N mutant of beta-phosphoglucomutase from Lactococcus lactis trapped with native reaction intermediate beta-glucose 1,6-bisphosphate to 2.2A resolution.

Robertson, A.J., Bisson, C.

(2018) ACS Catal

Released	2018-08-29
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Lactococcus lactis
Macromolecule	Beta-phosphoglucomutase (protein)
Unique Ligands	B16, MG, PDO

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5SXG \| pdb_00005sxg	Download File View File

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B

Shi, K., Kurahashi, K., Aihara, H.

(2017) Sci Rep 7: 17415-17415

Released	2017-12-27
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Homo sapiens
Macromolecule	DNA dC->dU-editing enzyme APOBEC-3B (protein)
Unique Ligands	IMD, PDO, ZN

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5WSQ \| pdb_00005wsq	Download File View File

Crystal structure of C-Hg-T pair containing DNA duplex

Gan, J.H., Liu, H.H.

(2017) Nucleic Acids Res 45: 2910-2918

Released	2017-02-08
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	unidentified
Macromolecule	DNA (5'-D(GPCPCPCPGPTPGPC)-3') (nucleic acid)
Unique Ligands	HG, PDO

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6BUM \| pdb_00006bum	Download File View File

Crystal structures of cyanuric acid hydrolase from Moorella thermoacetica

Shi, K., Cho, S., Seffernick, J.L., Bera, A., Wackett, L.P., Aihara, H.

(2019) PLoS One 14: e0216979-e0216979

Released	2019-06-12
Method	X-RAY DIFFRACTION 1.51 Å
Organisms	Moorella thermoacetica ATCC 39073
Macromolecule	Cyanuric acid amidohydrolase (protein)
Unique Ligands	CA, CL, MLI, PDO

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6BUN \| pdb_00006bun	Download File View File

Crystal structures of cyanuric acid hydrolase from Moorella thermoacetica

Shi, K., Aihara, H.

(2019) PLoS One 14: e0216979-e0216979

Released	2019-06-12
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Moorella thermoacetica ATCC 39073
Macromolecule	Cyanuric acid amidohydrolase (protein)
Unique Ligands	CA, CL, MLI, PDO

1 to 25 of 66 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

Symmetry Type

SCOP Classification

1D07 | pdb_00001d07

1IZ8 | pdb_00001iz8

1MR3 | pdb_00001mr3

1NAI | pdb_00001nai

1ZV9 | pdb_00001zv9

2O2I | pdb_00002o2i

2YMT | pdb_00002ymt

3FNK | pdb_00003fnk

3L8Q | pdb_00003l8q

4BCX | pdb_00004bcx

4HON | pdb_00004hon

4K1W | pdb_00004k1w

4L1F | pdb_00004l1f

4L68 | pdb_00004l68

4QVB | pdb_00004qvb

4XZ9 | pdb_00004xz9

4Y88 | pdb_00004y88

5EJ0 | pdb_00005ej0

5JA8 | pdb_00005ja8

5MED | pdb_00005med

5OK0 | pdb_00005ok0

5SXG | pdb_00005sxg

5WSQ | pdb_00005wsq

6BUM | pdb_00006bum

6BUN | pdb_00006bun