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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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Search Summary

This query matches 40 Structures.

Refinements

Structure Determination Methodology

experimental (40)

Scientific Name of Source Organism

	Homo sapiens (20)
	Escherichia coli K-12 (5)
	Human immunodeficiency virus type 1 (BRU ISOLATE) (3)
	Mus musculus (3)
	Rattus norvegicus (3)
	Serratia marcescens (2)
	Trypanosoma brucei brucei (2)
	synthetic construct (2)
	Aeropyrum pernix K1 (1)
	Human adenovirus 11 (1)

More...

Taxonomy

	Eukaryota (25)
	Bacteria (11)
	Riboviria (3)
	other sequences (2)
	Archaea (1)
	Varidnaviria (1)

Experimental Method

X-RAY DIFFRACTION (40)

Polymer Entity Type

Protein (40)

Refinement Resolution (Å)

	1.0 - 1.5 (13)
	1.5 - 2.0 (17)
	2.0 - 2.5 (7)
	2.5 - 3.0 (2)
	3.0 - 3.5 (1)

Release Date

	2000 - 2004 (4)
	2005 - 2009 (5)
	2010 - 2014 (19)
	2015 - 2019 (10)
	2020 - 2024 (2)

Enzyme Classification Name

	Hydrolases (15)
	Transferases (15)
	Oxidoreductases (4)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (26)
	Cyclic (13)
	Dihedral (3)

SCOP Classification

	Alpha and beta proteins (a/b) (12)
	Alpha and beta proteins (a+b) (13)
	All beta proteins (8)
	Artifacts (3)
	All alpha proteins (2)

AllSelected

1 to 25 of 40 Structures

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1E42 \| pdb_00001e42	Download File View File

Beta2-adaptin appendage domain, from clathrin adaptor AP2

Owen, D.J., Evans, P.R., McMahon, H.T.

(2000) EMBO J 19: 4216

Released	2000-08-21
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	AP-2 COMPLEX SUBUNIT BETA (protein)
Unique Ligands	CL, DTD, GOL, MG, NI

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1QTN \| pdb_00001qtn	Download File View File

CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TETRAPEPTIDE INHIBITOR ACE-IETD-ALDEHYDE

Watt, W., Watenpaugh, K.D.

(1999) Structure 7: 1135-1143

Released	2000-09-20
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Homo sapiens
Macromolecule	ACETYL-ILE-GLU-THR-ASP-ALDEHYDE (protein) CASPASE-8 (protein)
Unique Ligands	DTD

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1W80 \| pdb_00001w80	Download File View File

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170

Ford, M.G.J., Praefcke, G.J.K., McMahon, H.T.

(2004) EMBO J 23: 4371

Released	2004-10-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT (protein) SYNAPTOJANIN 1 (protein)
Unique Ligands	BEN, CO3, DTD, SO4

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2C2Z \| pdb_00002c2z	Download File View File

Crystal structure of caspase-8 in complex with aza-peptide Michael acceptor inhibitor

Ganesan, R., Jelakovic, S., Ekici, O.D., Li, Z.Z., James, K.E., Asgian, J.L., Campbell, A.J., Mikolajczyk, J., Salvesen, G.S., Powers, J.C., Gruetter, M.G.

(2006) J Med Chem 49: 5728

Released	2006-09-20
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	AZA-PEPTIDE INHIBITOR (5S, 8R, 11S)-8-(2-CARBOXYETHYL) -14-[4-(3,4-DIHYDROQUINOLIN-1(2H)-YL)-4-OXOBUTANOYL] -11-[(1R)-1-HYDROXYETHYL]-5-(2-METHYLPROPYL)-3,6,9,12-TETRAOXO -1-PHENYL-2-OXA-4,7,10,13,14-PENTAAZAHEXADECAN-16-OIC ACID (protein) CASPASE-8 P10 SUBUNIT (protein) CASPASE-8 P18 SUBUNIT (protein)
Unique Ligands	DTD

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2C97 \| pdb_00002c97	Download File View File

LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 4-(6- chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)butyl phosphate

Morgunova, E., Illarionov, B., Jin, G., Haase, I., Fischer, M., Cushman, M., Bacher, A., Ladenstein, R.

(2006) FEBS J 273: 4790

Released	2006-12-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE (protein)
Unique Ligands	ACT, DTD, JCL, K, MPD

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2IZX \| pdb_00002izx	Download File View File

Molecular Basis of AKAP Specificity for PKA Regulatory Subunits

Gold, M.G., Lygren, B., Dokurno, P., Hoshi, N., McConnachie, G., Tasken, K., Carlson, C.R., Scott, J.D., Barford, D.

(2006) Mol Cell 24: 383

Released	2006-11-08
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	AKAP-IS (protein) CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY SUBUNIT (protein)
Unique Ligands	DTD

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2PVA \| pdb_00002pva	Download File View File

OXIDIZED PENICILLIN V ACYLASE FROM B. SPHAERICUS

Suresh, C.G., Pundle, A.V., Rao, K.N., SivaRaman, H., Brannigan, J.A., McVey, C.E., Verma, C.S., Dauter, Z., Dodson, E.J., Dodson, G.G.

(1999) Nat Struct Biol 6: 414-416

Released	2000-07-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Lysinibacillus sphaericus
Macromolecule	PENICILLIN V ACYLASE (protein)
Unique Ligands	DTD

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2VJ0 \| pdb_00002vj0	Download File View File

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170

Ford, M.G.J., Praefcke, G.J.K., McMahon, H.T.

(2008) J Biological Chem 283: 5099

Released	2007-12-25
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens Mus musculus Rattus norvegicus
Macromolecule	AMPHIPHYSIN (protein) AP-2 COMPLEX SUBUNIT ALPHA-2 (protein) SYNAPTOJANIN-1 (protein)
Unique Ligands	BEN, CL, DTD, SO4

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2X9N \| pdb_00002x9n	Download File View File

High resolution structure of TbPTR1 in complex with cyromazine

Dawson, A., Tulloch, L.B., Barrack, K.L., Hunter, W.N.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1334

Released	2010-06-30
Method	X-RAY DIFFRACTION 1.15 Å
Organisms	Trypanosoma brucei brucei
Macromolecule	PTERIDINE REDUCTASE (protein)
Unique Ligands	ACT, AX3, D1D, DTD, NA, NAP

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3GVO \| pdb_00003gvo	Download File View File

Structure and RNA binding of the mouse Pumilio-2 Puf Domain

Jenkins, H.T., Edwards, T.A.

(2009) J Struct Biol 167: 271-276

Released	2009-06-30
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Mus musculus
Macromolecule	Pumilio homolog 2 (protein)
Unique Ligands	DTD, GOL

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3MW0 \| pdb_00003mw0	Download File View File

X-ray structure of the doubly hydroxylated iron complex-NikA species, NikA1/O2

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	BHR, DTD, FE

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3MZ9 \| pdb_00003mz9	Download File View File

X-ray structure of NikA in complex with HBED

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, BHN, CL, DTD, FE, GOL, SO4

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3MZB \| pdb_00003mzb	Download File View File

X-ray structure of NikA in complex with the doubly hydroxylated iron complex, 1-O2

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, BHR, CL, DTD, FE, GOL, SO4

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3O8E \| pdb_00003o8e	Download File View File

Structure of extracelllar portion of CD46 in complex with Adenovirus type 11 knob

Persson, B.D., Schmitz, N.B., Casasnovas, J.M., Stehle, T.

(2010) PLoS Pathog 6: e1001122-e1001122

Released	2010-10-13
Method	X-RAY DIFFRACTION 2.84 Å
Organisms	Homo sapiens Human adenovirus 11
Macromolecule	Fiber 36.1 kDa protein (protein) Membrane cofactor protein (protein)
Unique Ligands	DTD
Unique branched monosaccharides	NAG

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3OQV \| pdb_00003oqv	Download File View File

AlbC, a cyclodipeptide synthase from Streptomyces noursei

Sauguet, L., Ledu, M.H., Charbonnier, J.B., Gondry, M.

(2011) Nucleic Acids Res 39: 4475-4489

Released	2011-02-16
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Streptomyces noursei
Macromolecule	AlbC (protein)
Unique Ligands	DTD, PO4

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3QPJ \| pdb_00003qpj	Download File View File

HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor

Lindemann, I., Heine, A., Klebe, G.

To be published

Released	2012-02-15
Method	X-RAY DIFFRACTION 1.61 Å
Organisms	Human immunodeficiency virus type 1 (BRU ISOLATE)
Macromolecule	Protease (protein)
Unique Ligands	CL, DTD, N4I

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3QRM \| pdb_00003qrm	Download File View File

HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor

Lindemann, I., Heine, A., Klebe, G.

To be published

Released	2012-02-22
Method	X-RAY DIFFRACTION 1.731 Å
Organisms	Human immunodeficiency virus type 1 (BRU ISOLATE)
Macromolecule	Protease (protein)
Unique Ligands	CL, DTD, NK7

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3QRO \| pdb_00003qro	Download File View File

HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor

Lindemann, I., Heine, A., Klebe, G.

To be published

Released	2012-02-22
Method	X-RAY DIFFRACTION 1.616 Å
Organisms	Human immunodeficiency virus type 1 (BRU ISOLATE)
Macromolecule	Protease (protein)
Unique Ligands	CL, DTD, GOL, NK9

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3R6T \| pdb_00003r6t	Download File View File

Rat catechol o-methyltransferase in complex with the bisubstrate inhibitor 4'-fluoro-4,5-dihydroxy-biphenyl-3-carboxylic acid {(E)-3-[(2S,4R,5R)-4-hydroxy-5-(6-methyl-purin-9-yl)-tetrahydro-furan-2-yl]-allyl}-amide

Ehler, A., Schlatter, D., Stihle, M., Benz, J., Rudolph, M.G.

(2012) Acta Crystallogr D Biol Crystallogr 68: 253-260

Released	2012-02-01
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Rattus norvegicus
Macromolecule	Catechol O-methyltransferase (protein)
Unique Ligands	CL, DTD, LU1, MG, NHE, SO4

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3TH1 \| pdb_00003th1	Download File View File

Crystal structure of chlorocatechol 1,2-dioxygenase from Pseudomonas putida

Rustiguel, J.K., Nonato, M.C.

To be published

Released	2012-08-22
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Pseudomonas putida
Macromolecule	Chlorocatechol 1,2-dioxygenase (protein)
Unique Ligands	3PH, ACT, DTD, FE, GOL, MG

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3WD0 \| pdb_00003wd0	Download File View File

Serratia marcescens Chitinase B, tetragonal form

Hirose, T., Maita, N., Gouda, H., Koseki, J., Yamamoto, T., Sugawara, A., Nakano, H., Hirono, S., Shiomi, K., Watanabe, T., Taniguchi, H., Sharpless, K.B., Omura, S., Sunazuka, T.

(2013) Proc Natl Acad Sci U S A 110: 15892-15897

Released	2013-09-18
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Serratia marcescens
Macromolecule	Chitinase B (protein)
Unique Ligands	DTD, GOL, SO4

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3WD2 \| pdb_00003wd2	Download File View File

Serratia marcescens Chitinase B complexed with azide inhibitor

Hirose, T., Maita, N., Gouda, H., Koseki, J., Yamamoto, T., Sugawara, A., Nakano, H., Hirono, S., Shiomi, K., Watanabe, T., Taniguchi, H., Sharpless, K.B., Omura, S., Sunazuka, T.

(2013) Proc Natl Acad Sci U S A 110: 15892-15897

Released	2013-09-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Serratia marcescens
Macromolecule	Chitinase B (protein)
Unique Ligands	A1L, DTD, GOL, SO4

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4AW0 \| pdb_00004aw0	Download File View File

Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the PIF-Pocket

Schulze, J.O., Busschots, K., Lopez-Garcia, L.A., Lammi, C., Stroba, A., Zeuzem, S., Piiper, A., Alzari, P.M., Neimanis, S., Arencibia, J.M., Engel, M., Biondi, R.M.

(2012) Chem Biol 19: 1152

Released	2012-10-03
Method	X-RAY DIFFRACTION 1.43 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (protein)
Unique Ligands	ATP, DMS, DTD, MG, MJF

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4CLE \| pdb_00004cle	Download File View File

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor

Barrack, K.L., Hunter, W.N.

(2014) J Med Chem 57: 6479

Released	2015-01-21
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Trypanosoma brucei brucei
Macromolecule	PTERIDINE REDUCTASE 1 (protein)
Unique Ligands	DTD, JR2, NAP

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4CT1 \| pdb_00004ct1	Download File View File

Human PDK1-PKCzeta Kinase Chimera in Complex with Allosteric Compound PS315 Bound to the PIF-Pocket

Schulze, J.O., Zhang, H., Lopez-Garcia, L.A., Biondi, R.M.

(2014) Chem Biol 21: 754

Released	2014-05-28
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (protein)
Unique Ligands	31S, ATP, DMS, DTD

1 to 25 of 40 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

1E42 | pdb_00001e42

1QTN | pdb_00001qtn

1W80 | pdb_00001w80

2C2Z | pdb_00002c2z

2C97 | pdb_00002c97

2IZX | pdb_00002izx

2PVA | pdb_00002pva

2VJ0 | pdb_00002vj0

2X9N | pdb_00002x9n

3GVO | pdb_00003gvo

3MW0 | pdb_00003mw0

3MZ9 | pdb_00003mz9

3MZB | pdb_00003mzb

3O8E | pdb_00003o8e

3OQV | pdb_00003oqv

3QPJ | pdb_00003qpj

3QRM | pdb_00003qrm

3QRO | pdb_00003qro

3R6T | pdb_00003r6t

3TH1 | pdb_00003th1

3WD0 | pdb_00003wd0

3WD2 | pdb_00003wd2

4AW0 | pdb_00004aw0

4CLE | pdb_00004cle

4CT1 | pdb_00004ct1