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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 536 Structures.

Refinements

Structure Determination Methodology

experimental (536)

Scientific Name of Source Organism

	Homo sapiens (194)
	Escherichia coli (80)
	Tequatrovirus T4 (42)
	Rattus norvegicus (25)
	Thermus thermophilus HB8 (21)
	Cereibacter sphaeroides (20)
	Escherichia coli K-12 (19)
	Nonlabens marinus S1-08 (19)
	Methanocaldococcus jannaschii DSM 2661 (18)
	synthetic construct (18)

More...

Taxonomy

	Bacteria (295)
	Eukaryota (269)
	Archaea (63)
	Duplodnaviria (46)
	other sequences (18)
	Varidnaviria (4)
	Riboviria (2)

Experimental Method

	X-RAY DIFFRACTION (513)
	ELECTRON MICROSCOPY (22)
	ELECTRON CRYSTALLOGRAPHY (1)

Polymer Entity Type

Protein (536)

Refinement Resolution (Å)

	1.0 - 1.5 (11)
	1.5 - 2.0 (77)
	2.0 - 2.5 (174)
	2.5 - 3.0 (198)
	3.0 - 3.5 (68)
	3.5 - 4.0 (7)
	4.0 - 4.5 (1)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (1)
	2010 - 2014 (61)
	2015 - 2019 (223)
	2020 - 2024 (225)
	2025 - 2029 (25)

Enzyme Classification Name

	Hydrolases (60)
	Translocases (20)
	Oxidoreductases (25)
	Transferases (23)
	Lyases (1)

Membrane Protein Annotation

	PDBTM (508)
	MemProtMD (404)
	mpstruc (351)
	OPM (258)

Symmetry Type

	Asymmetric (388)
	Cyclic (151)
	Dihedral (1)

SCOP Classification

	Membrane and cell surface proteins and peptides (66)
	All beta proteins (25)
	Artifacts (9)
	Alpha and beta proteins (a+b) (3)

AllSelected

1 to 25 of 536 Structures

Page 1 of 22

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1E12 \| pdb_00001e12	Download File View File

Halorhodopsin, a light-driven chloride pump

Essen, L.-O., Kolbe, M., Oesterhelt, D.

(2000) Science 288: 1390

Released	2000-06-02
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Halobacterium salinarum
Macromolecule	HALORHODOPSIN (protein)
Unique Ligands	CL, K, OLC, PLM, RET

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3D4S \| pdb_00003d4s	Download File View File

Cholesterol bound form of human beta2 adrenergic receptor.

Hanson, M.A., Cherezov, V., Roth, C.B., Griffith, M.T., Jaakola, V.-P., Chien, E.Y.T., Velasquez, J., Kuhn, P., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

(2008) Structure 16: 897-905

Released	2008-06-17
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Beta-2 adrenergic receptor/T4-lysozyme chimera (protein)
Unique Ligands	CLR, OLC, TIM

Explore in 3D

3NY8 \| pdb_00003ny8	Download File View File

Crystal structure of the human beta2 adrenergic receptor in complex with the inverse agonist ICI 118,551

Wacker, D., Fenalti, G., Brown, M.A., Katritch, V., Abagyan, R., Cherezov, V., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

(2010) J Am Chem Soc 132: 11443-11445

Released	2010-08-11
Method	X-RAY DIFFRACTION 2.84 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Beta-2 adrenergic receptor, Lysozyme (protein)
Unique Ligands	CLR, JRZ, OLA, OLC, PGE

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3NY9 \| pdb_00003ny9	Download File View File

Crystal structure of the human beta2 adrenergic receptor in complex with a novel inverse agonist

Fenalti, G., Wacker, D., Brown, M.A., Katritch, V., Abagyan, R., Cherezov, V., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

(2010) J Am Chem Soc 132: 11443-11445

Released	2010-08-11
Method	X-RAY DIFFRACTION 2.84 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Beta-2 adrenergic receptor, Lysozyme (protein)
Unique Ligands	CLR, JSZ, OLC

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3ODU \| pdb_00003odu	Download File View File

The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t

Wu, B., Mol, C.D., Han, G.W., Katritch, V., Chien, E.Y.T., Liu, W., Cherezov, V., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

(2010) Science 330: 1066-1071

Released	2010-10-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	C-X-C chemokine receptor type 4, Lysozyme Chimera (protein)
Unique Ligands	ITD, OLA, OLC

Explore in 3D

3OE6 \| pdb_00003oe6	Download File View File

Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in I222 spacegroup

Wu, B., Mol, C.D., Han, G.W., Katritch, V., Chien, E.Y.T., Liu, W., Cherezov, V., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

(2010) Science 330: 1066-1071

Released	2010-10-27
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	C-X-C chemokine receptor type 4, Lysozyme Chimera (protein)
Unique Ligands	GOL, ITD, OLC

Explore in 3D

3POQ \| pdb_00003poq	Download File View File

Crystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, small unit cell

Efremov, R.G., Sazanov, L.A.

(2012) J Struct Biol 178: 311-318

Released	2012-03-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli BL21
Macromolecule	OmpF protein (protein)
Unique Ligands	OLC, SCN

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3POU \| pdb_00003pou	Download File View File

Crystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, large unit cell

Efremov, R.G., Sazanov, L.A.

(2012) J Struct Biol 178: 311-318

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli BL21
Macromolecule	OmpF protein (protein)
Unique Ligands	OLC

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3POX \| pdb_00003pox	Download File View File

Crystal Structure of E.coli OmpF porin in lipidic cubic phase: space group P1

Efremov, R.G., Sazanov, L.A.

(2012) J Struct Biol 178: 311-318

Released	2012-03-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli BL21
Macromolecule	OmpF protein (protein)
Unique Ligands	K, OLC, SCN

Explore in 3D

3QAK \| pdb_00003qak	Download File View File

Agonist bound structure of the human adenosine A2a receptor

Xu, F., Wu, H., Katritch, V., Han, G.W., Cherezov, V., Stevens, R., GPCR Network (GPCR)

(2011) Science 332: 322-327

Released	2011-03-09
Method	X-RAY DIFFRACTION 2.71 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Adenosine receptor A2a,lysozyme chimera (protein)
Unique Ligands	OLC, UKA

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3RZE \| pdb_00003rze	Download File View File

Structure of the human histamine H1 receptor in complex with doxepin

Shimamura, T., Han, G.W., Shiroishi, M., Weyand, S., Tsujimoto, H., Winter, G., Katritch, V., Abagyan, R., Cherezov, V., Liu, W., Kobayashi, T., Stevens, R., Iwata, S., GPCR Network (GPCR)

(2011) Nature 475: 65-70

Released	2011-06-15
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Histamine H1 receptor, Lysozyme chimera (protein)
Unique Ligands	5EH, D7V, OLC, PO4

Explore in 3D

3S8F \| pdb_00003s8f	Download File View File

1.8 A structure of ba3 cytochrome c oxidase from Thermus thermophilus in lipid environment

Tiefenbrunn, T., Liu, W., Chen, Y., Katritch, V., Stout, C.D., Fee, J.A., Cherezov, V.

(2011) PLoS One 6: e22348-e22348

Released	2011-08-03
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Cytochrome c oxidase polypeptide 2A (protein) Cytochrome c oxidase subunit 1 (protein) Cytochrome c oxidase subunit 2 (protein)
Unique Ligands	CU, CUA, HAS, HEM, OLC, PER

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3S8G \| pdb_00003s8g	Download File View File

1.8 A structure of ba3 cytochrome c oxidase mutant (A120F) from Thermus thermophilus in lipid environment

Tiefenbrunn, T., Liu, W., Chen, Y., Katritch, V., Stout, C.D., Fee, J.A., Cherezov, V.

(2011) PLoS One 6: e22348-e22348

Released	2011-08-03
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Cytochrome c oxidase polypeptide 2A (protein) Cytochrome c oxidase subunit 1 (protein) Cytochrome c oxidase subunit 2 (protein)
Unique Ligands	CU, CUA, HAS, HEM, OLC, PER

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3V5U \| pdb_00003v5u	Download File View File

Structure of Sodium/Calcium Exchanger from Methanocaldococcus jannaschii DSM 2661

Jiang, Y., Liao, J., Li, H., Zeng, W., Sauer, D., Belmares, R.

(2012) Science 335: 686-690

Released	2012-02-22
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Methanocaldococcus jannaschii DSM 2661
Macromolecule	Uncharacterized membrane protein MJ0091 (protein)
Unique Ligands	1PE, ACT, CA, MYS, NA, OLC

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3VVN \| pdb_00003vvn	Download File View File

Crystal structure of MATE in the straight conformation

Tanaka, Y., Ishitani, R., Nureki, O.

(2013) Nature 496: 247-251

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.398 Å
Organisms	Pyrococcus furiosus DSM 3638
Macromolecule	Putative uncharacterized protein (protein)
Unique Ligands	OLC

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3VVO \| pdb_00003vvo	Download File View File

Crystal structure of MATE in the bent conformation

Tanaka, Y., Ishitani, R., Nureki, O.

(2013) Nature 496: 247-251

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.504 Å
Organisms	Pyrococcus furiosus
Macromolecule	Putative uncharacterized protein (protein)
Unique Ligands	OLC

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3VVR \| pdb_00003vvr	Download File View File

Crystal structure of MATE in complex with MaD5

Tanaka, Y., Ishitani, R., Nureki, O.

(2013) Nature 496: 247-251

Released	2013-04-03
Method	X-RAY DIFFRACTION 3 Å
Organisms	Pyrococcus furiosus
Macromolecule	Putative uncharacterized protein (protein) macrocyclic peptide (protein)
Unique Ligands	OLC

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3VVS \| pdb_00003vvs	Download File View File

Crystal structure of MATE in complex with MaD3S

Tanaka, Y., Ishitani, R., Nureki, O.

(2013) Nature 496: 247-251

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus furiosus
Macromolecule	Putative uncharacterized protein (protein) macrocyclic peptide (protein)
Unique Ligands	OLC

Explore in 3D

3VW7 \| pdb_00003vw7	Download File View File

Crystal structure of human protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar at 2.2 angstrom

Zhang, C., Srinivasan, Y., Arlow, D.H., Fung, J.J., Palmer, D., Zheng, Y., Green, H.F., Pandey, A., Dror, R.O., Shaw, D.E., Weis, W.I., Coughlin, S.R., Kobilka, B.K.

(2012) Nature 492: 387-392

Released	2012-12-12
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Proteinase-activated receptor 1, Lysozyme (protein)
Unique Ligands	CL, NA, OLC, VPX

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3W4T \| pdb_00003w4t	Download File View File

Crystal structure of MATE P26A mutant

Tanaka, Y., Ishitani, R., Nureki, O.

(2013) Nature 496: 247-251

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.096 Å
Organisms	Pyrococcus furiosus DSM 3638
Macromolecule	Putative uncharacterized protein (protein)
Unique Ligands	OLC

Explore in 3D

3WBN \| pdb_00003wbn	Download File View File

Crystal structure of MATE in complex with MaL6

Tanaka, Y., Ishitani, R., Nureki, O.

(2013) Nature 496: 247-251

Released	2013-06-12
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Pyrococcus furiosus DSM 3638
Macromolecule	MaL6 (protein) Putative uncharacterized protein (protein)
Unique Ligands	OLC

Explore in 3D

3WO6 \| pdb_00003wo6	Download File View File

Crystal structure of YidC from Bacillus halodurans (form I)

Kumazaki, K., Tsukazaki, T., Ishitani, R., Nureki, O.

(2014) Nature 509: 516-520

Released	2014-04-23
Method	X-RAY DIFFRACTION 2.403 Å
Organisms	Halalkalibacterium halodurans C-125
Macromolecule	Membrane protein insertase YidC 2 (protein)
Unique Ligands	CD, OLC

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4BVN \| pdb_00004bvn	Download File View File

Ultra-thermostable beta1-adrenoceptor with cyanopindolol bound

Miller, J., Nehme, R., Warne, T., Edwards, P.C., Leslie, A.G.W., Schertler, G., Tate, C.G.

(2014) PLoS One 9: 92727

Released	2014-04-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Meleagris gallopavo
Macromolecule	BETA-1 ADRENERGIC RECEPTOR (protein)
Unique Ligands	MHA, NA, OLC, P32

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4CJZ \| pdb_00004cjz	Download File View File

Crystal structure of the integral membrane diacylglycerol kinase DgkA- 9.9, delta 4

Li, D., Aragao, D., Pye, V.E., Caffrey, M.

To be published

Released	2015-01-28
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Escherichia coli K-12
Macromolecule	DIACYLGLYCEROL KINASE (protein)
Unique Ligands	OLC

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4CK0 \| pdb_00004ck0	Download File View File

Crystal structure of the integral membrane diacylglycerol kinase - form 2

Li, D., Lyons, J.A., Vogeley, L., Aragao, D., Caffrey, M.

To be published

Released	2015-01-28
Method	X-RAY DIFFRACTION 2.924 Å
Organisms	Escherichia coli K-12
Macromolecule	DIACYLGLYCEROL KINASE (protein)
Unique Ligands	ACP, OLC, ZN

1 to 25 of 536 Structures

Page 1 of 22

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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

1E12 | pdb_00001e12

3D4S | pdb_00003d4s

3NY8 | pdb_00003ny8

3NY9 | pdb_00003ny9

3ODU | pdb_00003odu

3OE6 | pdb_00003oe6

3POQ | pdb_00003poq

3POU | pdb_00003pou

3POX | pdb_00003pox

3QAK | pdb_00003qak

3RZE | pdb_00003rze

3S8F | pdb_00003s8f

3S8G | pdb_00003s8g

3V5U | pdb_00003v5u

3VVN | pdb_00003vvn

3VVO | pdb_00003vvo

3VVR | pdb_00003vvr

3VVS | pdb_00003vvs

3VW7 | pdb_00003vw7

3W4T | pdb_00003w4t

3WBN | pdb_00003wbn

3WO6 | pdb_00003wo6

4BVN | pdb_00004bvn

4CJZ | pdb_00004cjz

4CK0 | pdb_00004ck0