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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "B2M"

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Search Summary

This query matches 57 Structures.

Refinements

Structure Determination Methodology

experimental (57)

Scientific Name of Source Organism

	Klebsiella pneumoniae (13)
	Halorhodospira halophila (12)
	synthetic construct (6)
	Homo sapiens (5)
	Pseudomonas aeruginosa PAO1 (4)
	Bacillus cereus (3)
	Escherichia coli K-12 (3)
	Aequorea victoria (2)
	Candida albicans (2)
	Actinomycetota bacterium (1)

More...

Taxonomy

	Bacteria (47)
	Eukaryota (11)
	other sequences (6)
	Archaea (1)
	Duplodnaviria (1)
	Riboviria (1)

Experimental Method

	X-RAY DIFFRACTION (53)
	ELECTRON MICROSCOPY (4)

Polymer Entity Type

	Protein (57)
	DNA (7)
	RNA (2)

Refinement Resolution (Å)

	0.5 - 1.0 (3)
	1.0 - 1.5 (16)
	1.5 - 2.0 (17)
	2.0 - 2.5 (10)
	2.5 - 3.0 (9)
	3.0 - 3.5 (1)
	> 4.5 (1)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (6)
	2005 - 2009 (12)
	2010 - 2014 (2)
	2015 - 2019 (13)
	2020 - 2024 (21)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (28)
	Oxidoreductases (3)
	Transferases (3)

Membrane Protein Annotation

	MemProtMD (1)
	OPM (1)
	PDBTM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (46)
	Cyclic (10)
	Dihedral (2)

SCOP Classification

	Alpha and beta proteins (a+b) (7)
	Multi-domain proteins (alpha and beta) (12)
	All alpha proteins (2)
	Alpha and beta proteins (a/b) (4)

AllSelected

1 to 25 of 57 Structures

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1BOO \| pdb_00001boo	Download File View File

PVUII DNA METHYLTRANSFERASE (CYTOSINE-N4-SPECIFIC)

Gong, W., O'Gara, M., Blumenthal, R.M., Cheng, X.

(1997) Nucleic Acids Res 25: 2702-2715

Released	1998-08-12
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Proteus vulgaris
Macromolecule	PROTEIN (N-4 CYTOSINE-SPECIFIC METHYLTRANSFERASE PVU II) (protein)
Unique Ligands	SAH

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1N9B \| pdb_00001n9b	Download File View File

Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme

Nukaga, M., Mayama, K., Hujer, A.M., Bonomo, R.A., Knox, J.R.

(2003) J Mol Biology 328: 289-301

Released	2003-04-08
Method	X-RAY DIFFRACTION 0.9 Å
Organisms	Klebsiella pneumoniae
Macromolecule	BETA-LACTAMASE SHV-2 (protein)
Unique Ligands	EPE, MA4, MPD

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1ONG \| pdb_00001ong	Download File View File

SHV-1 beta-lactamase with a penem inhibitor

Nukaga, M., Mayama, K., Bonomo, R.A., Knox, J.R.

(2003) Biochemistry 42: 13152-13159

Released	2003-12-09
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Klebsiella pneumoniae
Macromolecule	BETA-LACTAMASE SHV-1 (protein)
Unique Ligands	MA4, WY4

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1Q2P \| pdb_00001q2p	Download File View File

SHV-1 class A beta-lactamase complexed with penem WAY185229

Nukaga, M., Venkatesan, A.M., Mansour, T.S., Hujer, A., Bonomo, R.A., Knox, J.R.

(2004) J Med Chem 47: 6556-6568

Released	2004-09-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Klebsiella pneumoniae
Macromolecule	beta-lactamase SHV-1 (protein)
Unique Ligands	MA4, WY2

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1SHV \| pdb_00001shv	Download File View File

STRUCTURE OF SHV-1 BETA-LACTAMASE

Kuzin, A.P., Nukaga, M., Nukaga, Y., Hujer, A., Bonomo, R.A., Knox, J.R.

(1999) Biochemistry 38: 5720-5727

Released	1999-05-06
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Klebsiella pneumoniae
Macromolecule	PROTEIN (BETA-LACTAMASE SHV-1) (protein)
Unique Ligands	MA4

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1TDG \| pdb_00001tdg	Download File View File

Complex of S130G SHV-1 beta-lactamase with tazobactam

Sun, T., Bethel, C.R., Bonomo, R.A., Knox, J.R.

(2004) Biochemistry 43: 14111-14117

Released	2004-11-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase SHV-1 (protein)
Unique Ligands	MA4, MDD, MPD, MRD, TBE

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1TDL \| pdb_00001tdl	Download File View File

Structure of Ser130Gly SHV-1 beta-lactamase

Sun, T., Bethel, C.R., Bonomo, R.A., Knox, J.R.

(2004) Biochemistry 43: 14111-14117

Released	2004-11-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase SHV-1 (protein)
Unique Ligands	EPE, MA4

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1VM1 \| pdb_00001vm1	Download File View File

STRUCTURE OF SHV-1 BETA-LACTAMASE INHIBITED BY TAZOBACTAM

Kuzin, A.P., Nukaga, M., Nukaga, Y., Hujer, A., Bonomo, R.A., Knox, J.R.

(2001) Biochemistry 40: 1861-1866

Released	2004-09-07
Method	X-RAY DIFFRACTION 2.02 Å
Organisms	Klebsiella pneumoniae
Macromolecule	BETA-LACTAMASE SHV-1 (protein)
Unique Ligands	AKR, MA4, TAZ, TBE

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2G2U \| pdb_00002g2u	Download File View File

Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex

Reynolds, K.A., Thomson, J.M., Corbett, K.D., Bethel, C.R., Berger, J.M., Kirsch, J.F., Bonomo, R.A., Handel, T.M.

(2006) J Biological Chem 281: 26745-26753

Released	2006-07-04
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Klebsiella pneumoniae Streptomyces clavuligerus
Macromolecule	Beta-lactamase SHV-1 (protein) Beta-lactamase inhibitory protein (protein)

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2GS4 \| pdb_00002gs4	Download File View File

The crystal structure of the E.coli stress protein YciF.

Hindupur, A., Liu, D., Zhao, Y., Bellamy, H.D., White, M.A., Fox, R.O.

(2006) Protein Sci 15: 2605-2611

Released	2006-10-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	Protein yciF (protein)

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2H10 \| pdb_00002h10	Download File View File

Crystal structure of the M69V E166A double mutant of SHV-1 b-lactamase complexed to tazobactam

van den Akker, F., Padayatti, P.S.

(2006) Biochemistry 45: 11895-11904

Released	2007-01-30
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase SHV-1 (protein)
Unique Ligands	MA4, TBE

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2H5S \| pdb_00002h5s	Download File View File

SA2-13 penam sulfone complexed to wt SHV-1 beta-lactamase

van den Akker, F., Padayatti, P.S.

(2006) J Am Chem Soc 128: 13235-13242

Released	2006-10-17
Method	X-RAY DIFFRACTION 1.28 Å
Organisms	Klebsiella pneumoniae
Macromolecule	SHV-1 beta-lactamase (protein)
Unique Ligands	MA4, SA2

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2OV5 \| pdb_00002ov5	Download File View File

Crystal structure of the KPC-2 carbapenemase

Ke, W., Bethel, C.R., Thomson, J.M., Bonomo, R.A., van den Akker, F.

(2007) Biochemistry 46: 5732-5740

Released	2007-05-01
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Carbapenemase (protein)
Unique Ligands	BCN

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2V4E \| pdb_00002v4e	Download File View File

A non-cytotoxic DsRed variant for whole-cell labeling

Strack, R.L., Strongin, D.E., Bhattacharyya, D., Tao, W., Berman, A., Broxmeyer, H.E., Keenan, R.J., Glick, B.S.

(2008) Nat Methods 5: 955

Released	2008-11-04
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Discosoma sp.
Macromolecule	RED FLUORESCENT PROTEIN DRFP583 (protein)

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2WFE \| pdb_00002wfe	Download File View File

Structure of the Candida albicans cytosolic leucyl-tRNA synthetase editing domain

Seiradake, E., Mao, W., Hernandez, V., Baker, S.J., Plattner, J.J., Alley, M.R.K., Cusack, S.

(2009) J Mol Biology 390: 196

Released	2009-05-19
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Candida albicans
Macromolecule	CYTOSOLIC LEUCYL-TRNA SYNTHETASE (protein)

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2WFG \| pdb_00002wfg	Download File View File

Structure of the Candida albicans cytosolic leucyl-tRNA synthetase editing domain bound to a benzoxaborole-AMP adduct

Seiradake, E., Mao, W., Hernandez, V., Baker, S.J., Plattner, J.J., Alley, M.R.K., Cusack, S.

(2009) J Mol Biology 390: 196

Released	2009-05-19
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Candida albicans
Macromolecule	CYTOSOLIC LEUCYL-TRNA SYNTHETASE (protein)
Unique Ligands	ZZB

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2WYB \| pdb_00002wyb	Download File View File

The quorum quenching N-acyl homoserine lactone acylase PvdQ with a covalently bound dodecanoic acid

Bokhove, M., Nadal Jimenez, P., Quax, W.J., Dijkstra, B.W.

(2010) Proc Natl Acad Sci U S A 107: 686

Released	2009-12-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA (protein) ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA (protein)
Unique Ligands	DAO, GOL

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2WYC \| pdb_00002wyc	Download File View File

The quorum quenching N-acyl homoserine lactone acylase PvdQ in complex with 3-oxo-lauric acid

Bokhove, M., Nadal Jimenez, P., Quax, W.J., Dijkstra, B.W.

(2010) Proc Natl Acad Sci U S A 107: 686

Released	2009-12-29
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA (protein) ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA (protein)
Unique Ligands	3LA, DMS, GOL

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2WYD \| pdb_00002wyd	Download File View File

The quorum quenching N-acyl homoserine lactone acylase PvdQ in complex with dodecanoic acid

Bokhove, M., Nadal Jimenez, P., Quax, W.J., Dijkstra, B.W.

(2010) Proc Natl Acad Sci U S A 107: 686

Released	2009-12-29
Method	X-RAY DIFFRACTION 1.901 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA (protein) ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA (protein)
Unique Ligands	DAO, GOL

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2WYE \| pdb_00002wye	Download File View File

The quorum quenching N-acyl homoserine lactone acylase PvdQ is an Ntn- Hydrolase with an unusual substrate-binding pocket

Bokhove, M., Nadal Jimenez, P., Quax, W.J., Dijkstra, B.W.

(2010) Proc Natl Acad Sci U S A 107: 686

Released	2009-12-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA (protein) ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA (protein)
Unique Ligands	GOL

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3V50 \| pdb_00003v50	Download File View File

Complex of SHV S130G mutant beta-lactamase complexed to SA2-13

Wei, K., van den Akker, F.

(2012) ChemMedChem 7: 1002-1008

Released	2012-08-08
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase (protein)
Unique Ligands	MA4, SA2

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3V5M \| pdb_00003v5m	Download File View File

Crystal structure of M69V mutant of SHV beta-lactamase

van den Akker, F., Rodkey, E.A.

(2012) ChemMedChem 7: 1002-1008

Released	2012-08-08
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase (protein)
Unique Ligands	MA4

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4XSG \| pdb_00004xsg	Download File View File

The complex structure of C3cer exoenzyme and GTP bound RhoA (NADH-free state)

Toda, A., Tsurumura, T., Yoshida, T., Tsuge, H.

(2015) J Biological Chem 290: 19423-19432

Released	2015-06-24
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bacillus cereus Homo sapiens
Macromolecule	ADP-ribosyltransferase (protein) Transforming protein RhoA (protein)
Unique Ligands	EDO, GSP, MG

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4XSH \| pdb_00004xsh	Download File View File

The complex structure of C3cer exoenzyme and GTP bound RhoA (NADH-bound state)

Toda, A., Tsurumura, T., Yoshida, T., Tsuge, H.

(2015) J Biological Chem 290: 19423-19432

Released	2015-06-24
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bacillus cereus Homo sapiens
Macromolecule	ADP-ribosyltransferase (protein) Transforming protein RhoA (protein)
Unique Ligands	EDO, GSP, MG, NAI

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4ZSF \| pdb_00004zsf	Download File View File

Crystal structure of pre-specific restriction endonuclease BsaWI-DNA complex

Tamulaitiene, G., Rutkauskas, M., Grazulis, S., Siksnys, V.

(2015) Nucleic Acids Res 43: 8100-8110

Released	2015-10-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Geobacillus stearothermophilus synthetic construct
Macromolecule	BsaWI endonuclease (protein) DNA (nucleic acid)
Unique Ligands	CA, SIN

1 to 25 of 57 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

1BOO | pdb_00001boo

1N9B | pdb_00001n9b

1ONG | pdb_00001ong

1Q2P | pdb_00001q2p

1SHV | pdb_00001shv

1TDG | pdb_00001tdg

1TDL | pdb_00001tdl

1VM1 | pdb_00001vm1

2G2U | pdb_00002g2u

2GS4 | pdb_00002gs4

2H10 | pdb_00002h10

2H5S | pdb_00002h5s

2OV5 | pdb_00002ov5

2V4E | pdb_00002v4e

2WFE | pdb_00002wfe

2WFG | pdb_00002wfg

2WYB | pdb_00002wyb

2WYC | pdb_00002wyc

2WYD | pdb_00002wyd

2WYE | pdb_00002wye

3V50 | pdb_00003v50

3V5M | pdb_00003v5m

4XSG | pdb_00004xsg

4XSH | pdb_00004xsh

4ZSF | pdb_00004zsf