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Crystal structure of the oxa-10 V117T mutant at pH 8.0

Analyse Crystal structure of the oxa-10 V117T mutant at pH 8.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WGW
Type: protein
Length: 493 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase oxa-10
EC: 3.5.2.6
UniProt: P14489
Ligands: SO4
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	246	39% helix, 24% strand	P14489
B	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	247	37% helix, 23% strand	P14489

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · 9 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	162	0.75	0.92	33	GOL
2	139	0.74	0.93	29	GOL
3	206	0.48	0.75	31	SO4
4	183	0.46	0.75	32	SO4

Interfaces

1 interface between chains.

A–B · 1247 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 modified (disulfide, carboxylation).

Compared structures

2WGW · Crystal structure of the OXA-10 V117T mutant at pH 8.0 · the same entry in another collection · chain A against A, TM-score 1.00
P14489 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-10 (P14489) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P14489
Elsewhere: RCSB PDB 2WGW · PDBe 2WGW · UniProt P14489

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