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Crystal structure of oxa-10 with vnrx-5133

Analyse Crystal structure of oxa-10 with vnrx-5133 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RTN
Type: protein
Length: 491 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: KJK, CL
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	245	39% helix, 23% strand	P14489
B	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	246	41% helix, 24% strand	P14489

Ligands and binding sites

KJK · (3~{R})-3-[2-[4-(2-azanylethylamino) cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 12 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.81	0.89	68	CL
2	86	0.44	0.80	23	empty
3	82	0.31	0.73	16	KJK
4	51	0.31	0.77	12	empty
5	53	0.26	0.73	14	KJK

Interfaces

1 interface between chains.

A–B · 1020 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6RTN · Crystal structure of OXA-10 with VNRX-5133 · 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 6RTN · PDBe 6RTN · UniProt P14489

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