MolNFT v1 · #8717 · protein

Crystal structure of the class D beta-lactamase oxa-13

1H8Z: “Crystal structure of the class D beta-lactamase oxa-13”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.73). MolNFT v1 #8717 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1H8Z
Type: protein
Length: 474 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q51400
Ligands: SO4
Pockets: 6 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase (EC 3.5.2.6)	protein	237	39% helix, 24% strand	Q51400

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B

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

Pockets

6 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	191	0.73	0.89	29	empty
2	186	0.71	0.88	27	empty
3	89	0.37	0.76	21	empty
4	97	0.37	0.75	21	empty
5	65	0.34	0.77	17	SO4

Interfaces

1 interface between chains.

A–B · 1106 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1H8Z · Crystal structure of the class D beta-lactamase OXA-13 · the same entry in another collection · chain B against B, TM-score 1.00

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 Q51400
Elsewhere: RCSB PDB 1H8Z · PDBe 1H8Z · UniProt Q51400

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