MolNFT v1 · #151662 · protein

Crystal structure of oxa-427 class D beta-lactamase

6HUH: “Crystal structure of oxa-427 class D beta-lactamase”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.78). MolNFT v1 #151662 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HUH
Type: protein
Length: 484 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: A0A1Y6M6D7
Ligands: SO4
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase (EC 3.5.2.6)	protein	242	38% helix, 21% strand	A0A1Y6M6D7

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

3 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	956	0.78	0.80	83	SO4
2	51	0.31	0.77	10	empty
3	53	0.29	0.75	11	empty

Interfaces

1 interface between chains.

A–B · 296 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

6HUH · CRYSTAL STRUCTURE OF OXA-427 class D BETA-LACTAMASE · the same entry in another collection · chain A against A, 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 A0A1Y6M6D7
Elsewhere: RCSB PDB 6HUH · PDBe 6HUH · UniProt A0A1Y6M6D7

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