Research workbench

Class D beta-lactamase bat-2

Analyse Class D beta-lactamase bat-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W5G
Type: protein
Length: 474 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bat-2 beta-lactamase
EC: 3.5.2.6
UniProt: A0A0H3EA14
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Bat-2 beta-lactamase (EC 3.5.2.6)	protein	237	39% helix, 21% strand	A0A0H3EA14

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 6 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	658	0.70	0.78	43	EDO
2	155	0.46	0.76	27	EDO
3	132	0.45	0.77	23	empty
4	91	0.34	0.74	14	EDO
5	94	0.34	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 1089 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

6W5G · Class D beta-lactamase BAT-2 · 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 A0A0H3EA14
Elsewhere: RCSB PDB 6W5G · PDBe 6W5G · UniProt A0A0H3EA14

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