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Beta-lactamase from bacillus licheniformis BS3 complexed with cefoxitin

Analyse Beta-lactamase from bacillus licheniformis BS3 complexed with cefoxitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1I2W
Type: protein
Length: 511 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: P00808
Ligands: 1QL, OUT
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	255	42% helix, 18% strand	P00808
B	Beta-lactamase (EC 3.5.2.6)	protein	256	43% helix, 18% strand	P00808

Ligands and binding sites

1QL · (2R)-5-[(carbamoyloxy)methyl]-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains A, B
OUT · Carbamic acid · ligand · chains 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	237	0.64	0.83	39	empty
2	90	0.48	0.81	15	OUT
3	84	0.47	0.82	21	empty
4	116	0.36	0.74	21	1QL
5	80	0.34	0.76	19	1QL

Interfaces

1 interface between chains.

A–B · 670 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1I2W · Beta-lactamase from bacillus licheniformis BS3 complexed with cefoxitin · the same entry in another collection · chain B against B, TM-score 1.00
P00808 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00808) · a predicted model of the same protein · 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 P00808
Elsewhere: RCSB PDB 1I2W · PDBe 1I2W · UniProt P00808

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