MolNFT v1 · #168101 · protein

Class D beta-lactamase bsu-2 delta mutant

6W5F · Bsu-2DELTA mutant: “Class D beta-lactamase bsu-2 delta mutant”. X-ray diffraction, 9 pockets (best druggability 0.70). MolNFT v1 #168101 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6W5F
Type: protein
Length: 938 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bsu-2DELTA mutant
EC: 3.5.2.6
UniProt: P54427
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Bsu-2DELTA mutant (EC 3.5.2.6)	protein	235	39% helix, 21% strand	P54427
C, D	Bsu-2DELTA mutant (EC 3.5.2.6)	protein	234	38% helix, 21% strand	P54427

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, D
MLI · Malonate ion · additive · 3 copies · chains B, D
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	615	0.70	0.78	50	MLI
2	609	0.70	0.78	48	EDO
3	582	0.62	0.74	60	empty
4	174	0.43	0.74	37	EDO
5	94	0.37	0.76	19	MLI

Interfaces

4 interfaces between chains.

C–D · 1097 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1080 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 125 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 99 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

6W5F · Class D beta-lactamase BSU-2 delta mutant · the same entry in another collection · chain A against A, TM-score 1.00
P54427 · AlphaFold monomer V2.0 prediction for probable beta-lactamase ybxi (P54427) · a predicted model of the same protein · chain C 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 P54427
Elsewhere: RCSB PDB 6W5F · PDBe 6W5F · UniProt P54427

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