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Beta-lactamase, unmixed shards crystal form

Analyse Beta-lactamase, unmixed shards crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B5X
Type: protein
Length: 1,060 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: P9WKD3
Ligands: PO4
Pockets: 10 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-lactamase (EC 3.5.2.6)	protein	265	45% helix, 16% strand	P9WKD3

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	222	0.64	0.84	34	PO4
2	545	0.64	0.76	45	PO4
3	149	0.61	0.85	27	PO4
4	449	0.61	0.76	40	PO4
5	190	0.46	0.75	40	empty

Interfaces

4 interfaces between chains.

C–D · 800 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 795 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 642 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 638 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6B5X · Beta-Lactamase, unmixed shards crystal form · the same entry in another collection · chain D against D, TM-score 1.00
P9WKD3 · AlphaFold monomer V2.0 prediction for beta-lactamase (P9WKD3) · a predicted model of the same protein · chain B 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 P9WKD3
Elsewhere: RCSB PDB 6B5X · PDBe 6B5X · UniProt P9WKD3

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