MolNFT v1 · #143664 · protein

Beta-lactamase, 2SECS timepoint, mixed, shards crystal form

6B6A: “Beta-lactamase, 2SECS timepoint, mixed, shards crystal form”. X-ray diffraction, 3 ligands (9F2, FZS, PO4), 10 pockets (best druggability 0.59). MolNFT v1 #143664 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6B6A
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: 9F2, FZS, PO4
Pockets: 10 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-lactamase (EC 3.5.2.6)	protein	265	45% helix, 17% strand	P9WKD3

Ligands and binding sites

9F2 · Ceftriaxone · ligand · 4 copies · chains A, B, C, D
FZS · (2R)-2-[(1S)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-hydroxyethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 2 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	412	0.59	0.76	40	9F2, FZS
2	162	0.59	0.83	34	PO4
3	410	0.58	0.75	43	9F2, FZS
4	132	0.57	0.84	27	PO4
5	296	0.55	0.76	53	empty

Interfaces

4 interfaces between chains.

C–D · 755 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 753 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 689 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 668 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6B6A · Beta-Lactamase, 2secs timepoint, mixed, 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 6B6A · PDBe 6B6A · UniProt P9WKD3

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