MolNFT v1 · #56681 · protein

Metallo-beta-lactamase (cadmium-bound form)

2ZNB: “Metallo-beta-lactamase (cadmium-bound form)”. X-ray diffraction, 2 ligands (CD, NA), 2 pockets (best druggability 0.33). MolNFT v1 #56681 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ZNB
Type: protein
Length: 448 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallo-beta-lactamase
EC: 3.5.2.6
UniProt: P25910
Ligands: CD, NA
Pockets: 2 · best druggability 0.33

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metallo-beta-lactamase (EC 3.5.2.6)	protein	222	27% helix, 32% strand	P25910
B	Metallo-beta-lactamase (EC 3.5.2.6)	protein	226	27% helix, 33% strand	P25910

Ligands and binding sites

CD · Cadmium ion · metal · 4 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	76	0.33	0.75	14	CD
2	60	0.30	0.75	17	CD

Compared structures

2ZNB · Metallo-beta-lactamase (cadmium-bound form) · the same entry in another collection · chain A against A, TM-score 1.00
P25910 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (P25910) · a predicted model of the same protein · chain B 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 P25910
Elsewhere: RCSB PDB 2ZNB · PDBe 2ZNB · UniProt P25910

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