MolNFT v1 · #139758 · protein

Crystal structure of bismuth bound ndm-1

5XP9 · Metallo-beta-lactamase type 2: “Crystal structure of bismuth bound ndm-1”. X-ray diffraction, 1 ligand (BS3), 1 pocket (best druggability 0.37). MolNFT v1 #139758 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XP9
Type: protein
Length: 228 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallo-beta-lactamase type 2
EC: 3.5.2.6
UniProt: C7C422
Ligands: BS3
Pockets: 1 · best druggability 0.37

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metallo-beta-lactamase type 2 (EC 3.5.2.6)	protein	228	24% helix, 33% strand	C7C422

Ligands and binding sites

BS3 · Bismuth(III) ION · metal · chains A
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	93	0.37	0.75	20	empty

Compared structures

5XP9 · Crystal structure of Bismuth bound NDM-1 · the same entry in another collection · chain A against A, TM-score 1.00
C7C422 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (C7C422) · 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 C7C422
Elsewhere: RCSB PDB 5XP9 · PDBe 5XP9 · UniProt C7C422

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