MolNFT v1 · #107084 · protein

Structure of metallo-beta-lactamase

4TZE · Class B carbapenemase ndm-5: “Structure of metallo-beta-lactamase”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.49). MolNFT v1 #107084 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4TZE
Type: protein
Length: 459 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Class B carbapenemase ndm-5
UniProt: G3K399
Ligands: ZN
Pockets: 4 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Class B carbapenemase ndm-5	protein	230	25% helix, 30% strand	G3K399
B	Class B carbapenemase ndm-5	protein	229	25% helix, 30% strand	G3K399

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

4 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	225	0.49	0.75	21	empty
2	118	0.39	0.74	21	ZN
3	120	0.37	0.73	21	ZN
4	54	0.34	0.78	13	empty

Interfaces

1 interface between chains.

A–B · 271 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4TZE · Structure of metallo-beta-lactamase · the same entry in another collection · 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 G3K399
Elsewhere: RCSB PDB 4TZE · PDBe 4TZE · UniProt G3K399

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.