MolNFT v1 · #142041 · protein

Crystal structure of ndm-1 metallo-beta-lactamase

5ZR8: “Crystal structure of ndm-1 metallo-beta-lactamase”. X-ray diffraction, 2 ligands (ZN, SO4), 3 pockets (best druggability 0.78). MolNFT v1 #142041 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZR8
Type: protein
Length: 460 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
UniProt: E5KIY2
Ligands: ZN, SO4
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase	protein	229	24% helix, 32% strand	E5KIY2
E	Beta-lactamase	protein	231	24% helix, 31% strand	E5KIY2

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, E
SO4 · Sulfate ion · ion · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	104	0.78	0.98	21	empty
2	68	0.42	0.81	19	empty
3	115	0.40	0.75	19	empty

Interfaces

1 interface between chains.

A–E · 928 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5ZR8 · Crystal Structure Of NDM-1 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 E5KIY2
Elsewhere: RCSB PDB 5ZR8 · PDBe 5ZR8 · UniProt E5KIY2

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