MolNFT v1 · #175516 · protein

New delhi metallo-beta-lactamase 1 (NDM1) mutant - H116Q

7CT2 · Metallo beta lactamase ndm-1: “New delhi metallo-beta-lactamase 1 (NDM1) mutant - H116Q”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #175516 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7CT2
Type: protein
Length: 916 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallo beta lactamase ndm-1
UniProt: E9NWK5
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Metallo beta lactamase ndm-1	protein	229	25% helix, 29% strand	E9NWK5

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1143	0.76	0.79	96	empty
2	482	0.61	0.75	55	empty
3	115	0.38	0.74	21	empty
4	103	0.34	0.73	20	empty
5	63	0.29	0.73	11	empty

Interfaces

4 interfaces between chains.

A–D · 427 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 386 Å² buried · 1 hydrogen bond · protein-protein
A–B · 184 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 176 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

7CT2 · New Delhi metallo-beta-lactamase 1 (NDM1) mutant - H116Q · 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 E9NWK5
Elsewhere: RCSB PDB 7CT2 · PDBe 7CT2 · UniProt E9NWK5

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