MolNFT v1 · #78981 · protein

Apo ndm-1 crystal structure

3SPU · Beta-lactamase ndm-1: “Apo ndm-1 crystal structure”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.84). MolNFT v1 #78981 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SPU
Type: protein
Length: 1,160 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase ndm-1
EC: 3.5.2.6
UniProt: C7C422
Ligands: ZN
Pockets: 10 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 26% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Beta-lactamase ndm-1 (EC 3.5.2.6)	protein	232	25% helix, 32% strand	C7C422
B	Beta-lactamase ndm-1 (EC 3.5.2.6)	protein	238	26% helix, 31% strand	C7C422
D	Beta-lactamase ndm-1 (EC 3.5.2.6)	protein	231	29% helix, 29% strand	C7C422
E	Beta-lactamase ndm-1 (EC 3.5.2.6)	protein	227	24% helix, 32% strand	C7C422

Ligands and binding sites

ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1149	0.84	0.85	140	empty
2	118	0.80	0.98	21	empty
3	112	0.78	0.97	23	empty
4	348	0.66	0.81	46	ZN
5	345	0.56	0.75	38	ZN

Interfaces

9 interfaces between chains.

A–C · 1051 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 922 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 837 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 482 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 331 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3SPU · apo NDM-1 Crystal Structure · the same entry in another collection · chain E against E, 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 E against A, TM-score 0.99

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 3SPU · PDBe 3SPU · UniProt C7C422

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