MolNFT v1 · #90925 · protein

Crystal structure of ndm-1 bound to hydrolyzed oxacillin

4EYB · Beta-lactamase ndm-1: “Crystal structure of ndm-1 bound to hydrolyzed oxacillin”. X-ray diffraction, 2 ligands (0WO, ZN), 3 pockets (best druggability 0.83). MolNFT v1 #90925 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4EYB
Type: protein
Length: 482 residues
Chains: 2
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: 0WO, ZN
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase ndm-1 (EC 3.5.2.6)	protein	241	24% helix, 29% strand	C7C422

Ligands and binding sites

0WO · (2R,4S)-2-[(R)-carboxy{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carbo xylic acid · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 5 copies · chains A, B

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	650	0.83	0.88	75	ZN, 0WO
2	154	0.49	0.78	32	empty
3	152	0.49	0.78	31	empty

Interfaces

1 interface between chains.

A–B · 832 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4EYB · Crystal structure of NDM-1 bound to hydrolyzed oxacillin · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.94

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 4EYB · PDBe 4EYB · UniProt C7C422

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