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Crystal structure of hyperthermophilic nitrilase

Analyse Crystal structure of hyperthermophilic nitrilase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IW3
Type: protein
Length: 522 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrilase
EC: 3.5.1.6
UniProt: Q9UYV8
Ligands: MG
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nitrilase (EC 3.5.1.6)	protein	261	30% helix, 30% strand	Q9UYV8

Ligands and binding sites

MG · Magnesium ion · metal · chains A
ACY · Acetic acid · additive · 3 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.31	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 2166 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

3IW3 · Crystal structure of hyperthermophilic nitrilase · the same entry in another collection · chain A against A, TM-score 1.00
Q9UYV8 · AlphaFold monomer V2.0 prediction for nitrilase (Q9UYV8) · a predicted model of the same protein · 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 Q9UYV8
Elsewhere: RCSB PDB 3IW3 · PDBe 3IW3 · UniProt Q9UYV8

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