MolNFT v1 · #138844 · protein

Crystal structure of ATNUDX1

5WWD · Nudix hydrolase 1: “Crystal structure of ATNUDX1”. X-ray diffraction, 3 ligands (2ME, MG, NH4), 4 pockets (best druggability 0.72). MolNFT v1 #138844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5WWD
Type: protein
Length: 277 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nudix hydrolase 1
EC: 3.6.1.55, 3.6.1.67, 3.6.1.22
UniProt: Q9CA40
Ligands: 2ME, MG, NH4
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22)	protein	139	15% helix, 41% strand	Q9CA40
B	Nudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22)	protein	138	17% helix, 41% strand	Q9CA40

Ligands and binding sites

2ME · Methoxyethane · ligand · chains A
MG · Magnesium ion · metal · 6 copies · chains A, B
NH4 · Ammonium ion · ion · chains A
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

4 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	262	0.72	0.86	36	MG
2	254	0.72	0.86	35	NH4, MG
3	153	0.44	0.75	25	empty
4	80	0.31	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 968 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5WWD · Crystal structure of AtNUDX1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9CA40 · AlphaFold monomer V2.0 prediction for nudix hydrolase 1 (Q9CA40) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9CA40
Elsewhere: RCSB PDB 5WWD · PDBe 5WWD · UniProt Q9CA40

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