MolNFT v1 · #120096 · protein

Crystal structure of geraniol-NUDX1 complex

5GP0 · Nudix hydrolase 1: “Crystal structure of geraniol-NUDX1 complex”. X-ray diffraction, 1 ligand (GPP), 8 pockets (best druggability 0.73). MolNFT v1 #120096 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GP0
Type: protein
Length: 552 residues
Chains: 4
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: GPP
Pockets: 8 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Nudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22)	protein	137	18% helix, 42% strand	Q9CA40
F, A	Nudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22)	protein	138	15% helix, 41% strand	Q9CA40
I	Nudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22)	protein	139	17% helix, 41% strand	Q9CA40

Ligands and binding sites

GPP · Geranyl diphosphate · ligand · 4 copies · chains E, F, I, A
GOL · Glycerol · additive · 2 copies · chains E, I

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

Pockets

8 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	302	0.73	0.86	37	GPP
2	304	0.72	0.85	36	GPP
3	288	0.71	0.85	36	GPP
4	295	0.70	0.84	36	GPP
5	621	0.70	0.78	55	empty

Interfaces

5 interfaces between chains.

E–F · 959 Å² buried · 4 hydrogen bonds · protein-protein
I–A · 943 Å² buried · 4 hydrogen bonds · protein-protein
F–A · 259 Å² buried · 5 hydrogen bonds · protein-protein
E–I · 250 Å² buried · 1 hydrogen bond · protein-protein
E–A · 48 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5GP0 · Crystal structure of geraniol-NUDX1 complex · the same entry in another collection · chain E against E, TM-score 1.00
Q9CA40 · AlphaFold monomer V2.0 prediction for nudix hydrolase 1 (Q9CA40) · 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 Q9CA40
Elsewhere: RCSB PDB 5GP0 · PDBe 5GP0 · UniProt Q9CA40

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