MolNFT v1 · #120829 · protein

Gpn-loop GTPase NPA3 in complex with gmppcp

5HCN · Gpn-loop GTPase 1: “Gpn-loop GTPase NPA3 in complex with gmppcp”. X-ray diffraction, 3 ligands (DAO, GCP, MG), 2 pockets (best druggability 0.70). MolNFT v1 #120829 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HCN
Type: protein
Length: 253 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gpn-loop GTPase 1
EC: 3.6.5.-
UniProt: P47122
Ligands: DAO, GCP, MG
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gpn-loop GTPase 1 (EC 3.6.5.-)	protein	253	51% helix, 13% strand	P47122

Ligands and binding sites

DAO · Lauric acid · ligand · chains A
GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

2 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	160	0.70	0.88	23	DAO
2	57	0.27	0.73	14	empty

Compared structures

5HCN · GPN-loop GTPase Npa3 in complex with GMPPCP · the same entry in another collection · chain A against A, TM-score 1.00
P47122 · AlphaFold monomer V2.0 prediction for gpn-loop GTPase 1 (P47122) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P47122
Elsewhere: RCSB PDB 5HCN · PDBe 5HCN · UniProt P47122

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