MolNFT v1 · #120824 · protein

Gpn-loop GTPase NPA3 in complex with GDP

5HCI · Gpn-loop GTPase 1: “Gpn-loop GTPase NPA3 in complex with GDP”. X-ray diffraction, 2 ligands (GDP, MG), 9 pockets (best druggability 0.79). MolNFT v1 #120824 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HCI
Type: protein
Length: 1,527 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gpn-loop GTPase 1
EC: 3.6.5.-
UniProt: P47122
Ligands: GDP, MG
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 56% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gpn-loop GTPase 1 (EC 3.6.5.-)	protein	257	57% helix, 14% strand	P47122
B, D	Gpn-loop GTPase 1 (EC 3.6.5.-)	protein	258	55% helix, 14% strand	P47122
C	Gpn-loop GTPase 1 (EC 3.6.5.-)	protein	246	55% helix, 15% strand	P47122
E	Gpn-loop GTPase 1 (EC 3.6.5.-)	protein	259	57% helix, 14% strand	P47122
F	Gpn-loop GTPase 1 (EC 3.6.5.-)	protein	249	55% helix, 14% strand	P47122

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 4 copies · chains A, B, C, E

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

Pockets

9 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	996	0.79	0.81	93	GOL
2	152	0.67	0.87	24	empty
3	490	0.65	0.77	46	empty
4	280	0.60	0.79	35	empty
5	368	0.57	0.75	40	GDP

Interfaces

7 interfaces between chains.

D–E · 1348 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 571 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 439 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 345 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 184 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5HCI · GPN-loop GTPase Npa3 in complex with GDP · the same entry in another collection · chain E against E, 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 0.98

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

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