MolNFT v1 · #115419 · protein

Ran GDP Y39A mutant triclinic crystal form

5CJ2 · GTP-binding nuclear protein ran: “Ran GDP Y39A mutant triclinic crystal form”. X-ray diffraction, 3 ligands (GDP, MG, PO4), 16 pockets (best druggability 0.78). MolNFT v1 #115419 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5CJ2
Type: protein
Length: 1,583 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein ran
UniProt: P62826
Ligands: GDP, MG, PO4
Pockets: 16 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 36% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, G, H	GTP-binding nuclear protein ran	protein	197	35% helix, 27% strand	P62826
B	GTP-binding nuclear protein ran	protein	199	37% helix, 27% strand	P62826
C	GTP-binding nuclear protein ran	protein	198	36% helix, 27% strand	P62826
D	GTP-binding nuclear protein ran	protein	198	35% helix, 27% strand	P62826
E	GTP-binding nuclear protein ran	protein	200	37% helix, 27% strand	P62826

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, E, D, F, G, H
MG · Magnesium ion · metal · 12 copies · chains A, B, C, E, D, F, G, H
PO4 · Phosphate ion · ion · 2 copies · chains B, C

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

Pockets

16 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	1066	0.78	0.80	106	GDP, MG
2	500	0.73	0.82	51	empty
3	366	0.72	0.84	52	MG
4	209	0.54	0.78	28	empty
5	93	0.53	0.84	28	empty

Interfaces

14 interfaces between chains.

D–G · 750 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 720 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 494 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 419 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 290 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5CJ2 · Ran GDP Y39A mutant triclinic crystal form · the same entry in another collection · 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 P62826
Elsewhere: RCSB PDB 5CJ2 · PDBe 5CJ2 · UniProt P62826

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