MolNFT v1 · #9939 · protein

Complex of ran with importin beta

1IBR · GTP-binding nuclear protein ran: “Complex of ran with importin beta”. X-ray diffraction, 2 ligands (GNP, MG), 12 pockets (best druggability 0.83). MolNFT v1 #9939 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1IBR
Type: protein
Length: 1,232 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein ran; Importin beta-1 subunit
UniProt: P62826, Q14974
Ligands: GNP, MG
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 65% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	GTP-binding nuclear protein ran	protein	168	30% helix, 24% strand	P62826
B	Importin beta-1 subunit	protein	458	70% helix, 0% strand	Q14974
D	Importin beta-1 subunit	protein	438	72% helix, 0% strand	Q14974

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
MG · Magnesium ion · metal · 2 copies · chains A, C

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

Pockets

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1080	0.83	0.84	94	empty
2	1026	0.80	0.81	82	empty
3	395	0.71	0.83	54	empty
4	576	0.68	0.78	43	empty
5	546	0.67	0.77	43	empty

Interfaces

3 interfaces between chains.

C–D · 1801 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1798 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 152 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1IBR · Complex of ran with importin beta · the same entry in another collection · chain A against A, TM-score 1.00
Q14974 · AlphaFold monomer V2.0 prediction for importin subunit beta-1 (Q14974) · a predicted model of the same protein · chain D against A, TM-score 0.95

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
Every structure of UniProt Q14974
Elsewhere: RCSB PDB 1IBR · PDBe 1IBR · UniProt P62826 · UniProt Q14974

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