MolNFT v1 · #9630 · protein

Ran-RCC1-SO4 complex

1I2M · GTP-binding nuclear protein ran: “Ran-RCC1-SO4 complex”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.78). MolNFT v1 #9630 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1I2M
Type: protein
Length: 1,107 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein ran; Regulator of chromosome condensation 1
UniProt: P62826, P18754
Ligands: SO4
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein ran	protein	165	27% helix, 30% strand	P62826
B	Regulator of chromosome condensation 1	protein	388	6% helix, 45% strand	P18754
C	GTP-binding nuclear protein ran	protein	164	29% helix, 26% strand	P62826
D	Regulator of chromosome condensation 1	protein	390	4% helix, 44% strand	P18754

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	566	0.78	0.85	57	empty
2	600	0.78	0.85	62	empty
3	73	0.74	0.98	20	empty
4	64	0.72	0.98	22	empty
5	383	0.71	0.83	49	empty

Interfaces

4 interfaces between chains.

A–B · 1504 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 1442 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 727 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 535 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1I2M · Ran-RCC1-SO4 complex · the same entry in another collection · chain A against A, TM-score 1.00
P18754 · AlphaFold monomer V2.0 prediction for regulator of chromosome condensation (P18754) · a predicted model of the same protein · chain B 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 P62826
Every structure of UniProt P18754
Elsewhere: RCSB PDB 1I2M · PDBe 1I2M · UniProt P62826 · UniProt P18754

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