MolNFT v1 · #165446 · protein

Human CRM1-rangtp in complex with leptomycin B

6TVO · GTP-binding nuclear protein ran: “Human CRM1-rangtp in complex with leptomycin B”. X-ray diffraction, 3 ligands (GTP, LMB, MG), 16 pockets (best druggability 0.86). MolNFT v1 #165446 on GenesisL1: 3D structure, binding sites and…

PDB: 6TVO
Type: protein
Length: 1,186 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein ran; Exportin-1
UniProt: P62826, O14980
Ligands: GTP, LMB, MG
Pockets: 16 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	GTP-binding nuclear protein ran	protein	175	27% helix, 27% strand	P62826
A	Exportin-1	protein	1011	78% helix, 1% strand	O14980

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains B
LMB · Leptomycin B, bound form · ligand · chains A
MG · Magnesium ion · metal · chains B

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	1123	0.86	0.87	149	GTP, MG
2	354	0.65	0.80	30	empty
3	235	0.59	0.80	35	empty
4	263	0.57	0.78	23	empty
5	67	0.57	0.89	15	empty

Interfaces

1 interface between chains.

B–A · 2511 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6TVO · Human CRM1-RanGTP in complex with Leptomycin B · the same entry in another collection · chain B against B, TM-score 1.00
O14980 · AlphaFold monomer V2.0 prediction for exportin-1 (O14980) · a predicted model of the same protein · chain A 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 O14980
Elsewhere: RCSB PDB 6TVO · PDBe 6TVO · UniProt P62826 · UniProt O14980

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