Research workbench

Crystal structure of XPO1P-pki-GSP1P-GTP complex

Analyse Crystal structure of XPO1P-pki-GSP1P-GTP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WYG
Type: protein
Length: 1,193 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GSP1P; Exportin-1; Camp-dependent protein kinase inhibitor alpha
UniProt: E7KFU1, P30822, P61925
Ligands: GTP, MG
Pockets: 11 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 71% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GSP1P	protein	170	31% helix, 28% strand	E7KFU1
C	Exportin-1	protein	1003	79% helix, 1% strand	P30822
D	Camp-dependent protein kinase inhibitor alpha	protein	20	40% helix, 0% strand	P61925

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1104	0.85	0.86	101	GTP, MG
2	766	0.78	0.82	75	empty
3	338	0.68	0.82	39	empty
4	218	0.63	0.82	27	empty
5	464	0.62	0.76	39	empty

Interfaces

2 interfaces between chains.

A–C · 2482 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 1010 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3WYG · Crystal structure of Xpo1p-PKI-Gsp1p-GTP complex · the same entry in another collection · chain A against A, TM-score 1.00
P30822 · AlphaFold monomer V2.0 prediction for exportin-1 (P30822) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 E7KFU1
Every structure of UniProt P30822
Every structure of UniProt P61925
Elsewhere: RCSB PDB 3WYG · PDBe 3WYG · UniProt E7KFU1 · UniProt P30822 · UniProt P61925

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