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Crystal structure of XPO1P-pki-NUP42P-GSP1P-GTP complex

Analyse Crystal structure of XPO1P-pki-NUP42P-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: 5XOJ
Type: protein
Length: 1,212 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein; Exportin-1; Camp-dependent protein kinase inhibitor alpha…
UniProt: E7KFU1, P30822, P61925, E7Q297
Ligands: GTP, MG
Pockets: 12 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 68% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein	protein	170	28% helix, 28% strand	E7KFU1
C	Exportin-1	protein	999	77% helix, 1% strand	P30822
D	Camp-dependent protein kinase inhibitor alpha	protein	19	42% helix, 0% strand	P61925
E	NUP42P	protein	7	0% helix, 0% strand	E7Q297
F	NUP42P	protein	9	0% helix, 0% strand	E7Q297
G	NUP42P	protein	8	0% helix, 0% strand	E7Q297

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

12 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	1153	0.87	0.88	128	GTP, MG
2	321	0.67	0.82	27	empty
3	362	0.65	0.79	35	empty
4	60	0.64	0.93	17	empty
5	160	0.60	0.83	30	empty

Interfaces

5 interfaces between chains.

A–C · 2488 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 932 Å² buried · 5 hydrogen bonds · protein-protein
C–G · 532 Å² buried · 11 hydrogen bonds · protein-protein
C–F · 511 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 417 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5XOJ · Crystal structure of Xpo1p-PKI-Nup42p-Gsp1p-GTP complex · the same entry in another collection · chain D against D, 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
Every structure of UniProt E7Q297
Elsewhere: RCSB PDB 5XOJ · PDBe 5XOJ · UniProt E7KFU1 · UniProt P30822 · UniProt P61925 · UniProt E7Q297

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