MolNFT v1 · #136549 · protein

Crystal structure of fmrp nes peptide in complex with CRM1-ran-RANBP1

5UWJ · GTP-binding nuclear protein ran: “Crystal structure of fmrp nes peptide in complex with CRM1-ran-RANBP1”. X-ray diffraction, 2 ligands (GNP, MG), 15 pockets (best druggability 0.85). MolNFT v1 #136549 on GenesisL1: 3D structure…

PDB: 5UWJ
Type: protein
Length: 1,344 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein ran; Ran-specific GTPase-activating protein 1; Exportin-1…
UniProt: P62826, P41920, P30822
Ligands: GNP, MG
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 65% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein ran	protein	206	33% helix, 22% strand	P62826
B	Ran-specific GTPase-activating protein 1	protein	130	15% helix, 46% strand	P41920
C	Exportin-1	protein	997	79% helix, 0% strand	P30822
D	Synaptic functional regulator FMR1	protein	11	27% helix, 0% strand	—

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A
GOL · Glycerol · additive · 3 copies · chains A, C

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

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	842	0.85	0.87	95	GOL
2	149	0.65	0.87	29	GNP, MG
3	635	0.65	0.75	58	empty
4	80	0.64	0.91	27	empty
5	118	0.55	0.82	16	empty

Interfaces

4 interfaces between chains.

A–B · 2019 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 2017 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 730 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 175 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5UWJ · Crystal Structure of FMRP NES Peptide in complex with CRM1-Ran-RanBP1 · 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 0.99
P41920 · AlphaFold monomer V2.0 prediction for ran-specific GTPase-activating protein 1 (P41920) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P41920
Every structure of UniProt P30822
Elsewhere: RCSB PDB 5UWJ · PDBe 5UWJ · UniProt P62826 · UniProt P41920 · UniProt P30822

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