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Crystal structure of CPEB4 nes reverse mutant peptide in complex with CRM1-ran-RANBP1

Analyse Crystal structure of CPEB4 nes reverse mutant peptide in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DHA
Type: protein
Length: 1,341 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: 14 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 63% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein ran	protein	206	29% helix, 23% strand	P62826
B	Ran-specific GTPase-activating protein 1	protein	127	15% helix, 48% strand	P41920
C	Exportin-1	protein	994	77% helix, 0% strand	P30822
D	Engineered nuclear export signal peptide (CPEB4 nes reverse mutant)	protein	14	57% 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

14 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	832	0.85	0.87	112	GOL
2	717	0.67	0.75	63	empty
3	120	0.65	0.88	30	GNP, MG
4	144	0.55	0.82	30	empty
5	121	0.55	0.82	17	empty

Interfaces

4 interfaces between chains.

A–B · 2104 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 2022 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 873 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 171 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

P30822 · AlphaFold monomer V2.0 prediction for exportin-1 (P30822) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 0.96

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

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