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

Analyse Crystal structure of paxillin nes peptide in complex with CRM1-ran- RANBP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UWH
Type: protein
Length: 1,346 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 · 65% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein ran	protein	203	32% helix, 23% strand	P62826
B	Ran-specific GTPase-activating protein 1	protein	126	13% helix, 52% strand	P41920
C	Exportin-1	protein	1003	78% helix, 0% strand	P30822
D	Paxillin	protein	14	71% 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	797	0.85	0.88	99	GOL
2	635	0.65	0.75	57	empty
3	74	0.64	0.92	27	empty
4	146	0.64	0.87	30	GNP, MG
5	135	0.57	0.83	17	empty

Interfaces

4 interfaces between chains.

A–C · 2137 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2055 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 855 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 171 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5UWH · Crystal Structure of Paxillin 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 0.98
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 0.95

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 5UWH · PDBe 5UWH · UniProt P62826 · UniProt P41920 · UniProt P30822

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