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Crystal structure of human rangdp-NUP153ZNF4 complex

Analyse Crystal structure of human rangdp-NUP153ZNF4 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GJ5
Type: protein
Length: 454 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein ran; Nuclear pore complex protein NUP153
UniProt: P62826, P49791
Ligands: GDP, MG, ZN
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	GTP-binding nuclear protein ran	protein	201	37% helix, 26% strand	P62826
B, D	Nuclear pore complex protein NUP153	protein	26	0% helix, 23% strand	P49791

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
MG · Magnesium ion · metal · 2 copies · chains A, C
ZN · Zinc ion · metal · 2 copies · chains B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.62	0.88	26	empty
2	77	0.35	0.76	23	empty
3	70	0.34	0.76	19	empty

Interfaces

3 interfaces between chains.

A–C · 504 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 486 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 469 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3GJ5 · Crystal structure of human RanGDP-Nup153ZnF4 complex · the same entry in another collection · chain A against A, TM-score 1.00
P49791 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP153 (P49791) · a predicted model of the same protein · chain B against A, TM-score 0.82

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 P49791
Elsewhere: RCSB PDB 3GJ5 · PDBe 3GJ5 · UniProt P62826 · UniProt P49791

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