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Crystal structure of human rangdp

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

PDB: 3GJ0
Type: protein
Length: 400 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein ran
UniProt: P62826
Ligands: GDP, MG
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein ran	protein	207	34% helix, 27% strand	P62826
B	GTP-binding nuclear protein ran	protein	193	35% helix, 27% strand	P62826

Ligands and binding sites

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

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	426	0.67	0.80	55	MG
2	80	0.35	0.75	15	empty
3	53	0.30	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 398 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3GJ0 · Crystal structure of human RanGDP · the same entry in another collection · chain A against A, TM-score 1.00

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
Elsewhere: RCSB PDB 3GJ0 · PDBe 3GJ0 · UniProt P62826

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