MolNFT v2 · #115692 · protein

Ran GDP wild type tetragonal crystal form

5CIQ · GTP-binding nuclear protein Ran: “Ran GDP wild type tetragonal crystal form”. X-ray diffraction at 1.65, 2 ligands (GDP, MG), 4 pockets (best druggability 0.45). MolNFT v2 #115692 on GenesisL1: 3D structure, binding sites and…

PDB: 5CIQ
Type: protein
Length: 399 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.65
Source: Homo sapiens
Molecule: GTP-binding nuclear protein Ran
UniProt: P62826
Ligands: GDP, MG
Pockets: 4 · best druggability 0.45

Structure

x-ray diffraction · resolution 1.65 · 2 distinct chains · 36% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein Ran	protein	199	36% helix, 27% strand	P62826
B	GTP-binding nuclear protein Ran	protein	200	37% helix, 28% 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

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	198	0.45	0.74	35	GDP, MG
2	114	0.40	0.75	18	empty
3	103	0.38	0.76	21	GDP, MG
4	70	0.35	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 79 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5CIQ · Ran GDP wild type tetragonal crystal form · the same entry in another collection · chain A against A, TM-score 1.00
P62826 · AlphaFold monomer V2.0 prediction for GTP-binding nuclear protein ran (P62826) · a predicted model of the same protein · chain B against A, TM-score 0.77

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 5CIQ · PDBe 5CIQ · UniProt P62826

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