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Structure of the NTF2:RANGDP complex

Analyse Structure of the NTF2:RANGDP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BXQ
Type: protein
Length: 841 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear transport factor 2; GTP-binding nuclear protein ran
UniProt: P61972, P62825
Ligands: GDP, MG, SO4
Pockets: 7 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nuclear transport factor 2	protein	124	28% helix, 48% strand	P61972
C	GTP-binding nuclear protein ran	protein	192	33% helix, 29% strand	P62825
D	GTP-binding nuclear protein ran	protein	198	34% helix, 28% strand	P62825
E	GTP-binding nuclear protein ran	protein	203	33% helix, 27% strand	P62825

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains C, D, E
MG · Magnesium ion · metal · 3 copies · chains C, A, D, E
SO4 · Sulfate ion · ion · chains E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	128	0.57	0.83	24	empty
2	248	0.52	0.76	29	empty
3	243	0.52	0.76	40	empty
4	177	0.42	0.74	29	empty
5	97	0.39	0.77	27	GDP, MG

Interfaces

7 interfaces between chains.

A–B · 1661 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 874 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 804 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 493 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 75 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5BXQ · Structure of the NTF2:RanGDP complex · the same entry in another collection · chain E against E, TM-score 1.00
P61972 · AlphaFold monomer V2.0 prediction for nuclear transport factor 2 (P61972) · a predicted model of the same protein · chain A against A, TM-score 0.98
P62825 · AlphaFold monomer V2.0 prediction for GTP-binding nuclear protein ran (P62825) · a predicted model of the same protein · chain C against A, TM-score 0.89

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 P61972
Every structure of UniProt P62825
Elsewhere: RCSB PDB 5BXQ · PDBe 5BXQ · UniProt P61972 · UniProt P62825

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