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Crystal structure of importin 13 - rangtp - EIF1A complex

Analyse Crystal structure of importin 13 - rangtp - EIF1A complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZJY
Type: protein
Length: 3,223 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein ran; Importin-13; Eukaryotic translation initiation factor…
UniProt: P62826, O94829, P47813
Ligands: GTP, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein ran	protein	169	25% helix, 28% strand	P62826
B	Importin-13	protein	908	78% helix, 0% strand	O94829
C	Eukaryotic translation initiation factor 1A, X-chromosomal	protein	74	15% helix, 45% strand	P47813
D, F	GTP-binding nuclear protein ran	protein	170	24% helix, 28% strand	P62826
E	Importin-13	protein	825	76% helix, 0% strand	O94829
G	Importin-13	protein	907	76% helix, 0% strand	O94829

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, D, F, G
MG · Magnesium ion · metal · 3 copies · chains A, D, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	752	0.85	0.88	106	empty
2	779	0.84	0.86	74	empty
3	1080	0.82	0.83	118	empty
4	993	0.81	0.82	101	empty
5	384	0.81	0.89	63	empty

Interfaces

8 interfaces between chains.

F–G · 1356 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1263 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 1002 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 789 Å² buried · 10 hydrogen bonds · protein-protein
E–G · 633 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3ZJY · Crystal Structure of Importin 13 - RanGTP - eIF1A complex · the same entry in another collection · chain G against G, TM-score 1.00
O94829 · AlphaFold monomer V2.0 prediction for importin-13 (O94829) · a predicted model of the same protein · chain E against A, TM-score 0.98
P47813 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 1A… · a predicted model of the same protein · chain C against A, TM-score 0.92

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 O94829
Every structure of UniProt P47813
Elsewhere: RCSB PDB 3ZJY · PDBe 3ZJY · UniProt P62826 · UniProt O94829 · UniProt P47813

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