MolNFT v1 · #53663 · protein

Crystal structure of IMPORTIN13 - mago-Y14 complex

2X1G · RNA-binding protein 8A: “Crystal structure of IMPORTIN13 - mago-Y14 complex”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #53663 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2X1G
Type: protein
Length: 2,252 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding protein 8A; Protein mago nashi; Cadmus
UniProt: Q9V535, P49028, Q9VEC5
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	RNA-binding protein 8A	protein	90	18% helix, 32% strand	Q9V535
B, D	Protein mago nashi	protein	140	30% helix, 35% strand	P49028
F, G	Cadmus	protein	896	77% helix, 0% strand	Q9VEC5

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	934	0.78	0.80	89	empty
2	992	0.78	0.79	85	empty
3	1141	0.76	0.78	105	empty
4	933	0.74	0.78	100	empty
5	188	0.73	0.89	29	empty

Interfaces

9 interfaces between chains.

B–F · 1079 Å² buried · 18 hydrogen bonds · protein-protein
D–G · 1077 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1024 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1022 Å² buried · 10 hydrogen bonds · protein-protein
C–G · 501 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2X1G · Crystal structure of Importin13 - Mago-Y14 complex · the same entry in another collection · chain G against G, TM-score 1.00
P49028 · AlphaFold monomer V2.0 prediction for protein mago nashi (P49028) · a predicted model of the same protein · chain B against A, TM-score 0.95
Q9V535 · AlphaFold monomer V2.0 prediction for RNA-binding protein 8A (Q9V535) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9V535
Every structure of UniProt P49028
Every structure of UniProt Q9VEC5
Elsewhere: RCSB PDB 2X1G · PDBe 2X1G · UniProt Q9V535 · UniProt P49028 · UniProt Q9VEC5

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