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Crystal structure of human karyopherin-BETA2 bound to the histone H3 tail

Analyse Crystal structure of human karyopherin-BETA2 bound to the histone H3 tail in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5J3V
Type: protein
Length: 1,682 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transportin-1,TRANSPORTIN-1; Histone H3
UniProt: Q92973
Pockets: 15 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transportin-1,TRANSPORTIN-1	protein	835	73% helix, 0% strand	Q92973
C, D	Histone H3	protein	17	35% helix, 0% strand	—
B	Transportin-1,TRANSPORTIN-1	protein	813	67% helix, 0% strand	Q92973

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.66	0.94	16	empty
2	577	0.66	0.77	45	empty
3	262	0.64	0.82	28	empty
4	489	0.63	0.76	40	empty
5	264	0.63	0.81	39	empty

Interfaces

3 interfaces between chains.

B–D · 977 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 939 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 634 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5J3V · Crystal structure of human Karyopherin-beta2 bound to the histone H3 tail · the same entry in another collection · chain A against A, TM-score 1.00
Q92973 · AlphaFold monomer V2.0 prediction for transportin-1 (Q92973) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q92973
Elsewhere: RCSB PDB 5J3V · PDBe 5J3V · UniProt Q92973

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