Research workbench

Unliganded transportin 3

Analyse Unliganded transportin 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4C0P
Type: protein
Length: 3,557 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transportin-3
UniProt: Q9Y5L0
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Transportin-3	protein	889	75% helix, 0% strand	Q9Y5L0
D	Transportin-3	protein	890	76% helix, 0% strand	Q9Y5L0

Ligands and binding sites

DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	862	0.79	0.82	112	empty
2	1177	0.77	0.79	102	empty
3	1016	0.77	0.79	88	empty
4	489	0.74	0.83	65	empty
5	554	0.72	0.81	51	empty

Interfaces

3 interfaces between chains.

A–D · 2066 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 2020 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 856 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4C0P · Unliganded Transportin 3 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y5L0 · AlphaFold monomer V2.0 prediction for transportin-3 (Q9Y5L0) · a predicted model of the same protein · chain A against A, TM-score 0.84

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 Q9Y5L0
Elsewhere: RCSB PDB 4C0P · PDBe 4C0P · UniProt Q9Y5L0

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