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Structure of the C-terminal domain of human tubby-like protein 1

Analyse Structure of the C-terminal domain of human tubby-like protein 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FIM
Type: protein
Length: 456 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubby related protein 1
UniProt: O00294
Ligands: 3DP, SO4
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubby related protein 1	protein	224	12% helix, 38% strand	O00294
B	Tubby related protein 1	protein	232	12% helix, 38% strand	O00294

Ligands and binding sites

3DP · 3-(N,N-dimethyloctylammonio)propanesulfonate · ligand · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	995	0.74	0.77	95	3DP
2	80	0.42	0.79	17	empty
3	66	0.37	0.78	21	empty
4	62	0.32	0.76	19	empty
5	64	0.31	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 398 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2FIM · Structure of the C-terminal domain of Human Tubby-like protein 1 · the same entry in another collection · chain A against A, TM-score 1.00
O00294 · AlphaFold monomer V2.0 prediction for tubby-related protein 1 (O00294) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O00294
Elsewhere: RCSB PDB 2FIM · PDBe 2FIM · UniProt O00294

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