Research workbench

Rat transthyretin complex with thyroxine (T4)

Analyse Rat transthyretin complex with thyroxine (T4) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IE4
Type: protein
Length: 480 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transthyretin
UniProt: P02767
Ligands: T44
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transthyretin	protein	120	7% helix, 50% strand	P02767

Ligands and binding sites

T44 · 3,5,3',5'-tetraiodo-L-thyronine · ligand · 2 copies · chains A, C, B, D

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	366	0.71	0.83	41	T44
2	451	0.70	0.81	57	T44
3	67	0.38	0.79	18	empty
4	73	0.36	0.77	16	empty
5	75	0.34	0.76	17	empty

Interfaces

6 interfaces between chains.

A–B · 961 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 957 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 370 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 351 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 349 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1IE4 · Rat transthyretin complex with thyroxine (T4) · the same entry in another collection · chain A against A, TM-score 1.00
P02767 · AlphaFold monomer V2.0 prediction for transthyretin (P02767) · 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 P02767
Elsewhere: RCSB PDB 1IE4 · PDBe 1IE4 · UniProt P02767

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