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Crystal structure of transthyretin from sparus aurata

Analyse Crystal structure of transthyretin from sparus aurata in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OO2
Type: protein
Length: 464 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transthyretin
UniProt: O93330
Ligands: CD
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transthyretin	protein	116	9% helix, 49% strand	O93330

Ligands and binding sites

CD · Cadmium ion · metal · 2 copies · chains C

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	283	0.65	0.81	38	empty
2	278	0.65	0.81	44	empty
3	83	0.38	0.77	18	empty
4	64	0.28	0.73	19	empty
5	52	0.26	0.73	15	empty

Interfaces

6 interfaces between chains.

C–D · 968 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 932 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 408 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 396 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 363 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1OO2 · Crystal structure of transthyretin from Sparus aurata · the same entry in another collection · chain A against A, TM-score 1.00

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 O93330
Elsewhere: RCSB PDB 1OO2 · PDBe 1OO2 · UniProt O93330

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