MolNFT v1 · #61523 · protein

Crystal structure of transthyretin variant T60A at acidic pH

3DO4: “Crystal structure of transthyretin variant T60A at acidic pH”. X-ray diffraction, 14 pockets (best druggability 0.78). MolNFT v1 #61523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3DO4
Type: protein
Length: 928 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transthyretin
UniProt: P02766
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Transthyretin	protein	116	5% helix, 53% strand	P02766

Ligands and binding sites

ACT · Acetate ion · additive · 5 copies · chains A, B, E, G, H

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1025	0.78	0.80	68	empty
2	786	0.76	0.80	70	empty
3	87	0.74	0.97	28	empty
4	94	0.74	0.96	28	ACT
5	314	0.68	0.82	45	empty

Interfaces

17 interfaces between chains.

C–E · 933 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 928 Å² buried · 20 hydrogen bonds · protein-protein
D–F · 922 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 915 Å² buried · 21 hydrogen bonds · protein-protein
F–G · 395 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3DO4 · Crystal structure of transthyretin variant T60A at acidic pH · 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 P02766
Elsewhere: RCSB PDB 3DO4 · PDBe 3DO4 · UniProt P02766

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