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Crystal structure of the wild type ttr binding naringenin (TTRWT:NAR)

Analyse Crystal structure of the wild type ttr binding naringenin (TTRWT:NAR) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DEU
Type: protein
Length: 232 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transthyretin
UniProt: P02766
Ligands: NAR, CA
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transthyretin	protein	117	5% helix, 50% strand	P02766
B	Transthyretin	protein	115	6% helix, 51% strand	P02766

Ligands and binding sites

NAR · Naringenin · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · chains B
EDO · 1,2-ethanediol · additive · 10 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.38	0.76	16	empty
2	70	0.35	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 907 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

4DEU · Crystal Structure of the Wild Type TTR Binding Naringenin (TTRwt:NAR) · 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 4DEU · PDBe 4DEU · UniProt P02766

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