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Crystal structure of the wild type ttr binding apigenin (TTRWT:API)

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

PDB: 4DER
Type: protein
Length: 231 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transthyretin
UniProt: P02766
Ligands: AGI
Pockets: 2 · best druggability 0.29

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transthyretin	protein	116	6% helix, 51% strand	P02766
B	Transthyretin	protein	115	7% helix, 51% strand	P02766

Ligands and binding sites

AGI · 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · chains A

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	56	0.29	0.75	14	empty
2	54	0.29	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 924 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

4DER · Crystal Structure of the Wild Type TTR Binding Apigenin (TTRwt:API) · 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 4DER · PDBe 4DER · UniProt P02766

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