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Crystal structure of human transthyretin complexed with glabridin

Analyse Crystal structure of human transthyretin complexed with glabridin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4N86
Type: protein
Length: 230 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transthyretin
UniProt: P02766
Ligands: GBJ, CA
Pockets: 3 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 51% strand (DSSP).

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

Ligands and binding sites

GBJ · 4-[(3R)-8,8-dimethyl-3,4-dihydro-2H,8H-pyrano[2,3-f]chromen-3-yl]benzene-1,3-diol · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · chains A

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

Pockets

3 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	91	0.38	0.76	18	empty
2	65	0.34	0.77	16	empty
3	64	0.26	0.72	18	empty

Interfaces

1 interface between chains.

A–B · 902 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

4N86 · Crystal structure of human transthyretin complexed with glabridin · 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 4N86 · PDBe 4N86 · UniProt P02766

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