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Human transthyretin (ttr) complexed with 4-hydroxy-chalcone

Analyse Human transthyretin (ttr) complexed with 4-hydroxy-chalcone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EZP
Type: protein
Length: 936 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transthyretin
UniProt: P02766
Ligands: IPJ
Pockets: 17 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transthyretin	protein	115	6% helix, 51% strand	P02766
B, C, F	Transthyretin	protein	117	5% helix, 50% strand	P02766
D	Transthyretin	protein	116	6% helix, 51% strand	P02766
E	Transthyretin	protein	122	6% helix, 48% strand	P02766
G	Transthyretin	protein	118	6% helix, 50% strand	P02766
H	Transthyretin	protein	114	6% helix, 52% strand	P02766

Ligands and binding sites

IPJ · 4-hydroxy-chalcone · ligand · 5 copies · chains A, D, B, C, F, H, E, G
EDO · 1,2-ethanediol · additive · chains G

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

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1174	0.79	0.81	96	empty
2	101	0.74	0.96	28	empty
3	100	0.73	0.95	28	empty
4	427	0.71	0.82	50	IPJ
5	334	0.69	0.83	38	IPJ

Interfaces

17 interfaces between chains.

C–D · 905 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 904 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 902 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 891 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 410 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5EZP · Human transthyretin (TTR) complexed with 4-hydroxy-chalcone · 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 5EZP · PDBe 5EZP · UniProt P02766

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