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Crystal structure of chalcone isomerase from medicago truncatula complexed with (2S) naringenin

Analyse Crystal structure of chalcone isomerase from medicago truncatula complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MS8
Type: protein
Length: 1,660 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chalcone-flavonone isomerase family protein
UniProt: B7FJK3
Ligands: NAR
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 8 distinct chains · 39% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chalcone-flavonone isomerase family protein	protein	208	40% helix, 29% strand	B7FJK3
B	Chalcone-flavonone isomerase family protein	protein	207	40% helix, 27% strand	B7FJK3
C	Chalcone-flavonone isomerase family protein	protein	209	38% helix, 28% strand	B7FJK3
D	Chalcone-flavonone isomerase family protein	protein	207	39% helix, 28% strand	B7FJK3
E	Chalcone-flavonone isomerase family protein	protein	208	39% helix, 29% strand	B7FJK3
F	Chalcone-flavonone isomerase family protein	protein	207	39% helix, 28% strand	B7FJK3
G	Chalcone-flavonone isomerase family protein	protein	209	39% helix, 30% strand	B7FJK3
H	Chalcone-flavonone isomerase family protein	protein	205	39% helix, 29% strand	B7FJK3

Ligands and binding sites

NAR · Naringenin · ligand · 5 copies · chains A, D, E, F, G

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1042	0.73	0.76	83	NAR
2	696	0.73	0.80	69	empty
3	360	0.65	0.80	41	empty
4	108	0.64	0.88	17	empty
5	97	0.64	0.89	15	NAR

Interfaces

17 interfaces between chains.

D–H · 356 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 344 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 342 Å² buried · 3 hydrogen bonds · protein-protein
D–G · 341 Å² buried · 4 hydrogen bonds · protein-protein
C–F · 320 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6MS8 · Crystal Structure of Chalcone Isomerase from Medicago Truncatula Complexed with (2S)… · 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 B7FJK3
Elsewhere: RCSB PDB 6MS8 · PDBe 6MS8 · UniProt B7FJK3

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