MolNFT v1 · #124280 · protein

Crystal structure of a dioxygenase in the crotonase superfamily in P21, V425T mutant

5KAH · (3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase: “Crystal structure of a dioxygenase in the crotonase superfamily in P21, V425T mutant”. X-ray diffraction, 1 ligand (YE1), 20 pockets (best druggability 0.83). MolNFT v1 #124280 on…

PDB: 5KAH
Type: protein
Length: 5,033 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: (3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase
EC: 1.13.11.80
UniProt: Q8KLK7
Ligands: YE1
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 56% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, F, I	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	421	56% helix, 13% strand	Q8KLK7
B, H	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	418	58% helix, 12% strand	Q8KLK7
C	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	417	56% helix, 13% strand	Q8KLK7
D	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	421	56% helix, 13% strand	Q8KLK7
G	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	419	56% helix, 12% strand	Q8KLK7
J	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	419	56% helix, 13% strand	Q8KLK7
K	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	419	58% helix, 13% strand	Q8KLK7
L	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	418	56% helix, 13% strand	Q8KLK7

Ligands and binding sites

YE1 · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-4-({3-[(2-{[(3,5-dihydroxyphenyl)acetyl]amino}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate · ligand · 12 copies · chains A, B, C, L, D, E, F, I, G, H, J, K

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	925	0.83	0.85	98	empty
2	874	0.82	0.85	85	empty
3	1173	0.81	0.83	99	empty
4	757	0.81	0.84	71	empty
5	1046	0.76	0.78	76	empty

Interfaces

21 interfaces between chains.

E–F · 1448 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1442 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 1427 Å² buried · 12 hydrogen bonds · protein-protein
J–K · 1424 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 1419 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5KAH · Crystal structure of a dioxygenase in the Crotonase superfamily in P21, V425T mutant · the same entry in another collection · chain L against L, 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 Q8KLK7
Elsewhere: RCSB PDB 5KAH · PDBe 5KAH · UniProt Q8KLK7

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