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Crystal structure of a dioxygenase in the crotonase superfamily in P21, A319C mutant

Analyse Crystal structure of a dioxygenase in the crotonase superfamily in P21, A319C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KAJ
Type: protein
Length: 4,991 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: YE2
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 5 distinct chains · 56% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	414	56% helix, 13% strand	Q8KLK7
B, D, K	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	416	57% helix, 13% strand	Q8KLK7
C, F, L	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	416	56% helix, 13% strand	Q8KLK7
E, G, H	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	417	56% helix, 13% strand	Q8KLK7
I, J	(3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80)	protein	415	55% helix, 13% strand	Q8KLK7

Ligands and binding sites

YE2 · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[(~{E})-2-[3,5-bis(oxidanyl)phenyl]-1-oxidanyl-ethenyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate · ligand · 12 copies · chains A, B, C, D, E, F, I, G, H, J, K, L

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	1161	0.82	0.83	90	empty
2	775	0.82	0.85	70	empty
3	751	0.81	0.85	64	empty
4	755	0.81	0.85	66	empty
5	996	0.76	0.78	67	empty

Interfaces

20 interfaces between chains.

K–L · 1507 Å² buried · 19 hydrogen bonds · protein-protein
H–I · 1490 Å² buried · 16 hydrogen bonds · protein-protein
J–K · 1463 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1457 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1442 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5KAJ · Crystal structure of a dioxygenase in the Crotonase superfamily in P21, A319C 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 5KAJ · PDBe 5KAJ · UniProt Q8KLK7

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