Research workbench
Crystal structure of a dioxygenase in the crotonase superfamily in P21
Analyse Crystal structure of a dioxygenase in the crotonase superfamily in P21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KAG
- Type
- protein
- Length
- 5,059 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, OXY
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F, I, L | (3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80) | protein | 421 | 56% helix, 13% strand | Q8KLK7 |
| B, G, H, K | (3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80) | protein | 422 | 57% helix, 13% strand | Q8KLK7 |
| D | (3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80) | protein | 423 | 57% helix, 13% strand | Q8KLK7 |
| J | (3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase (EC 1.13.11.80) | protein | 422 | 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, D, E, F, G, H, I, J, K, L
- OXY · Oxygen molecule · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.83 | 0.85 | 88 | empty |
| 2 | 830 | 0.82 | 0.85 | 72 | empty |
| 3 | 1195 | 0.81 | 0.83 | 98 | empty |
| 4 | 1027 | 0.81 | 0.83 | 72 | empty |
| 5 | 1124 | 0.76 | 0.78 | 71 | empty |
Interfaces
21 interfaces between chains.
- K–L · 1496 Ų buried · 19 hydrogen bonds · protein-protein
- J–K · 1488 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1485 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1475 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1454 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5KAG · Crystal structure of a dioxygenase in the Crotonase superfamily in P21 · 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 5KAG · PDBe 5KAG · UniProt Q8KLK7
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