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Crystal structure of oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide
Analyse Crystal structure of oryza sativa fatty acid alpha-dioxygenase with hydrogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KVJ
- Type
- protein
- Length
- 611 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid alpha-oxidase
- UniProt
- Q9M5J1
- Ligands
- HEM, PEO, NA, CA, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fatty acid alpha-oxidase | protein | 611 | 45% helix, 9% strand | Q9M5J1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- PEO · Hydrogen peroxide · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- DMU · Decyl-beta-D-maltopyranoside · additive · chains A
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.85 | 0.92 | 52 | HEM, PEO |
| 2 | 136 | 0.73 | 0.92 | 28 | PG4, CL |
| 3 | 155 | 0.57 | 0.82 | 32 | empty |
| 4 | 124 | 0.56 | 0.83 | 23 | empty |
| 5 | 170 | 0.52 | 0.79 | 26 | P33, NA |
Compared structures
- 4KVJ · Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide · 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 Q9M5J1
- Elsewhere: RCSB PDB 4KVJ · PDBe 4KVJ · UniProt Q9M5J1
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