Research workbench
Crystal structure of oryza sativa fatty acid alpha-dioxygenase Y379F with palmitic acid
Analyse Crystal structure of oryza sativa fatty acid alpha-dioxygenase Y379F with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KVL
- Type
- protein
- Length
- 610 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid alpha-oxidase
- UniProt
- Q9M5J1
- Ligands
- PLM, HEM, CA, CL
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fatty acid alpha-oxidase | protein | 610 | 46% helix, 9% strand | Q9M5J1 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PGE · Triethylene glycol · additive · 6 copies · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A
- IMD · Imidazole · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.86 | 0.92 | 49 | HEM, IMD |
| 2 | 172 | 0.79 | 0.94 | 31 | PLM |
| 3 | 162 | 0.58 | 0.82 | 31 | PG4 |
| 4 | 170 | 0.53 | 0.80 | 24 | 1PE |
| 5 | 102 | 0.49 | 0.81 | 15 | CL |
Compared structures
- 4KVL · Crystal structure of Oryza sativa fatty acid alpha-dioxygenase Y379F with palmitic acid · 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 4KVL · PDBe 4KVL · UniProt Q9M5J1
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