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Crystal structure of ornithine 4,5 aminomutase backsoaked complex
Analyse Crystal structure of ornithine 4,5 aminomutase backsoaked complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KOW
- Type
- protein
- Length
- 3,345 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-ornithine aminomutase E component; D-ornithine aminomutase S component
- UniProt
- Q8VPJ5, Q8VPJ6
- Ligands
- B12, PLP, 5AD
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | D-ornithine aminomutase E component | protein | 727 | 38% helix, 15% strand | Q8VPJ5 |
| E, F, G, H | D-ornithine aminomutase S component | protein | 109 | 72% helix, 2% strand | Q8VPJ6 |
| B | D-ornithine aminomutase E component | protein | 728 | 39% helix, 15% strand | Q8VPJ5 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 4 copies · chains A, C, B, D
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
- 5AD · 5'-deoxyadenosine · ligand · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.83 | 0.85 | 91 | empty |
| 2 | 959 | 0.79 | 0.80 | 102 | PLP, B12 |
| 3 | 91 | 0.75 | 0.97 | 22 | empty |
| 4 | 576 | 0.75 | 0.82 | 67 | PLP |
| 5 | 656 | 0.75 | 0.81 | 64 | PLP |
Interfaces
11 interfaces between chains.
- A–C · 6758 Ų buried · 82 hydrogen bonds · protein-protein
- B–D · 6690 Ų buried · 79 hydrogen bonds · protein-protein
- B–F · 3074 Ų buried · 42 hydrogen bonds · protein-protein
- D–H · 3058 Ų buried · 43 hydrogen bonds · protein-protein
- C–G · 3019 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3KOW · Crystal Structure of ornithine 4,5 aminomutase backsoaked complex · 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 Q8VPJ5
- Every structure of UniProt Q8VPJ6
- Elsewhere: RCSB PDB 3KOW · PDBe 3KOW · UniProt Q8VPJ5 · UniProt Q8VPJ6
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