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Crystal structure of ornithine 4,5 aminomutase in complex with 2,4- diaminobutyrate (anaerobic)
Analyse Crystal structure of ornithine 4,5 aminomutase in complex with 2,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KOX
- Type
- protein
- Length
- 3,348 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, 5AD, Z98
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-ornithine aminomutase E component | protein | 728 | 42% helix, 16% strand | Q8VPJ5 |
| E, F, G, H | D-ornithine aminomutase S component | protein | 109 | 78% helix, 2% strand | Q8VPJ6 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 4 copies · chains A, C, B, D
- 5AD · 5'-deoxyadenosine · ligand · 4 copies · chains A, C, B, D
- Z98 · (2S)-2-amino-4-{[(1Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}butanoic acid · ligand · 4 copies · chains A, C, B, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.79 | 0.81 | 112 | Z98, B12 |
| 2 | 941 | 0.79 | 0.81 | 95 | B12, Z98 |
| 3 | 752 | 0.77 | 0.82 | 93 | Z98 |
| 4 | 1094 | 0.77 | 0.79 | 68 | empty |
| 5 | 979 | 0.75 | 0.78 | 103 | Z98 |
Interfaces
12 interfaces between chains.
- B–D · 6758 Ų buried · 85 hydrogen bonds · protein-protein
- A–C · 6688 Ų buried · 91 hydrogen bonds · protein-protein
- D–H · 3023 Ų buried · 51 hydrogen bonds · protein-protein
- B–F · 3006 Ų buried · 45 hydrogen bonds · protein-protein
- A–E · 2984 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 3KOX · Crystal Structure of ornithine 4,5 aminomutase in complex with 2,4-diaminobutyrate… · 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 3KOX · PDBe 3KOX · UniProt Q8VPJ5 · UniProt Q8VPJ6
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