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Crystal Structure of ORNITHINE 4,5 AMINOMUTASE in complex with 2,4-diaminobutyrate (DAB) (Aerobic)
Analyse Crystal Structure of ORNITHINE 4,5 AMINOMUTASE in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KP0
- Type
- protein
- Length
- 3,048 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Clostridium sticklandii
- Molecule
- D-ornithine aminomutase E component; D-ornithine aminomutase S component
- UniProt
- Q8VPJ5, Q8VPJ6
- Ligands
- Z98, 5AD, B12
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.8 · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | D-ornithine aminomutase E component | protein | 578 | 39% helix, 15% strand | Q8VPJ5 |
| E, F, G, H | D-ornithine aminomutase S component | protein | 109 | 76% helix, 2% strand | Q8VPJ6 |
| B, C | D-ornithine aminomutase E component | protein | 728 | 40% helix, 15% strand | Q8VPJ5 |
Ligands and binding sites
- 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
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, C, B, D
- B12 · Cobalamin · ligand · 2 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.80 | 0.82 | 111 | B12, Z98 |
| 2 | 867 | 0.78 | 0.81 | 63 | empty |
| 3 | 467 | 0.75 | 0.84 | 47 | empty |
| 4 | 454 | 0.75 | 0.84 | 57 | Z98 |
| 5 | 84 | 0.73 | 0.96 | 21 | empty |
Interfaces
11 interfaces between chains.
- A–C · 6065 Ų buried · 76 hydrogen bonds · protein-protein
- B–D · 6035 Ų buried · 78 hydrogen bonds · protein-protein
- B–F · 3032 Ų buried · 45 hydrogen bonds · protein-protein
- C–G · 3024 Ų buried · 45 hydrogen bonds · protein-protein
- A–E · 3014 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 3KP0 · Crystal structure of ornithine 4,5 aminomutase in complex with 2,4- diaminobutyrate (dab)… · 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 3KP0 · PDBe 3KP0 · UniProt Q8VPJ5 · UniProt Q8VPJ6
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