MolNFT v1 · #69388 · protein
Crystal structure of ornithine 4,5 aminomutase (resting state)
3KP1 · D-ornithine aminomutase E component: “Crystal structure of ornithine 4,5 aminomutase (resting state)”. X-ray diffraction, 3 ligands (PLP, B12, 5AD), 20 pockets (best druggability 0.84). MolNFT v1 #69388 on GenesisL1: 3D structure…
- PDB
- 3KP1
- Type
- protein
- Length
- 3,340 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
- PLP, B12, 5AD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C | D-ornithine aminomutase E component | protein | 726 | 42% helix, 15% strand | Q8VPJ5 |
| E, F, H, G | D-ornithine aminomutase S component | protein | 109 | 77% helix, 2% strand | Q8VPJ6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
- B12 · Cobalamin · ligand · 4 copies · chains A, C, B, D
- 5AD · 5'-deoxyadenosine · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.84 | 0.85 | 95 | empty |
| 2 | 1167 | 0.80 | 0.81 | 148 | PLP, B12 |
| 3 | 935 | 0.79 | 0.81 | 106 | PLP, B12 |
| 4 | 604 | 0.75 | 0.82 | 65 | PLP |
| 5 | 596 | 0.74 | 0.81 | 63 | PLP |
Interfaces
12 interfaces between chains.
- A–C · 6731 Ų buried · 93 hydrogen bonds · protein-protein
- B–D · 6730 Ų buried · 97 hydrogen bonds · protein-protein
- D–H · 3058 Ų buried · 47 hydrogen bonds · protein-protein
- A–E · 2993 Ų buried · 44 hydrogen bonds · protein-protein
- B–F · 2990 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3KP1 · Crystal structure of ornithine 4,5 aminomutase (Resting State) · the same entry in another collection · chain D against D, 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 3KP1 · PDBe 3KP1 · UniProt Q8VPJ5 · UniProt Q8VPJ6
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