MolNFT v1 · #179109 · protein
Structure of the M101A variant of the sida ornithine hydroxylase with the FAD in the "out" conformation
7JVK · L-ornithine N(5)-monooxygenase: “Structure of the M101A variant of the sida ornithine hydroxylase with the FAD in the "out" conformation”. X-ray diffraction, 2 ligands (FAD, CA), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 7JVK
- Type
- protein
- Length
- 1,797 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-ornithine N(5)-monooxygenase
- EC
- 1.14.13.196
- UniProt
- E9QYP0
- Ligands
- FAD, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 455 | 34% helix, 22% strand | E9QYP0 |
| B | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 448 | 34% helix, 22% strand | E9QYP0 |
| C | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 446 | 34% helix, 22% strand | E9QYP0 |
| D | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 448 | 34% helix, 22% strand | E9QYP0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.85 | 0.86 | 104 | FAD, ACT |
| 2 | 762 | 0.85 | 0.88 | 81 | FAD, PGE, ACT |
| 3 | 672 | 0.84 | 0.88 | 76 | FAD, PGE, ACT |
| 4 | 991 | 0.84 | 0.85 | 95 | FAD, ACT |
| 5 | 321 | 0.68 | 0.82 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1300 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1290 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1046 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1026 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 936 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7JVK · Structure of the M101A variant of the SidA ornithine hydroxylase with the FAD in the out"… · the same entry in another collection · chain D against D, TM-score 1.00
- E9QYP0 · AlphaFold monomer V2.0 prediction for L-ornithine N(5)-monooxygenase (E9QYP0) · a predicted model of the same protein · 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 E9QYP0
- Elsewhere: RCSB PDB 7JVK · PDBe 7JVK · UniProt E9QYP0
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