Research workbench
Structure of the M101A variant of the sida ornithine hydroxylase complexed with NADP and the FAD in the "out" conformation
Analyse Structure of the M101A variant of the sida ornithine hydroxylase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JVL
- Type
- protein
- Length
- 1,762 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, NAP, CA
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 439 | 34% helix, 22% strand | E9QYP0 |
| B | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 442 | 35% helix, 22% strand | E9QYP0 |
| C | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 441 | 35% helix, 22% strand | E9QYP0 |
| D | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 440 | 34% helix, 22% strand | E9QYP0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.85 | 0.87 | 94 | FAD, NAP, ACT, CA |
| 2 | 818 | 0.85 | 0.88 | 75 | FAD, NAP, ACT, CA |
| 3 | 1058 | 0.84 | 0.85 | 89 | FAD, NAP, ACT |
| 4 | 1152 | 0.84 | 0.85 | 104 | FAD, NAP, ACT |
| 5 | 331 | 0.68 | 0.82 | 42 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1300 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1298 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 1115 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1106 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 911 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7JVL · Structure of the M101A variant of the SidA ornithine hydroxylase complexed with NADP and… · 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 7JVL · PDBe 7JVL · UniProt E9QYP0
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