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Structure of dithionite-reduced sida ornithine hydroxylase with the FAD "in" and complexed with L-ornithine
Analyse Structure of dithionite-reduced sida ornithine hydroxylase with the FAD "in"… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X0K
- Type
- protein
- Length
- 3,510 residues
- Chains
- 8
- 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
- FDA, ORN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 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 | 440 | 34% helix, 23% strand | E9QYP0 |
| B | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 442 | 33% helix, 23% strand | E9QYP0 |
| C | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 433 | 34% helix, 22% strand | E9QYP0 |
| D | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 441 | 34% helix, 22% strand | E9QYP0 |
| E | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 441 | 32% helix, 22% strand | E9QYP0 |
| F | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 436 | 36% helix, 22% strand | E9QYP0 |
| G | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 440 | 34% helix, 22% strand | E9QYP0 |
| H | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 437 | 34% helix, 22% strand | E9QYP0 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ORN · L-ornithine · ligand · 6 copies · chains A, B, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.85 | 0.86 | 91 | FDA, ORN |
| 2 | 954 | 0.85 | 0.86 | 85 | FDA, ORN |
| 3 | 906 | 0.85 | 0.87 | 80 | FDA, ORN |
| 4 | 939 | 0.84 | 0.86 | 102 | FDA |
| 5 | 916 | 0.84 | 0.86 | 78 | FDA, ORN |
Interfaces
15 interfaces between chains.
- C–D · 1335 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1333 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 1325 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 1318 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1049 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6X0K · Structure of dithionite-reduced SidA ornithine hydroxylase with the FAD in" and complexed… · the same entry in another collection · chain H against H, 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 C 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 6X0K · PDBe 6X0K · UniProt E9QYP0
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