Research workbench
Structure of oxidized sida ornithine hydroxylase with the FAD "in" and complexed with NADP
Analyse Structure of oxidized sida ornithine hydroxylase with the FAD "in" and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X0I
- Type
- protein
- Length
- 1,771 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 · 3 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 | 443 | 34% helix, 22% strand | E9QYP0 |
| B, C | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 443 | 34% helix, 23% strand | E9QYP0 |
| D | L-ornithine N(5)-monooxygenase (EC 1.14.13.196) | protein | 442 | 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 · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.85 | 0.87 | 90 | ACT, FAD, NAP, CA |
| 2 | 871 | 0.85 | 0.87 | 77 | ACT, FAD, NAP, CA |
| 3 | 858 | 0.85 | 0.87 | 79 | ACT, FAD, NAP, CA |
| 4 | 1134 | 0.84 | 0.85 | 100 | ACT, FAD, NAP, CA |
| 5 | 412 | 0.69 | 0.81 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1290 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1288 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1128 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1111 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 888 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6X0I · Structure of oxidized SidA ornithine hydroxylase with the FAD in" and complexed with NADP" · the same entry in another collection · chain A against A, 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 6X0I · PDBe 6X0I · UniProt E9QYP0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.