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Crystal structure of salicylate 5-hydroxylase naggh (a rieske non-heme iron-dependent monooxgenase)
Analyse Crystal structure of salicylate 5-hydroxylase naggh (a rieske non-heme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C8Z
- Type
- protein
- Length
- 2,176 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Salicylate 5-hydroxylase, large oxygenase component; Salicylate 5-hydroxylase, small…
- EC
- 1.14.13.172
- UniProt
- O52379, O52380
- Ligands
- FES, FE
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Salicylate 5-hydroxylase, large oxygenase component (EC 1.14.13.172) | protein | 383 | 25% helix, 28% strand | O52379 |
| B, D, F, H | Salicylate 5-hydroxylase, small oxygenase component (EC 1.14.13.172) | protein | 161 | 26% helix, 46% strand | O52380 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, C, E, G
- FE · Fe (III) ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.73 | 0.84 | 50 | empty |
| 2 | 398 | 0.72 | 0.83 | 55 | empty |
| 3 | 479 | 0.69 | 0.80 | 58 | empty |
| 4 | 283 | 0.67 | 0.82 | 40 | FE |
| 5 | 426 | 0.66 | 0.79 | 40 | empty |
Interfaces
14 interfaces between chains.
- C–D · 1651 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1650 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1644 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 1636 Ų buried · 37 hydrogen bonds · protein-protein
- A–E · 1564 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7C8Z · Crystal structure of salicylate 5-hydroxylase NagGH (a Rieske non-heme iron-dependent… · the same entry in another collection · chain H against H, TM-score 1.00
- O52379 · AlphaFold monomer V2.0 prediction for salicylate 5-hydroxylase, large oxygenase component… · a predicted model of the same protein · chain A against A, TM-score 0.99
- O52380 · AlphaFold monomer V2.0 prediction for salicylate 5-hydroxylase, small oxygenase component… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O52379
- Every structure of UniProt O52380
- Elsewhere: RCSB PDB 7C8Z · PDBe 7C8Z · UniProt O52379 · UniProt O52380
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