MolNFT v1 · #187861 · protein
Structure of the rieske non-heme iron oxygenase gxta with beta- saxitoxinol bound
7SZF · Sxtdiox: “Structure of the rieske non-heme iron oxygenase gxta with beta- saxitoxinol bound”. X-ray diffraction, 4 ligands (D82, FES, FE), 11 pockets (best druggability 0.80). MolNFT v1 #187861 on GenesisL1: 3D structure, binding…
- PDB
- 7SZF
- Type
- protein
- Length
- 962 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sxtdiox
- UniProt
- C3RVP5
- Ligands
- D82, FES, FE, CL
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sxtdiox | protein | 318 | 20% helix, 34% strand | C3RVP5 |
| B | Sxtdiox | protein | 318 | 22% helix, 35% strand | C3RVP5 |
| C | Sxtdiox | protein | 326 | 21% helix, 32% strand | C3RVP5 |
Ligands and binding sites
- D82 · beta-Saxitoxinol · ligand · 3 copies · chains A, B, C
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 7 copies · chains A, B, C
- GOL · Glycerol · additive · 14 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.80 | 0.86 | 52 | D82 |
| 2 | 306 | 0.79 | 0.90 | 34 | D82, FE |
| 3 | 353 | 0.76 | 0.87 | 38 | D82 |
| 4 | 434 | 0.67 | 0.79 | 46 | GOL |
| 5 | 289 | 0.56 | 0.77 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–C · 853 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 199 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7SZF · Structure of the Rieske Non-heme Iron Oxygenase GxtA with beta-Saxitoxinol Bound · the same entry in another collection · 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 C3RVP5
- Elsewhere: RCSB PDB 7SZF · PDBe 7SZF · UniProt C3RVP5
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