MolNFT v1 · #187862 · protein
Structure of the rieske non-heme iron oxygenase gxta pressurized with xenon
7SZG · Sxtdiox: “Structure of the rieske non-heme iron oxygenase gxta pressurized with xenon”. X-ray diffraction, 4 ligands (FES, FE, XE), 15 pockets (best druggability 0.80). MolNFT v1 #187862 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7SZG
- Type
- protein
- Length
- 958 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sxtdiox
- UniProt
- C3RVP5
- Ligands
- FES, FE, XE, CL
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sxtdiox | protein | 315 | 21% helix, 33% strand | C3RVP5 |
| B | Sxtdiox | protein | 316 | 20% helix, 35% strand | C3RVP5 |
| C | Sxtdiox | protein | 327 | 20% helix, 32% strand | C3RVP5 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- XE · Xenon · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.80 | 0.86 | 52 | XE, DTT |
| 2 | 358 | 0.79 | 0.88 | 38 | DTT, XE |
| 3 | 335 | 0.78 | 0.88 | 40 | XE, DTT |
| 4 | 538 | 0.68 | 0.78 | 59 | GOL |
| 5 | 68 | 0.57 | 0.88 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 812 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 230 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 218 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 7SZG · Structure of the Rieske Non-heme Iron Oxygenase GxtA Pressurized with Xenon · 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 7SZG · PDBe 7SZG · UniProt C3RVP5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.