Research workbench
The soxax complex of rhodovulum sulfidophilum
Analyse The soxax complex of rhodovulum sulfidophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OZ1
- Type
- protein
- Length
- 1,592 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diheme cytochrome C; Cytochrome C
- UniProt
- Q939U1, Q939U4
- Ligands
- HEC
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Diheme cytochrome C | protein | 261 | 38% helix, 15% strand | Q939U1 |
| B | Cytochrome C | protein | 135 | 29% helix, 4% strand | Q939U4 |
| D | Cytochrome C | protein | 137 | 31% helix, 4% strand | Q939U4 |
| F, H | Cytochrome C | protein | 138 | 31% helix, 4% strand | Q939U4 |
Ligands and binding sites
- HEC · Heme C · ligand · 12 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.87 | 0.88 | 114 | HEC |
| 2 | 1074 | 0.86 | 0.87 | 120 | HEC |
| 3 | 831 | 0.82 | 0.84 | 80 | HEC |
| 4 | 1149 | 0.81 | 0.82 | 114 | HEC |
| 5 | 575 | 0.67 | 0.77 | 66 | HEC |
Interfaces
13 interfaces between chains.
- A–B · 1336 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1326 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1320 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1290 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 520 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 cofactor, 4 modified (heme c attachment, oxidation).
Compared structures
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 Q939U1
- Every structure of UniProt Q939U4
- Elsewhere: RCSB PDB 2OZ1 · PDBe 2OZ1 · UniProt Q939U1 · UniProt Q939U4
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