Research workbench
Rhodobacter sphaeroides bc1 with azoxystrobin
Analyse Rhodobacter sphaeroides bc1 with azoxystrobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NHH
- Type
- protein
- Length
- 1,722 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
- Molecule
- Cytochrome b; Cytochrome c1; Ubiquinol-cytochrome c reductase iron-sulfur subunit
- EC
- 1.10.2.2
- UniProt
- A0A344Q9J3, A0A344Q9J2, A0A344Q9J4
- Ligands
- HEM, AZO, 6PE, 8SP, HEC, FES, SR
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 3 · 3 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Cytochrome b | protein | 430 | 68% helix, 2% strand | A0A344Q9J3 |
| B, F | Cytochrome c1 | protein | 256 | 40% helix, 7% strand | A0A344Q9J2 |
| C, G | Ubiquinol-cytochrome c reductase iron-sulfur subunit (EC 1.10.2.2) | protein | 175 | 23% helix, 29% strand | A0A344Q9J4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, E
- AZO · Methyl (2Z)-2-(2-{[6-(2-cyanophenoxy)pyrimidin-4-yl]oxy}phenyl)-3-methoxyacrylate · ligand · 2 copies · chains A, E
- 6PE · 1,2-dihexanoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, E
- 8SP · O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy) phosphoryl]-L-serine · ligand · 2 copies · chains A, B, E, F
- HEC · Heme C · ligand · 2 copies · chains B, F
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, G
- SR · Strontium ion · metal · 3 copies · chains B, F
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.87 | 0.91 | 67 | HEM, BOG |
| 2 | 636 | 0.86 | 0.91 | 68 | HEM, BOG |
| 3 | 1179 | 0.82 | 0.83 | 96 | HEC, 8SP |
| 4 | 824 | 0.82 | 0.85 | 94 | 8SP, HEC |
| 5 | 395 | 0.80 | 0.88 | 44 | HEM |
Interfaces
11 interfaces between chains.
- E–F · 1991 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1963 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1573 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 732 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 656 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 disulfide (heme c attachment, disulfide).
Compared structures
- 6NHH · Rhodobacter sphaeroides BC1 with azoxystrobin · 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 A0A344Q9J3
- Every structure of UniProt A0A344Q9J2
- Every structure of UniProt A0A344Q9J4
- Elsewhere: RCSB PDB 6NHH · PDBe 6NHH · UniProt A0A344Q9J3 · UniProt A0A344Q9J2 · UniProt A0A344Q9J4
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