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Crystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin inhibited
Analyse Crystal structure of wild type rhodobacter sphaeroides with stigmatellin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QJP
- Type
- protein
- Length
- 3,452 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B; Cytochrome C1; Ubiquinol-cytochrome C reductase iron-sulfur subunit
- EC
- 1.10.2.2
- UniProt
- Q02761, Q3IY11, Q02762
- Ligands
- HEM, BGL, SMA, LOP, ANJ, FES, SR
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Cytochrome B | protein | 428 | 69% helix, 2% strand | Q02761 |
| B, E, H, K | Cytochrome C1 | protein | 256 | 37% helix, 5% strand | Q3IY11 |
| C, F, I, L | Ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 1.10.2.2) | protein | 179 | 20% helix, 27% strand | Q02762 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, D, E, G, H, J, K
- BGL · 2-O-octyl-beta-D-glucopyranose · ligand · 4 copies · chains A, B, D, E, G, H, J, K
- SMA · Stigmatellin A · ligand · 4 copies · chains A, F, C, D, G, L, I, J
- LOP · (1R)-2-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(dodecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 4 copies · chains A, D, G, J
- ANJ · (2R,3S,6S,7R,8R)-3-{[3-(formylamino)-2-hydroxybenzoyl]amino}-8-hexyl-2,6-dimethyl-4,9-dioxo-1,5-dioxonan-7-yl (2S)-2-methylbutanoate · ligand · 4 copies · chains A, D, G, J
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains C, F, I, L
- SR · Strontium ion · metal · 6 copies · chains B, E, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.89 | 0.91 | 93 | BGL, HEM |
| 2 | 845 | 0.88 | 0.91 | 96 | HEM |
| 3 | 1181 | 0.87 | 0.88 | 134 | BGL, HEM |
| 4 | 697 | 0.87 | 0.91 | 76 | HEM |
| 5 | 458 | 0.81 | 0.88 | 49 | HEM, ANJ |
Interfaces
26 interfaces between chains.
- J–K · 1961 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1960 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1947 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1931 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1554 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 8 disulfide (heme attachment, disulfide).
Compared structures
- 2QJP · Crystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin… · the same entry in another collection · chain L against L, 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 Q02761
- Every structure of UniProt Q3IY11
- Every structure of UniProt Q02762
- Elsewhere: RCSB PDB 2QJP · PDBe 2QJP · UniProt Q02761 · UniProt Q3IY11 · UniProt Q02762
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