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Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2
Analyse Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QJY
- Type
- protein
- Length
- 5,178 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Rhodobacter sphaeroides
- Molecule
- Cytochrome b; Cytochrome c1; Ubiquinol-cytochrome c reductase iron-sulfur subunit
- EC
- 1.10.2.2
- UniProt
- Q02761, Q3IY11, Q02762
- Ligands
- HEM, SMA, LOP, UQ2, FES, BGL, SR, NA, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 2.4 · 3 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P | Cytochrome b | protein | 428 | 68% helix, 2% strand | Q02761 |
| B, E, H, K, N, Q | Cytochrome c1 | protein | 256 | 39% helix, 7% strand | Q3IY11 |
| C, F, I, L, O, R | Ubiquinol-cytochrome c reductase iron-sulfur subunit (EC 1.10.2.2) | protein | 179 | 23% helix, 28% strand | Q02762 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 18 copies · chains A, B, D, E, G, H, J, K, M, N, P, Q
- SMA · Stigmatellin A · ligand · 6 copies · chains A, F, C, D, G, L, I, J, M, R, O, P
- LOP · (1R)-2-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(dodecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 6 copies · chains A, D, G, J, M, P
- UQ2 · Ubiquinone-2 · ligand · 6 copies · chains A, D, G, J, M, P
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains C, F, I, L, O, R
- BGL · 2-O-octyl-beta-D-glucopyranose · sugar · 6 copies · chains A, B, D, E, G, H, J, K, M, N, P, Q
- SR · Strontium ion · metal · 9 copies · chains B, E, H, K, J, M, N, Q
- NA · Sodium ion · metal · chains I, R
- CL · Chloride ion · ion · 2 copies · chains I, R
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 | 983 | 0.89 | 0.91 | 105 | HEM, BGL |
| 2 | 945 | 0.89 | 0.91 | 102 | HEM, BGL |
| 3 | 1008 | 0.89 | 0.90 | 116 | HEM, BGL |
| 4 | 901 | 0.89 | 0.91 | 103 | BGL, HEM |
| 5 | 861 | 0.89 | 0.91 | 103 | BGL, HEM |
Interfaces
39 interfaces between chains.
- P–Q · 1982 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1979 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1970 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1967 Ų buried · 19 hydrogen bonds · protein-protein
- J–K · 1962 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 12 disulfide (heme attachment, disulfide).
Compared structures
- 2QJY · Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2 · the same entry in another collection · chain K against K, 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 2QJY · PDBe 2QJY · UniProt Q02761 · UniProt Q3IY11 · UniProt Q02762
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