Research workbench
E(L212)A, D(L213)A, N(M5)D triple mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides
Analyse E(L212)A, D(L213)A, N(M5)D triple mutant structure of photosynthetic reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DUQ
- Type
- protein
- Length
- 819 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Rhodobacter sphaeroides
- Molecule
- Reaction center protein L chain; Reaction center protein M chain; Reaction center protein…
- UniProt
- P0C0Y8, P0C0Y9, P0C0Y7
- Ligands
- BCL, BPH, U10, SPN, CDL, FE
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.7 · 3 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Reaction center protein L chain | protein | 281 | 63% helix, 4% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 298 | 64% helix, 4% strand | P0C0Y9 |
| H | Reaction center protein H chain | protein | 240 | 26% helix, 25% strand | P0C0Y7 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
- SPN · Speroidenone · ligand · chains M
- CDL · Cardiolipin · ligand · chains L, M, H
- FE · Fe (III) ion · metal · chains L, M
- LDA · Lauryl dimethylamine-N-oxide · additive · 4 copies · chains L, M, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.82 | 0.84 | 70 | BCL |
| 2 | 264 | 0.74 | 0.87 | 45 | U10 |
| 3 | 214 | 0.71 | 0.87 | 36 | U10 |
| 4 | 283 | 0.66 | 0.82 | 56 | empty |
| 5 | 101 | 0.60 | 0.86 | 16 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4536 Ų buried · 64 hydrogen bonds · protein-protein
- M–H · 2755 Ų buried · 39 hydrogen bonds · protein-protein
- L–H · 1638 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3DUQ · E(L212)A, D(L213)A, N(M5)D triple mutant structure of photosynthetic reaction center from… · the same entry in another collection · chain H against H, TM-score 1.00
- P0C0Y8 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P0C0Y8) · a predicted model of the same protein · chain L against A, TM-score 1.00
- P0C0Y9 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P0C0Y9) · a predicted model of the same protein · chain M against A, TM-score 0.99
- P0C0Y7 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P0C0Y7) · a predicted model of the same protein · chain H against A, TM-score 0.99
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 P0C0Y8
- Every structure of UniProt P0C0Y9
- Every structure of UniProt P0C0Y7
- Elsewhere: RCSB PDB 3DUQ · PDBe 3DUQ · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7
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