Research workbench
Photosynthetic reaction center from rhodopseudomonas viridis (qb- depleted)
Analyse Photosynthetic reaction center from rhodopseudomonas viridis (qb- depleted) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PRC
- Type
- protein
- Length
- 1,186 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center
- UniProt
- P07173, P06009, P06010, P06008
- Ligands
- HEM, BCB, BPB, MQ7, NS5, FE2, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Photosynthetic reaction center | protein | 332 | 43% helix, 4% strand | P07173 |
| L | Photosynthetic reaction center | protein | 273 | 66% helix, 4% strand | P06009 |
| M | Photosynthetic reaction center | protein | 323 | 63% helix, 5% strand | P06010 |
| H | Photosynthetic reaction center | protein | 258 | 26% helix, 24% strand | P06008 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, L, M
- BCB · Bacteriochlorophyll B · ligand · 4 copies · chains L, M
- BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
- MQ7 · Menaquinone-7 · ligand · chains L, M
- NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains M
- FE2 · Fe (II) ion · metal · chains L, M
- SO4 · Sulfate ion · ion · 4 copies · chains L, M, H
- LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains L, M, H
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 | 857 | 0.88 | 0.90 | 104 | HEM |
| 2 | 844 | 0.84 | 0.85 | 79 | BCB |
| 3 | 100 | 0.77 | 0.98 | 31 | empty |
| 4 | 219 | 0.74 | 0.88 | 38 | MQ7 |
| 5 | 58 | 0.72 | 0.99 | 22 | empty |
Interfaces
6 interfaces between chains.
- L–M · 4394 Ų buried · 62 hydrogen bonds · protein-protein
- M–H · 2884 Ų buried · 47 hydrogen bonds · protein-protein
- C–M · 2742 Ų buried · 37 hydrogen bonds · protein-protein
- L–H · 1865 Ų buried · 25 hydrogen bonds · protein-protein
- C–L · 1775 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 1 modified (heme attachment, formylation).
Compared structures
- 3PRC · Photosynthetic reaction center from rhodopseudomonas viridis (qb-depleted) · the same entry in another collection · chain H against H, TM-score 1.00
- P07173 · AlphaFold monomer V2.0 prediction for photosynthetic reaction center cytochrome C subunit… · a predicted model of the same protein · chain C against A, TM-score 1.00
- P06009 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P06009) · a predicted model of the same protein · chain L against A, TM-score 0.99
- P06010 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P06010) · a predicted model of the same protein · chain M against A, TM-score 0.97
- P06008 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P06008) · a predicted model of the same protein · chain H against A, TM-score 0.94
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 P07173
- Every structure of UniProt P06009
- Every structure of UniProt P06010
- Every structure of UniProt P06008
- Elsewhere: RCSB PDB 3PRC · PDBe 3PRC · UniProt P07173 · UniProt P06009 · UniProt P06010 · UniProt P06008
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