MolNFT v1 · #20964 · protein
Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213 replaced with asn and arg H177 replaced with his
1RVJ · Reaction center protein L chain: “Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213 replaced with asn and…”. X-ray diffraction, 7 ligands (BCL, BPH, U10), 13 pockets (best druggability 0.83).…
- PDB
- 1RVJ
- Type
- protein
- Length
- 820 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reaction center protein L chain; Reaction center protein M chain; Reaction center protein…
- UniProt
- P02954, P02953, P11846
- Ligands
- BCL, BPH, U10, SPO, CDL, FE2, PO4
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 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 | P02954 |
| M | Reaction center protein M chain | protein | 301 | 65% helix, 4% strand | P02953 |
| H | Reaction center protein H chain | protein | 238 | 25% helix, 25% strand | P11846 |
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
- SPO · Spheroidene · ligand · chains M
- CDL · Cardiolipin · ligand · chains L, M, H
- FE2 · Fe (II) ion · metal · chains L, M
- PO4 · Phosphate ion · ion · chains M
- LDA · Lauryl dimethylamine-N-oxide · additive · 3 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.83 | 0.84 | 83 | BCL |
| 2 | 209 | 0.68 | 0.85 | 30 | U10 |
| 3 | 93 | 0.58 | 0.87 | 19 | empty |
| 4 | 91 | 0.55 | 0.84 | 21 | empty |
| 5 | 134 | 0.46 | 0.78 | 27 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4506 Ų buried · 67 hydrogen bonds · protein-protein
- M–H · 2907 Ų buried · 38 hydrogen bonds · protein-protein
- L–H · 1637 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1RVJ · Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213… · 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 P02954
- Every structure of UniProt P02953
- Every structure of UniProt P11846
- Elsewhere: RCSB PDB 1RVJ · PDBe 1RVJ · UniProt P02954 · UniProt P02953 · UniProt P11846
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