Research workbench
Photosynthetic reaction center from rhodobacter sphaeroides
Analyse Photosynthetic reaction center from rhodobacter sphaeroides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z9J
- Type
- protein
- Length
- 821 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
- P0C0Y8, P0C0Y9, P0C0Y7
- Ligands
- BCL, BPH, U10, FE, MN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reaction center protein L chain | protein | 281 | 60% helix, 4% strand | P0C0Y8 |
| B | Reaction center protein M chain | protein | 302 | 57% helix, 5% strand | P0C0Y9 |
| C | Reaction center protein H chain | protein | 238 | 24% helix, 21% strand | P0C0Y7 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains A, B
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains A, B
- U10 · Ubiquinone-10 · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · chains A, B
- MN · Manganese (II) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.81 | 0.82 | 74 | BCL |
| 2 | 201 | 0.75 | 0.90 | 42 | U10 |
| 3 | 72 | 0.72 | 0.97 | 30 | empty |
| 4 | 152 | 0.61 | 0.84 | 32 | empty |
| 5 | 135 | 0.57 | 0.82 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4567 Ų buried · 67 hydrogen bonds · protein-protein
- B–C · 2856 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1580 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1Z9J · Photosynthetic Reaction Center from Rhodobacter sphaeroides · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.99
- P0C0Y9 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P0C0Y9) · a predicted model of the same protein · chain B 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 C against A, TM-score 0.98
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 1Z9J · PDBe 1Z9J · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7
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