Research workbench
Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LSP co-crystallization with spheroidene
Analyse Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LSP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z1J
- Type
- protein
- Length
- 823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Rhodobacter sphaeroides
- Molecule
- Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
- UniProt
- P0C0Y7, P0C0Y8, P0C0Y9
- Ligands
- UNL, BCL, BPH, NKP, U10, SPN, FE, PO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.1 · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Reaction center protein H chain | protein | 241 | 24% helix, 25% strand | P0C0Y7 |
| L | Reaction center protein L chain | protein | 281 | 62% helix, 4% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 301 | 64% helix, 4% strand | P0C0Y9 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 5 copies · chains L, M, H
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- NKP · (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate · ligand · 2 copies · chains M, H, L
- U10 · Ubiquinone-10 · ligand · chains L, M
- SPN · Speroidenone · ligand · chains M
- FE · Fe (III) ion · metal · chains L, M
- PO4 · Phosphate ion · ion · chains H, M
- LDA · Lauryl dimethylamine-N-oxide · additive · 4 copies · chains H, M, L
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.82 | 0.84 | 74 | BCL |
| 2 | 67 | 0.71 | 0.97 | 25 | empty |
| 3 | 171 | 0.68 | 0.87 | 28 | U10 |
| 4 | 139 | 0.60 | 0.84 | 24 | OLC |
| 5 | 107 | 0.57 | 0.84 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4599 Ų buried · 71 hydrogen bonds · protein-protein
- H–M · 2904 Ų buried · 46 hydrogen bonds · protein-protein
- H–L · 1613 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6Z1J · Photosynthetic reaction center from rhodobacter sphaeroides strain rv lsp… · the same entry in another collection · chain H against H, 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
- 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 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 0.98
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 P0C0Y7
- Every structure of UniProt P0C0Y8
- Every structure of UniProt P0C0Y9
- Elsewhere: RCSB PDB 6Z1J · PDBe 6Z1J · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.