Research workbench
Photosynthetic reaction center mutant with ala M248 replaced with TRP (chain M, AM248W)
Analyse Photosynthetic reaction center mutant with ala M248 replaced with TRP (chain M… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JJ0
- Type
- protein
- Length
- 817 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
- UniProt
- P0C0Y7, P0C0Y8, P0C0Y9
- Ligands
- BCL, BPH, U10, CDL, SPN, FE, CL
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Reaction center protein H chain | protein | 235 | 23% helix, 26% strand | P0C0Y7 |
| L | Reaction center protein L chain | protein | 281 | 63% helix, 4% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 301 | 63% helix, 4% strand | P0C0Y9 |
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 · chains L
- CDL · Cardiolipin · ligand · chains H, L, M
- SPN · Speroidenone · ligand · chains M
- FE · Fe (III) ion · metal · chains L, M
- CL · Chloride ion · ion · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.83 | 0.85 | 84 | BCL |
| 2 | 99 | 0.75 | 0.96 | 32 | empty |
| 3 | 148 | 0.62 | 0.85 | 28 | U10 |
| 4 | 180 | 0.60 | 0.82 | 38 | empty |
| 5 | 73 | 0.57 | 0.87 | 16 | CL |
Interfaces
3 interfaces between chains.
- L–M · 4539 Ų buried · 76 hydrogen bonds · protein-protein
- H–M · 2806 Ų buried · 39 hydrogen bonds · protein-protein
- H–L · 1623 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2JJ0 · Photosynthetic reaction center mutant with ala M248 replaced with TRP (chain M, AM248W) · 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 P0C0Y7
- Every structure of UniProt P0C0Y8
- Every structure of UniProt P0C0Y9
- Elsewhere: RCSB PDB 2JJ0 · PDBe 2JJ0 · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9
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