Research workbench
Photosynthetic reaction center mutant with glu L212 replaced with ala (chain L, EL212W), asp L213 replaced with ala (chain L, DL213A) and leu M215 replaced with ala (chain M, LM215A)
Analyse Photosynthetic reaction center mutant with glu L212 replaced with ala (chain L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LSE
- 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
- D12, BCL, BPH, U10, SPN, CDL, FE, PO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Reaction center protein L chain | protein | 281 | 63% helix, 4% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 300 | 64% helix, 4% strand | P0C0Y9 |
| H | Reaction center protein H chain | protein | 240 | 23% helix, 25% strand | P0C0Y7 |
Ligands and binding sites
- D12 · Dodecane · ligand · 5 copies · chains L, H
- 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
- SPN · Speroidenone · ligand · chains M
- CDL · Cardiolipin · ligand · chains L, M, H
- FE · Fe (III) 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
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.83 | 0.84 | 69 | BCL |
| 2 | 89 | 0.73 | 0.96 | 29 | empty |
| 3 | 213 | 0.73 | 0.88 | 39 | U10 |
| 4 | 200 | 0.72 | 0.88 | 33 | U10 |
| 5 | 54 | 0.69 | 0.97 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4531 Ų buried · 70 hydrogen bonds · protein-protein
- M–H · 2801 Ų buried · 41 hydrogen bonds · protein-protein
- L–H · 1627 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5LSE · PHOTOSYNTHETIC REACTION CENTER MUTANT WITH Glu L212 replaced with Ala (CHAIN L, EL212W)… · 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 P0C0Y8
- Every structure of UniProt P0C0Y9
- Every structure of UniProt P0C0Y7
- Elsewhere: RCSB PDB 5LSE · PDBe 5LSE · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7
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