MolNFT v1 · #126057 · protein
Photosynthetic reaction center mutant with GLUL212 replaced with TRP (chain L, EL212W)
5LRI · Reaction center protein L chain: “Photosynthetic reaction center mutant with GLUL212 replaced with TRP (chain L, EL212W)”. X-ray diffraction, 6 ligands (BCL, BPH, U10), 16 pockets (best druggability 0.81). MolNFT v1 #126057 on…
- PDB
- 5LRI
- 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
- Q3J1A5, Q3J1A6, Q3J170
- Ligands
- BCL, BPH, U10, SPN, CDL, FE
- Pockets
- 16 · best druggability 0.81
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 | 64% helix, 4% strand | Q3J1A5 |
| M | Reaction center protein M chain | protein | 300 | 64% helix, 4% strand | Q3J1A6 |
| H | Reaction center protein H chain | protein | 239 | 25% helix, 24% strand | Q3J170 |
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
- SPN · Speroidenone · ligand · chains M
- CDL · Cardiolipin · ligand · chains L, M, H
- FE · Fe (III) ion · metal · chains L, M
- LDA · Lauryl dimethylamine-N-oxide · additive · 5 copies · chains L, M, H
- DD9 · nonane · additive · 3 copies · chains L, 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 | 739 | 0.81 | 0.84 | 55 | BCL |
| 2 | 105 | 0.76 | 0.96 | 30 | empty |
| 3 | 55 | 0.69 | 0.97 | 17 | empty |
| 4 | 178 | 0.68 | 0.87 | 31 | U10 |
| 5 | 128 | 0.60 | 0.84 | 21 | U10 |
Interfaces
3 interfaces between chains.
- L–M · 4590 Ų buried · 71 hydrogen bonds · protein-protein
- M–H · 2750 Ų buried · 35 hydrogen bonds · protein-protein
- L–H · 1617 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5LRI · Photosynthetic reaction center mutant with GLUL212 replaced with TRP (chain L, EL212W) · the same entry in another collection · chain L against L, TM-score 1.00
- Q3J1A5 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (Q3J1A5) · a predicted model of the same protein · chain L against A, TM-score 1.00
- Q3J1A6 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (Q3J1A6) · a predicted model of the same protein · chain M against A, TM-score 1.00
- Q3J170 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (Q3J170) · 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 Q3J1A5
- Every structure of UniProt Q3J1A6
- Every structure of UniProt Q3J170
- Elsewhere: RCSB PDB 5LRI · PDBe 5LRI · UniProt Q3J1A5 · UniProt Q3J1A6 · UniProt Q3J170
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