MolNFT v1 · #53801 · protein
80 microsecond laue diffraction snapshot from crystals of a photosynthetic reaction centre without illumination.
2X5U · Photosynthetic reaction center cytochrome C subunit: “80 microsecond laue diffraction snapshot from crystals of a photosynthetic reaction centre without…”. X-ray diffraction, 5 ligands (HEC, BCB, BPB), 17 pockets (best druggability…
- PDB
- 2X5U
- Type
- protein
- Length
- 1,171 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center cytochrome C subunit; Reaction center protein H chain…
- UniProt
- P07173, P06008, P06009, P06010
- Ligands
- HEC, BCB, BPB, MQ7, FE2
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Photosynthetic reaction center cytochrome C subunit | protein | 332 | 43% helix, 4% strand | P07173 |
| H | Reaction center protein H chain | protein | 243 | 26% helix, 26% strand | P06008 |
| L | Reaction center protein L chain | protein | 273 | 64% helix, 5% strand | P06009 |
| M | Reaction center protein M chain | protein | 323 | 60% helix, 6% strand | P06010 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains C, L, M
- BCB · Bacteriochlorophyll B · ligand · 4 copies · chains L, M
- BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
- MQ7 · Menaquinone-7 · ligand · chains L, M
- FE2 · Fe (II) ion · metal · chains L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.85 | 0.89 | 78 | HEC |
| 2 | 1193 | 0.83 | 0.83 | 87 | BCB |
| 3 | 233 | 0.80 | 0.93 | 32 | HEC |
| 4 | 77 | 0.72 | 0.97 | 26 | empty |
| 5 | 179 | 0.71 | 0.88 | 24 | MQ7 |
Interfaces
6 interfaces between chains.
- L–M · 4464 Ų buried · 61 hydrogen bonds · protein-protein
- H–M · 2922 Ų buried · 50 hydrogen bonds · protein-protein
- C–M · 2762 Ų buried · 37 hydrogen bonds · protein-protein
- H–L · 1843 Ų buried · 21 hydrogen bonds · protein-protein
- C–L · 1792 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 1 modified (heme c attachment, formylation).
Compared structures
- 2X5U · 80 microsecond Laue diffraction snapshot from crystals of a photosynthetic reaction… · the same entry in another collection · chain M against M, TM-score 1.00
- P07173 · AlphaFold monomer V2.0 prediction for photosynthetic reaction center cytochrome C subunit… · a predicted model of the same protein · chain C against A, TM-score 1.00
- P06009 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P06009) · a predicted model of the same protein · chain L against A, TM-score 0.99
- P06010 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P06010) · a predicted model of the same protein · chain M against A, TM-score 0.98
- P06008 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P06008) · a predicted model of the same protein · chain H against A, TM-score 0.95
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 P07173
- Every structure of UniProt P06008
- Every structure of UniProt P06009
- Every structure of UniProt P06010
- Elsewhere: RCSB PDB 2X5U · PDBe 2X5U · UniProt P07173 · UniProt P06008 · UniProt P06009 · UniProt P06010
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