Research workbench
Ultrafast structural response to charge redistribution within a photosynthetic reaction centre - 300 ps (a) structure
Analyse Ultrafast structural response to charge redistribution within a photosynthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZI5
- Type
- protein
- Length
- 1,186 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, HTO, BPB, DGA, MQ7, NS5, FE, SO4
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 8% 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 | 258 | 25% helix, 23% strand | P06008 |
| L | Reaction center protein L chain | protein | 273 | 67% helix, 4% strand | P06009 |
| M | Reaction center protein M chain | protein | 323 | 62% helix, 5% 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
- HTO · Heptane-1,2,3-triol · ligand · 2 copies · chains C, H, M, L
- BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
- DGA · Diacyl glycerol · ligand · chains C, L, M
- MQ7 · Menaquinone-7 · ligand · chains L, M
- NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains M
- FE · Fe (III) ion · metal · chains L, M
- SO4 · Sulfate ion · ion · 12 copies · chains C, M, H, L
- LDA · Lauryl dimethylamine-N-oxide · additive · 4 copies · chains H, M, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.85 | 0.89 | 87 | HEC |
| 2 | 1026 | 0.83 | 0.84 | 85 | BCB |
| 3 | 222 | 0.79 | 0.92 | 32 | HEC |
| 4 | 377 | 0.77 | 0.87 | 59 | BPB, MQ7 |
| 5 | 85 | 0.75 | 0.98 | 31 | empty |
Interfaces
6 interfaces between chains.
- L–M · 4388 Ų buried · 58 hydrogen bonds · protein-protein
- H–M · 2903 Ų buried · 44 hydrogen bonds · protein-protein
- C–M · 2733 Ų buried · 35 hydrogen bonds · protein-protein
- H–L · 1882 Ų buried · 24 hydrogen bonds · protein-protein
- C–L · 1786 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 1 covalent, 1 modified (heme c attachment, covalent ligand, formylation).
Compared structures
- 6ZI5 · Ultrafast Structural Response to Charge Redistribution Within 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 0.97
- 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 0.94
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 6ZI5 · PDBe 6ZI5 · UniProt P07173 · UniProt P06008 · UniProt P06009 · UniProt P06010
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