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Serial femtosecond crystallography structure of a photosynthetic reaction center
Analyse Serial femtosecond crystallography structure of a photosynthetic reaction center in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CAS
- 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 L chain…
- UniProt
- P07173, P06009, P06010, P06008
- Ligands
- HEC, BCL, MPG, BPB, DGA, MQ7, NS5, OTP, FE2, PO4
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosynthetic reaction center cytochrome C subunit | protein | 332 | 43% helix, 4% strand | P07173 |
| B | Reaction center protein L chain | protein | 273 | 64% helix, 4% strand | P06009 |
| C | Reaction center protein M chain | protein | 323 | 62% helix, 5% strand | P06010 |
| D | Reaction center protein H chain | protein | 243 | 25% helix, 25% strand | P06008 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains B, C
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 3 copies · chains B, C
- BPB · Bacteriopheophytin B · ligand · 2 copies · chains B, C
- DGA · Diacyl glycerol · ligand · chains A, B, C
- MQ7 · Menaquinone-7 · ligand · chains B, C
- NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains C
- OTP · (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl trihydrogen diphosphate · ligand · chains B, C, D
- FE2 · Fe (II) ion · metal · chains B, C
- PO4 · Phosphate ion · ion · 2 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.88 | 0.90 | 112 | HEC |
| 2 | 810 | 0.83 | 0.85 | 81 | BCL |
| 3 | 356 | 0.75 | 0.85 | 48 | BPB, MQ7 |
| 4 | 80 | 0.73 | 0.97 | 24 | empty |
| 5 | 65 | 0.72 | 0.98 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4379 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 2753 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2642 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1753 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1733 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 1 covalent, 1 modified (heme c attachment, covalent ligand, formylation).
Compared structures
- 4CAS · Serial femtosecond crystallography structure of a photosynthetic reaction center · the same entry in another collection · chain D against D, 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 A 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 B 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 C 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 D 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 P06009
- Every structure of UniProt P06010
- Every structure of UniProt P06008
- Elsewhere: RCSB PDB 4CAS · PDBe 4CAS · UniProt P07173 · UniProt P06009 · UniProt P06010 · UniProt P06008
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