Research workbench
Lipidic sponge phase crystal structure of the bl. viridis reaction centre solved using serial femtosecond crystallography
Analyse Lipidic sponge phase crystal structure of the bl. viridis reaction centre… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AC5
- 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
- HEM, BCB, BPB, MQ7, NS5, FE2
- Pockets
- 18 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Photosynthetic reaction center cytochrome C subunit | protein | 332 | 38% helix, 5% strand | P07173 |
| H | Reaction center protein H chain | protein | 243 | 22% helix, 23% strand | P06008 |
| L | Reaction center protein L chain | protein | 273 | 55% helix, 4% strand | P06009 |
| M | Reaction center protein M chain | protein | 323 | 56% helix, 6% strand | P06010 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · 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
- NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains 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
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.90 | 0.93 | 109 | HEM |
| 2 | 253 | 0.76 | 0.89 | 42 | BCB |
| 3 | 107 | 0.75 | 0.95 | 32 | empty |
| 4 | 264 | 0.73 | 0.86 | 40 | MQ7 |
| 5 | 51 | 0.72 | 0.99 | 19 | empty |
Interfaces
6 interfaces between chains.
- L–M · 4480 Ų buried · 51 hydrogen bonds · protein-protein
- H–M · 2953 Ų buried · 52 hydrogen bonds · protein-protein
- C–M · 2819 Ų buried · 39 hydrogen bonds · protein-protein
- H–L · 1870 Ų buried · 19 hydrogen bonds · protein-protein
- C–L · 1759 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (formylation).
Compared structures
- 4AC5 · Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using… · 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 0.95
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 4AC5 · PDBe 4AC5 · UniProt P07173 · UniProt P06008 · UniProt P06009 · UniProt P06010
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