MolNFT v1 · #85428 · protein
Lipidic sponge phase crystal structure of the bl. viridis reaction centre solved using serial femtosecond crystallography
4AC5 · Photosynthetic reaction center cytochrome C subunit: “Lipidic sponge phase crystal structure of the bl. viridis reaction centre solved using serial femtosecond…”. X-ray diffraction, 6 ligands (HEM, BCB, BPB), 18 pockets (best…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.