Research workbench
Crystal structure of the reaction centre from blastochloris viridis strain dsm 133 (atcc 19567) substrain-94
Analyse Crystal structure of the reaction centre from blastochloris viridis strain dsm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T6E
- Type
- protein
- Length
- 1,188 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
- HTO, HEC, DGA, BCB, BPB, UQ9, MQ9, NS5, FE2, SO4
- Pockets
- 18 · best druggability 0.88
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 | 334 | 43% helix, 4% strand | P07173 |
| H | Reaction center protein H chain | protein | 258 | 26% helix, 23% strand | P06008 |
| L | Reaction center protein L chain | protein | 273 | 66% helix, 4% strand | P06009 |
| M | Reaction center protein M chain | protein | 323 | 63% helix, 5% strand | P06010 |
Ligands and binding sites
- HTO · Heptane-1,2,3-triol · ligand · 8 copies · chains C, L, H, M
- HEC · Heme C · ligand · 4 copies · chains C, L, M
- DGA · Diacyl glycerol · ligand · 4 copies · chains C, L, M, H
- BCB · Bacteriochlorophyll B · ligand · 4 copies · chains L, M
- BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
- UQ9 · Ubiquinone-9 · ligand · 2 copies · chains L, M
- MQ9 · Menaquinone-9 · ligand · chains L, M
- NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains M
- FE2 · Fe (II) ion · metal · chains L, M
- SO4 · Sulfate ion · ion · 26 copies · chains C, L, M, H
- GOL · Glycerol · additive · 41 copies · chains C, L, H, M
- LDA · Lauryl dimethylamine-N-oxide · additive · 16 copies · chains C, L, H, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.88 | 0.88 | 127 | HEC |
| 2 | 860 | 0.84 | 0.85 | 81 | BCB |
| 3 | 290 | 0.77 | 0.89 | 49 | empty |
| 4 | 82 | 0.74 | 0.97 | 23 | GOL |
| 5 | 60 | 0.73 | 0.99 | 25 | empty |
Interfaces
6 interfaces between chains.
- L–M · 4430 Ų buried · 63 hydrogen bonds · protein-protein
- H–M · 2876 Ų buried · 42 hydrogen bonds · protein-protein
- C–M · 2741 Ų buried · 33 hydrogen bonds · protein-protein
- H–L · 1912 Ų buried · 28 hydrogen bonds · protein-protein
- C–L · 1772 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 2 modified, 1 covalent (heme c attachment, covalent ligand, formylation, oxidation).
Compared structures
- 3T6E · Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC… · 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 3T6E · PDBe 3T6E · UniProt P07173 · UniProt P06008 · UniProt P06009 · UniProt P06010
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