MolNFT v1 · #171360 · protein
Photosynthetic reaction center from rhodobacter sphaeroides strain rv lcp crystallization
6Z27 · Reaction center protein H chain: “Photosynthetic reaction center from rhodobacter sphaeroides strain rv lcp crystallization”. X-ray diffraction, 5 ligands (BCL, BPH, U10), 11 pockets (best druggability 0.82). MolNFT v1 #171360 on…
- PDB
- 6Z27
- Type
- protein
- Length
- 812 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
- UniProt
- P0C0Y7, P0C0Y8, P0C0Y9
- Ligands
- BCL, BPH, U10, FE, PO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Reaction center protein H chain | protein | 240 | 23% helix, 23% strand | P0C0Y7 |
| L | Reaction center protein L chain | protein | 270 | 66% helix, 3% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 302 | 64% helix, 3% strand | P0C0Y9 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- U10 · Ubiquinone-10 · ligand · chains L, M
- FE · Fe (III) ion · metal · chains L, M
- PO4 · Phosphate ion · ion · 8 copies · chains H, L, M
- LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains H, L, M
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 copies · chains L, M
- EDO · 1,2-ethanediol · additive · chains H, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.82 | 0.84 | 70 | BCL |
| 2 | 69 | 0.72 | 0.97 | 30 | empty |
| 3 | 166 | 0.70 | 0.88 | 28 | U10 |
| 4 | 123 | 0.60 | 0.85 | 23 | OLC |
| 5 | 95 | 0.57 | 0.85 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4328 Ų buried · 65 hydrogen bonds · protein-protein
- H–M · 2913 Ų buried · 43 hydrogen bonds · protein-protein
- H–L · 1569 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6Z27 · Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LCP crystallization · the same entry in another collection · chain H against H, TM-score 1.00
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 P0C0Y7
- Every structure of UniProt P0C0Y8
- Every structure of UniProt P0C0Y9
- Elsewhere: RCSB PDB 6Z27 · PDBe 6Z27 · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9
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