MolNFT v1 · #18059 · protein
Structure of the photosynthetic reaction centre from rhodobacter sphaeroides at 2.65 ångströms resolution: cofactors and protein- cofactor interactions
1PCR · Photosynthetic reaction center: “Structure of the photosynthetic reaction centre from rhodobacter sphaeroides at 2.65 ångströms resolution…”. X-ray diffraction, 6 ligands (BCL, BPH, U10), 11 pockets (best druggability 0.82). MolNFT…
- PDB
- 1PCR
- Type
- protein
- Length
- 823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center
- UniProt
- P02954, P02953, P11846
- Ligands
- BCL, BPH, U10, SPO, FE, PO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Photosynthetic reaction center | protein | 281 | 62% helix, 4% strand | P02954 |
| M | Photosynthetic reaction center | protein | 302 | 62% helix, 4% strand | P02953 |
| H | Photosynthetic reaction center | protein | 240 | 23% helix, 25% strand | P11846 |
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 · 2 copies · chains L, M
- SPO · Spheroidene · ligand · chains M
- FE · Fe (III) ion · metal · chains L, M
- PO4 · Phosphate ion · ion · chains L, M, H
- LDA · Lauryl dimethylamine-N-oxide · additive · 9 copies · chains L, M, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.82 | 0.82 | 91 | BCL |
| 2 | 68 | 0.72 | 0.97 | 25 | empty |
| 3 | 203 | 0.69 | 0.86 | 30 | U10 |
| 4 | 51 | 0.69 | 0.97 | 23 | empty |
| 5 | 118 | 0.60 | 0.85 | 29 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4510 Ų buried · 71 hydrogen bonds · protein-protein
- M–H · 2814 Ų buried · 32 hydrogen bonds · protein-protein
- L–H · 1589 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1PCR · Structure of the photosynthetic reaction centre from rhodobacter sphaeroides at 2.65… · the same entry in another collection · chain L against L, 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 P02954
- Every structure of UniProt P02953
- Every structure of UniProt P11846
- Elsewhere: RCSB PDB 1PCR · PDBe 1PCR · UniProt P02954 · UniProt P02953 · UniProt P11846
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