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X-ray structure of the cytochrome-C(2)-photosynthetic reaction center electron transfer complex from rhodobacter sphaeroides in type I co- crystals
Analyse X-ray structure of the cytochrome-C(2)-photosynthetic reaction center electron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L9J
- Type
- protein
- Length
- 1,836 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reaction center protein L chain; Reaction center protein M chain; Reaction center protein…
- UniProt
- P02954, P02953, P11846, P00095
- Ligands
- BCL, BPH, U10, HEM, FE2, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, R | Reaction center protein L chain | protein | 281 | 65% helix, 4% strand | P02954 |
| M, S | Reaction center protein M chain | protein | 267 | 73% helix, 2% strand | P02953 |
| H, T | Reaction center protein H chain | protein | 246 | 23% helix, 21% strand | P11846 |
| C, D | Cytochrome C-2 | protein | 124 | 41% helix, 7% strand | P00095 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 8 copies · chains L, M, R, S
- BPH · Bacteriopheophytin A · ligand · 4 copies · chains L, M, R, S
- U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M, R, S
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains L, M, C, R, S, D
- FE2 · Fe (II) ion · metal · 2 copies · chains L, M, R, S
- CL · Chloride ion · ion · 2 copies · chains M, R, S
- LDA · Lauryl dimethylamine-N-oxide · additive · 4 copies · chains L, M, H, R, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.82 | 0.82 | 94 | BCL, BPH |
| 2 | 705 | 0.80 | 0.84 | 57 | BCL |
| 3 | 673 | 0.77 | 0.82 | 76 | HEM |
| 4 | 212 | 0.76 | 0.90 | 37 | U10 |
| 5 | 1004 | 0.76 | 0.78 | 80 | empty |
Interfaces
10 interfaces between chains.
- R–S · 3889 Ų buried · 44 hydrogen bonds · protein-protein
- L–M · 3884 Ų buried · 43 hydrogen bonds · protein-protein
- M–H · 1876 Ų buried · 29 hydrogen bonds · protein-protein
- S–T · 1873 Ų buried · 23 hydrogen bonds · protein-protein
- R–T · 1527 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme attachment).
Compared structures
- 1L9J · X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer… · 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 P02954
- Every structure of UniProt P02953
- Every structure of UniProt P11846
- Every structure of UniProt P00095
- Elsewhere: RCSB PDB 1L9J · PDBe 1L9J · UniProt P02954 · UniProt P02953 · UniProt P11846 · UniProt P00095
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