Research workbench
Crystal structure analysis of the mutant reaction center pro L209-> glu from the photosynthetic purple bacterium rhodobacter sphaeroides
Analyse Crystal structure analysis of the mutant reaction center pro L209-> glu from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FNQ
- Type
- protein
- Length
- 822 residues
- Chains
- 3
- 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
- Ligands
- BCL, BPH, U10, SPO, FE, PO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Reaction center protein L chain | protein | 281 | 62% helix, 3% strand | P02954 |
| M | Reaction center protein M chain | protein | 302 | 62% helix, 4% strand | P02953 |
| H | Reaction center protein H chain | protein | 239 | 23% helix, 23% 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
- LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains L, M, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.81 | 0.84 | 55 | BCL |
| 2 | 266 | 0.76 | 0.88 | 41 | U10 |
| 3 | 77 | 0.73 | 0.97 | 28 | empty |
| 4 | 115 | 0.58 | 0.84 | 18 | SPO |
| 5 | 136 | 0.57 | 0.83 | 22 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4616 Ų buried · 63 hydrogen bonds · protein-protein
- M–H · 2852 Ų buried · 44 hydrogen bonds · protein-protein
- L–H · 1641 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1FNQ · Crystal structure analysis of the mutant reaction center pro L209-> glu from the… · 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 1FNQ · PDBe 1FNQ · UniProt P02954 · UniProt P02953 · UniProt P11846
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