Research workbench
Bacterial photosynthetic reaction center from rhodobacter sphaeroides with ile M265 replaced with thr
Analyse Bacterial photosynthetic reaction center from rhodobacter sphaeroides with ile… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H99
- Type
- protein
- Length
- 823 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
- P0C0Y8, P0C0Y9, P0C0Y7
- Ligands
- BCL, BPH, U10, SPO, FE
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Reaction center protein L chain | protein | 281 | 62% helix, 3% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 302 | 63% helix, 4% strand | P0C0Y9 |
| H | Reaction center protein H chain | protein | 240 | 23% helix, 25% strand | P0C0Y7 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.82 | 0.82 | 92 | BCL, BPH |
| 2 | 125 | 0.78 | 0.96 | 32 | empty |
| 3 | 252 | 0.74 | 0.88 | 47 | U10 |
| 4 | 56 | 0.69 | 0.97 | 20 | empty |
| 5 | 152 | 0.63 | 0.85 | 29 | U10 |
Interfaces
3 interfaces between chains.
- L–M · 4555 Ų buried · 64 hydrogen bonds · protein-protein
- M–H · 2860 Ų buried · 39 hydrogen bonds · protein-protein
- L–H · 1590 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4H99 · Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides with ILE M265… · 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 P0C0Y8
- Every structure of UniProt P0C0Y9
- Every structure of UniProt P0C0Y7
- Elsewhere: RCSB PDB 4H99 · PDBe 4H99 · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7
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