MolNFT v1 · #61728 · protein
E(L212)A mutant structure of photosynthetic reaction center from rhodobacter sphaeroides
3DU2 · Reaction center protein L chain: “E(L212)A mutant structure of photosynthetic reaction center from rhodobacter sphaeroides”. X-ray diffraction, 6 ligands (BCL, BPH, U10), 15 pockets (best druggability 0.82). MolNFT v1 #61728 on…
- PDB
- 3DU2
- 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, SPN, CDL, FE
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Reaction center protein L chain | protein | 281 | 63% helix, 4% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 302 | 63% helix, 4% strand | P0C0Y9 |
| H | Reaction center protein H chain | protein | 240 | 26% 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
- SPN · Speroidenone · ligand · chains M
- CDL · Cardiolipin · ligand · chains L, M, H
- FE · Fe (III) ion · metal · chains L, M
- LDA · Lauryl dimethylamine-N-oxide · additive · 4 copies · chains L, M, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.82 | 0.82 | 86 | BCL, BPH |
| 2 | 99 | 0.77 | 0.98 | 31 | empty |
| 3 | 207 | 0.70 | 0.87 | 31 | empty |
| 4 | 207 | 0.68 | 0.85 | 28 | U10 |
| 5 | 121 | 0.58 | 0.84 | 17 | SPN |
Interfaces
3 interfaces between chains.
- L–M · 4560 Ų buried · 67 hydrogen bonds · protein-protein
- M–H · 2827 Ų buried · 39 hydrogen bonds · protein-protein
- L–H · 1601 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3DU2 · E(L212)A mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides · 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 3DU2 · PDBe 3DU2 · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7
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