MolNFT v1 · #12103 · protein
E(L212)A,D(L213)A double mutant structure of photosynthetic reaction center from rhodobacter sphaeroides
1K6N · Photosynthetic reaction center L subunit: “E(L212)A,D(L213)A double mutant structure of photosynthetic reaction center from rhodobacter sphaeroides”. X-ray diffraction, 6 ligands (BCL, BPH, U10), 15 pockets (best druggability 0.82).…
- PDB
- 1K6N
- Type
- protein
- Length
- 823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center L subunit; Photosynthetic reaction center M subunit…
- UniProt
- P02954, P02953, P11846
- 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 | Photosynthetic reaction center L subunit | protein | 281 | 63% helix, 4% strand | P02954 |
| M | Photosynthetic reaction center M subunit | protein | 302 | 64% helix, 4% strand | P02953 |
| H | Photosynthetic reaction center H subunit | protein | 240 | 26% 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
- 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.82 | 0.83 | 88 | BCL |
| 2 | 95 | 0.76 | 0.97 | 30 | empty |
| 3 | 225 | 0.73 | 0.88 | 39 | U10 |
| 4 | 205 | 0.68 | 0.85 | 28 | U10 |
| 5 | 50 | 0.66 | 0.96 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4575 Ų buried · 65 hydrogen bonds · protein-protein
- M–H · 2822 Ų buried · 42 hydrogen bonds · protein-protein
- L–H · 1613 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1K6N · E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center from… · 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 1K6N · PDBe 1K6N · UniProt P02954 · UniProt P02953 · UniProt P11846
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