Research workbench
Photosynthetic reaction center mutant with TRP M115 replaced with phe (chain M, WM115F) phe M197 replaced with arg (chain M, FM197R)
Analyse Photosynthetic reaction center mutant with TRP M115 replaced with phe (chain M… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E6D
- Type
- protein
- Length
- 823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center H subunit; Photosynthetic reaction center L subunit…
- UniProt
- P11846, P02954, P02953
- Ligands
- BCL, BPH, U10, SPN, FE, PO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Photosynthetic reaction center H subunit | protein | 240 | 25% helix, 24% strand | P11846 |
| L | Photosynthetic reaction center L subunit | protein | 281 | 63% helix, 4% strand | P02954 |
| M | Photosynthetic reaction center M subunit | protein | 302 | 63% helix, 4% strand | P02953 |
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
- FE · Fe (III) ion · metal · chains L, M
- PO4 · Phosphate ion · ion · 2 copies · chains L, M
- LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains H, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.80 | 0.84 | 52 | BCL |
| 2 | 110 | 0.76 | 0.96 | 31 | empty |
| 3 | 144 | 0.72 | 0.90 | 20 | U10 |
| 4 | 144 | 0.61 | 0.84 | 28 | empty |
| 5 | 109 | 0.60 | 0.85 | 20 | empty |
Interfaces
3 interfaces between chains.
- L–M · 4518 Ų buried · 70 hydrogen bonds · protein-protein
- H–M · 2840 Ų buried · 42 hydrogen bonds · protein-protein
- H–L · 1589 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1E6D · Photosynthetic reaction center mutant with TRP M115 replaced with phe (chain M, WM115F)… · 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 P11846
- Every structure of UniProt P02954
- Every structure of UniProt P02953
- Elsewhere: RCSB PDB 1E6D · PDBe 1E6D · UniProt P11846 · UniProt P02954 · UniProt P02953
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