MolNFT v1 · #5052 · protein
Photosynthetic reaction center mutant with TRP M115 replaced with phe (chain M, WM115F) phe M197 replaced with arg (chain M, FM197R)
1E6D · Photosynthetic reaction center H subunit: “Photosynthetic reaction center mutant with TRP M115 replaced with phe (chain M, WM115F) phe M197 replaced…”. X-ray diffraction, 6 ligands (BCL, BPH, U10), 13 pockets (best druggability…
- 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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