Research workbench
Homodimeric reaction center of H. modesticaldum
Analyse Homodimeric reaction center of H. modesticaldum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V8K
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P800 reaction center core protein; Proteinsubunit pshx
- UniProt
- Q1MX24, B0TAT4
- Ligands
- GBF, GB0, DGG, AOH, SF4, C4D, CA
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P800 reaction center core protein | protein | 600 | 68% helix, 1% strand | Q1MX24 |
| B | Proteinsubunit pshx | protein | 25 | 76% helix, 0% strand | B0TAT4 |
Ligands and binding sites
- GBF · Bacteriochlorophyll g · ligand · 27 copies · chains A, B
- GB0 · Bacteriochlorophyll g · ligand · 2 copies · chains A
- DGG · 1-[glycerolylphosphonyl]-2-[8-(2-hexyl-cyclopropyl)-octanal-1-yl]-3-[hexadecanal-1-yl]-glycerol · ligand · 2 copies · chains A, B
- AOH · 8(1)-OH-Chlorophyll aF · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
- C4D · 4,4'-Diaponeurosporene · ligand · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.68 | 0.79 | 45 | GBF |
| 2 | 431 | 0.63 | 0.76 | 35 | GBF, DGG |
| 3 | 577 | 0.63 | 0.74 | 55 | GBF, CA |
| 4 | 452 | 0.60 | 0.74 | 36 | GBF |
| 5 | 243 | 0.58 | 0.78 | 33 | GB0 |
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5V8K · Homodimeric reaction center of H. modesticaldum · the same entry in another collection · chain A against A, 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 Q1MX24
- Every structure of UniProt B0TAT4
- Elsewhere: RCSB PDB 5V8K · PDBe 5V8K · UniProt Q1MX24 · UniProt B0TAT4
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