Research workbench
De novo photosynthetic reaction center protein variant equipped with his-tyr H-bond, heme B, and CD(II) ions
Analyse De novo photosynthetic reaction center protein variant equipped with his-tyr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VJU
- Type
- protein
- Length
- 196 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reaction center maquette LEU71HIS variant
- Ligands
- HEM, CD
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 90% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reaction center maquette LEU71HIS variant | protein | 196 | 90% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- CD · Cadmium ion · metal · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.68 | 0.83 | 28 | HEM |
| 2 | 106 | 0.56 | 0.85 | 24 | empty |
Compared structures
- 5VJU · De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-bond, Heme… · 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
- Elsewhere: RCSB PDB 5VJU · PDBe 5VJU
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