Research workbench
Unique behavior of a histidine responsible for an engineered green-to- red photoconversion process
Analyse Unique behavior of a histidine responsible for an engineered green-to- red… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DDD
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photoconvertible fluorescent protein
- UniProt
- Q53UG8
- Ligands
- CR8, MG, NA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photoconvertible fluorescent protein | protein | 223 | 5% helix, 55% strand | Q53UG8 |
| B | Photoconvertible fluorescent protein | protein | 224 | 5% helix, 55% strand | Q53UG8 |
Ligands and binding sites
- CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.74 | 0.96 | 25 | CR8 |
| 2 | 82 | 0.73 | 0.96 | 25 | CR8 |
| 3 | 245 | 0.58 | 0.79 | 49 | empty |
| 4 | 83 | 0.38 | 0.77 | 20 | empty |
| 5 | 54 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 910 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2DDD · Unique behavior of a histidine responsible for an engineered green-to-red photoconversion… · 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 Q53UG8
- Elsewhere: RCSB PDB 2DDD · PDBe 2DDD · UniProt Q53UG8
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