Research workbench
Cellular response to a crystal-forming protein
Analyse Cellular response to a crystal-forming protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P76
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photoconvertible fluorescent protein
- UniProt
- Q53UG8
- Ligands
- CR8, NA
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photoconvertible fluorescent protein | protein | 223 | 2% helix, 55% strand | Q53UG8 |
| B | Photoconvertible fluorescent protein | protein | 219 | 2% helix, 56% 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
- NA · Sodium ion · metal · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.75 | 0.98 | 26 | CR8 |
| 2 | 85 | 0.75 | 0.97 | 30 | CR8 |
| 3 | 130 | 0.47 | 0.79 | 32 | empty |
| 4 | 121 | 0.45 | 0.78 | 24 | empty |
| 5 | 67 | 0.37 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 934 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4P76 · Cellular response to a crystal-forming protein · 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 4P76 · PDBe 4P76 · UniProt Q53UG8
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