Research workbench
Photoproduct of the wild-type aequorea victoria green fluorescent protein
Analyse Photoproduct of the wild-type aequorea victoria green fluorescent protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HCJ
- Type
- protein
- Length
- 905 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- GYS
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Green fluorescent protein | protein | 226 | 12% helix, 52% strand | P42212 |
| C | Green fluorescent protein | protein | 227 | 11% helix, 52% strand | P42212 |
Ligands and binding sites
- GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.82 | 0.98 | 28 | GYS |
| 2 | 146 | 0.82 | 0.98 | 27 | GYS |
| 3 | 144 | 0.80 | 0.97 | 26 | GYS |
| 4 | 140 | 0.80 | 0.97 | 27 | GYS |
| 5 | 474 | 0.61 | 0.76 | 55 | empty |
Interfaces
4 interfaces between chains.
- A–D · 594 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 588 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 124 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 modified (chromophore, nonstandard).
Compared structures
- 1HCJ · Photoproduct of the wild-type Aequorea victoria Green Fluorescent Protein · the same entry in another collection · chain D against D, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain B 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 P42212
- Elsewhere: RCSB PDB 1HCJ · PDBe 1HCJ · UniProt P42212
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