Research workbench
Photoproduct of the wild-type aequorea victoria green fluorescent protein after structural annealing at 170K
Analyse Photoproduct of the wild-type aequorea victoria green fluorescent protein after… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W7U
- Type
- protein
- Length
- 907 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- GYS
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Green fluorescent protein | protein | 227 | 11% helix, 52% strand | P42212 |
| B | Green fluorescent protein | protein | 226 | 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
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.86 | 0.87 | 143 | empty |
| 2 | 143 | 0.82 | 0.98 | 26 | GYS |
| 3 | 132 | 0.81 | 0.98 | 28 | GYS |
| 4 | 128 | 0.80 | 0.97 | 23 | GYS |
| 5 | 131 | 0.80 | 0.97 | 28 | GYS |
Interfaces
6 interfaces between chains.
- B–D · 695 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 676 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 628 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 621 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 198 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 modified (chromophore, nonstandard).
Compared structures
- 1W7U · Photoproduct of the Wild-Type Aequorea victoria Green Fluorescent Protein after… · 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 C 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 1W7U · PDBe 1W7U · UniProt P42212
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