Research workbench
Crystal structure of sfgfp-66-hqala
Analyse Crystal structure of sfgfp-66-hqala in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JFG
- Type
- protein
- Length
- 1,785 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- HQY, CS
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Green fluorescent protein | protein | 226 | 10% helix, 52% strand | P42212 |
| B | Green fluorescent protein | protein | 223 | 9% helix, 50% strand | P42212 |
| C, H | Green fluorescent protein | protein | 226 | 11% helix, 52% strand | P42212 |
| D | Green fluorescent protein | protein | 218 | 8% helix, 52% strand | P42212 |
| F | Green fluorescent protein | protein | 218 | 6% helix, 50% strand | P42212 |
| G | Green fluorescent protein | protein | 222 | 11% helix, 51% strand | P42212 |
Ligands and binding sites
- HQY · quinolin-8-ol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CS · Cesium ion · metal · 31 copies · chains A, B, C, D, E, F, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.72 | 0.98 | 23 | HQY |
| 2 | 625 | 0.69 | 0.77 | 65 | empty |
| 3 | 499 | 0.66 | 0.78 | 64 | HQY |
| 4 | 412 | 0.62 | 0.77 | 65 | CS, HQY |
| 5 | 220 | 0.61 | 0.81 | 26 | empty |
Interfaces
10 interfaces between chains.
- C–D · 762 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 757 Ų buried · 18 hydrogen bonds · protein-protein
- F–H · 751 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 745 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 656 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 8 modified (covalent ligand, nonstandard).
Compared structures
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 4JFG · PDBe 4JFG · UniProt P42212
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