Research workbench
Crystal structure of green fluorescent protein (GFP); S65T, Y66(3,5- F2Y), H148D; circular permutant (50-51)
Analyse Crystal structure of green fluorescent protein (GFP); S65T, Y66(3,5- F2Y)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OG9
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crystal structure of green fluorescent protein (GFP)
- Ligands
- MHY
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Crystal structure of green fluorescent protein (GFP) | protein | 226 | 11% helix, 52% strand | — |
| A | Crystal structure of green fluorescent protein (GFP) | protein | 224 | 11% helix, 52% strand | — |
Ligands and binding sites
- MHY · {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.78 | 0.97 | 25 | MHY |
| 2 | 111 | 0.78 | 0.97 | 26 | MHY |
| 3 | 450 | 0.61 | 0.76 | 59 | empty |
| 4 | 272 | 0.53 | 0.76 | 32 | empty |
| 5 | 121 | 0.42 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 672 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6OG9 · Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3,5-F2Y), H148D; circular… · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 6OG9 · PDBe 6OG9
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