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Crystal structure of green fluorescent protein (GFP); S65T, H148D with globally incorporated 3-F1Y; circular permutant (50-51)
Analyse Crystal structure of green fluorescent protein (GFP); S65T, H148D with globally… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OG8
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crystal structure of green fluorescent protein (GFP)
- Ligands
- MFC
- Pockets
- 7 · 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 | 227 | 11% helix, 52% strand | — |
| A | Crystal structure of green fluorescent protein (GFP) | protein | 226 | 11% helix, 53% strand | — |
Ligands and binding sites
- MFC · 5-[1-(3-fluoro-4-hydroxy-phenyl)-meth-(Z)-ylidene]-3,5-dihydro-imidazol-4-one · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.78 | 0.97 | 25 | MFC |
| 2 | 103 | 0.77 | 0.97 | 23 | MFC |
| 3 | 436 | 0.59 | 0.75 | 58 | empty |
| 4 | 266 | 0.53 | 0.76 | 30 | empty |
| 5 | 110 | 0.40 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 635 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 4 covalent (nonstandard, covalent ligand).
Compared structures
- 6OG8 · Crystal structure of Green Fluorescent Protein (GFP); S65T, H148D with globally… · 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 6OG8 · PDBe 6OG8
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