Research workbench
Crystal structure of green fluorescent protein (GFP); S65T, Y66(3- CH3Y); ih circular permutant (50-51)
Analyse Crystal structure of green fluorescent protein (GFP); S65T, Y66(3- CH3Y); ih… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OFM
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein (GFP)
- Ligands
- MFV
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein (GFP) | protein | 229 | 10% helix, 51% strand | — |
| B | Green fluorescent protein (GFP) | protein | 237 | 9% helix, 49% strand | — |
Ligands and binding sites
- MFV · {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-hydroxy-3-methylphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.77 | 0.97 | 24 | MFV |
| 2 | 104 | 0.77 | 0.97 | 25 | MFV |
| 3 | 402 | 0.57 | 0.75 | 62 | empty |
| 4 | 217 | 0.51 | 0.77 | 23 | empty |
| 5 | 93 | 0.41 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 659 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6OFM · Crystal structure of green fluorescent protein (GFP); S65T, Y66(3-CH3Y); ih circular… · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 6OFM · PDBe 6OFM
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