Research workbench
Crystal structure of green fluorescent protein (GFP); S65T, T203(3- omey); ih circular permutant (50-51)
Analyse Crystal structure of green fluorescent protein (GFP); S65T, T203(3- omey); ih… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OFN
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein (GFP)
- Ligands
- CRO
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein (GFP) | protein | 224 | 10% helix, 52% strand | — |
| B | Green fluorescent protein (GFP) | protein | 236 | 11% helix, 50% strand | — |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.72 | 0.96 | 23 | CRO |
| 2 | 67 | 0.72 | 0.97 | 22 | CRO |
| 3 | 317 | 0.55 | 0.75 | 36 | empty |
| 4 | 201 | 0.49 | 0.76 | 24 | empty |
| 5 | 145 | 0.37 | 0.72 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 757 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 modified (chromophore, nonstandard).
Compared structures
- 6OFN · Crystal structure of green fluorescent protein (GFP); S65T, T203(3-OMeY); 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 6OFN · PDBe 6OFN
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