MolNFT v1 · #159139 · protein
Crystal structure of green fluorescent protein (GFP); S65T, Y66(3- cly); ih circular permutant (50-51)
6OFL: “Crystal structure of green fluorescent protein (GFP); S65T, Y66(3- cly); ih circular permutant (50-51)”. X-ray diffraction, 1 ligand (4NT), 8 pockets (best druggability 0.77). MolNFT v1 #159139 on GenesisL1: 3D structure, binding…
- PDB
- 6OFL
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein (GFP)
- Ligands
- 4NT
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein (GFP) | protein | 229 | 11% helix, 51% strand | — |
| B | Green fluorescent protein (GFP) | protein | 227 | 11% helix, 51% strand | — |
Ligands and binding sites
- 4NT · [(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(3-chloro-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
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 | 100 | 0.77 | 0.97 | 24 | 4NT |
| 2 | 100 | 0.77 | 0.97 | 27 | 4NT |
| 3 | 284 | 0.54 | 0.76 | 38 | empty |
| 4 | 292 | 0.53 | 0.75 | 48 | empty |
| 5 | 58 | 0.37 | 0.79 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 672 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6OFL · Crystal structure of green fluorescent protein (GFP); S65T, Y66(3-ClY); 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 6OFL · PDBe 6OFL
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