MolNFT v1 · #159162 · protein
Crystal structure of green fluorescent protein (GFP); S65T, Y66(2,3- F2Y), H148D; circular permutant (50-51)
6OGC: “Crystal structure of green fluorescent protein (GFP); S65T, Y66(2,3- F2Y), H148D; circular permutant (50-51)”. X-ray diffraction, 1 ligand (MJ1), 6 pockets (best druggability 0.77). MolNFT v1 #159162 on GenesisL1: 3D structure…
- PDB
- 6OGC
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crystal structure of green fluorescent protein (GFP)
- Ligands
- MJ1
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Crystal structure of green fluorescent protein (GFP) | protein | 233 | 11% helix, 50% strand | — |
| A | Crystal structure of green fluorescent protein (GFP) | protein | 227 | 9% helix, 51% strand | — |
Ligands and binding sites
- MJ1 · {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(2,3-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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.77 | 0.97 | 26 | MJ1 |
| 2 | 94 | 0.77 | 0.98 | 24 | MJ1 |
| 3 | 206 | 0.50 | 0.76 | 34 | empty |
| 4 | 220 | 0.49 | 0.75 | 35 | empty |
| 5 | 62 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 670 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6OGC · Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(2,3-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 6OGC · PDBe 6OGC
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