MolNFT v1 · #71511 · protein
Crystal structure of monomeric kusabira-orange (mko), orange-emitting GFP-like protein, at pH 7.5
3MGF · Fluorescent protein: “Crystal structure of monomeric kusabira-orange (mko), orange-emitting GFP-like protein, at pH 7.5”. X-ray diffraction, 1 ligand (CFY), 13 pockets (best druggability 0.81). MolNFT v1 #71511 on GenesisL1: 3D…
- PDB
- 3MGF
- Type
- protein
- Length
- 845 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein
- UniProt
- Q6I7B2
- Ligands
- CFY
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Fluorescent protein | protein | 212 | 5% helix, 58% strand | Q6I7B2 |
| B | Fluorescent protein | protein | 209 | 5% helix, 58% strand | Q6I7B2 |
Ligands and binding sites
- CFY · [(4Z)-2-{(2R)-2-[(1S)-1-amino-2-phenylethyl]-2-hydroxy-2,5-dihydro-1,3-thiazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.81 | 0.98 | 39 | CFY |
| 2 | 127 | 0.80 | 0.98 | 34 | CFY |
| 3 | 129 | 0.80 | 0.97 | 35 | CFY |
| 4 | 70 | 0.74 | 0.98 | 19 | CFY |
| 5 | 63 | 0.72 | 0.97 | 22 | CFY |
Interfaces
5 interfaces between chains.
- C–D · 989 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 981 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 77 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 3MGF · Crystal Structure of Monomeric Kusabira-Orange (MKO), Orange-Emitting GFP-like Protein… · 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
- Every structure of UniProt Q6I7B2
- Elsewhere: RCSB PDB 3MGF · PDBe 3MGF · UniProt Q6I7B2
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