MolNFT v1 · #56674 · protein
Crystal structure of monomeric kusabira-orange (mko), orange-emitting GFP-like protein, at pH 6.0
2ZMW · Fluorescent protein: “Crystal structure of monomeric kusabira-orange (mko), orange-emitting GFP-like protein, at pH 6.0”. X-ray diffraction, 1 ligand (CFY), 9 pockets (best druggability 0.82). MolNFT v1 #56674 on GenesisL1: 3D…
- PDB
- 2ZMW
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein
- UniProt
- Q6I7B2
- Ligands
- CFY
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fluorescent protein | protein | 213 | 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.82 | 0.97 | 32 | CFY |
| 2 | 144 | 0.82 | 0.98 | 36 | CFY |
| 3 | 146 | 0.82 | 0.98 | 32 | CFY |
| 4 | 143 | 0.81 | 0.97 | 32 | CFY |
| 5 | 80 | 0.41 | 0.79 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 966 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 957 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 2ZMW · 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 2ZMW · PDBe 2ZMW · UniProt Q6I7B2
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