Research workbench
Crystal structure of the yfpnano fusion protein
Analyse Crystal structure of the yfpnano fusion protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HR1
- Type
- protein
- Length
- 807 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin light chain kinase 2, SKELETAL/CARDIAC muscle, unconventional myosin-X,GREEN…
- EC
- 2.7.11.18
- UniProt
- P07313, P79114, P42212, P0DP23
- Ligands
- CR2, CA, NA
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin light chain kinase 2, SKELETAL/CARDIAC muscle, unconventional myosin-X,GREEN fluorescent PROTEIN,CALMODULIN-1 (EC 2.7.11.18) | protein | 406 | 35% helix, 31% strand | P07313, P79114, P42212, P0DP23 |
| B | Myosin light chain kinase 2, SKELETAL/CARDIAC muscle, unconventional myosin-X,GREEN fluorescent PROTEIN,CALMODULIN-1 (EC 2.7.11.18) | protein | 401 | 36% helix, 31% strand | P07313, P79114, P42212, P0DP23 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.68 | 0.97 | 22 | CR2 |
| 2 | 272 | 0.53 | 0.76 | 39 | GOL |
| 3 | 174 | 0.47 | 0.76 | 27 | empty |
| 4 | 176 | 0.47 | 0.76 | 24 | empty |
| 5 | 180 | 0.45 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 838 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 6HR1 · Crystal structure of the YFPnano fusion protein · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain B against A, TM-score 0.57
- P79114 · AlphaFold monomer V2.0 prediction for unconventional myosin-X (P79114) · a predicted model of the same protein · chain B against A, TM-score 0.29
- P07313 · AlphaFold monomer V2.0 prediction for myosin light chain kinase 2, SKELETAL/CARDIAC… · a predicted model of the same protein · chain A against A, TM-score 0.23
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain A against A, TM-score 0.20
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 P07313
- Every structure of UniProt P79114
- Every structure of UniProt P42212
- Every structure of UniProt P0DP23
- Elsewhere: RCSB PDB 6HR1 · PDBe 6HR1 · UniProt P07313 · UniProt P79114 · UniProt P42212 · UniProt P0DP23
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