MolNFT v1 · #12549 · protein
Scallop myosin (S1-ADP-befx) in the actin-detached conformation
1KK8 · Myosin heavy chain, striated muscle: “Scallop myosin (S1-ADP-befx) in the actin-detached conformation”. X-ray diffraction, 4 ligands (BEF, ADP, MG), 11 pockets (best druggability 0.81). MolNFT v1 #12549 on GenesisL1: 3D structure…
- PDB
- 1KK8
- Type
- protein
- Length
- 1,086 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin heavy chain, striated muscle; Myosin regulatory light chain, striated adductor…
- UniProt
- P24733, P13543, P07291
- Ligands
- BEF, ADP, MG, CA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin heavy chain, striated muscle | protein | 793 | 49% helix, 15% strand | P24733 |
| B | Myosin regulatory light chain, striated adductor muscle | protein | 139 | 55% helix, 4% strand | P13543 |
| C | Myosin essential light CHAIN,STRIATED adductor muscle | protein | 154 | 55% helix, 6% strand | P07291 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.81 | 0.85 | 99 | MG, BEF, ADP, GOL |
| 2 | 305 | 0.75 | 0.87 | 34 | empty |
| 3 | 453 | 0.61 | 0.76 | 47 | empty |
| 4 | 250 | 0.54 | 0.76 | 32 | empty |
| 5 | 241 | 0.49 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2429 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1842 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 232 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1KK8 · SCALLOP MYOSIN (S1-ADP-BeFx) IN THE ACTIN-DETACHED CONFORMATION · the same entry in another collection · chain A against A, TM-score 1.00
- P07291 · AlphaFold monomer V2.0 prediction for myosin essential light chain, striated adductor… · a predicted model of the same protein · chain C against A, TM-score 0.98
- P13543 · AlphaFold monomer V2.0 prediction for myosin regulatory light chain, striated adductor… · a predicted model of the same protein · chain B against A, TM-score 0.89
- P24733 · AlphaFold monomer V2.0 prediction for myosin heavy chain, striated muscle (P24733) · a predicted model of the same protein · chain A against A, TM-score 0.81
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 P24733
- Every structure of UniProt P13543
- Every structure of UniProt P07291
- Elsewhere: RCSB PDB 1KK8 · PDBe 1KK8 · UniProt P24733 · UniProt P13543 · UniProt P07291
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