Research workbench
The crystal structure of rigor like squid myosin S1 in the absence of nucleotide
Analyse The crystal structure of rigor like squid myosin S1 in the absence of nucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I5H
- Type
- protein
- Length
- 1,109 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin heavy chain isoform a; Myosin regulatory light chain lc-2, mantle muscle; Myosin…
- UniProt
- O44934, P08052, P05945
- Ligands
- CA
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin heavy chain isoform a | protein | 808 | 48% helix, 13% strand | O44934 |
| B | Myosin regulatory light chain lc-2, mantle muscle | protein | 145 | 48% helix, 3% strand | P08052 |
| C | Myosin catalytic light chain lc-1, mantle muscle | protein | 156 | 53% helix, 6% strand | P05945 |
Ligands and binding sites
- CA · Calcium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.78 | 0.84 | 77 | empty |
| 2 | 1058 | 0.78 | 0.79 | 102 | empty |
| 3 | 409 | 0.73 | 0.84 | 59 | empty |
| 4 | 264 | 0.63 | 0.81 | 32 | empty |
| 5 | 64 | 0.51 | 0.86 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2233 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1966 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3I5H · The crystal structure of rigor like squid myosin S1 in the absence of nucleotide · the same entry in another collection · chain A against A, TM-score 1.00
- P08052 · AlphaFold monomer V2.0 prediction for myosin regulatory light chain lc-2, mantle muscle… · a predicted model of the same protein · chain B against A, TM-score 0.62
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 O44934
- Every structure of UniProt P08052
- Every structure of UniProt P05945
- Elsewhere: RCSB PDB 3I5H · PDBe 3I5H · UniProt O44934 · UniProt P08052 · UniProt P05945
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