Research workbench
Thin filament at low calcium concentration
Analyse Thin filament at low calcium concentration in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MVY
- Type
- protein
- Length
- 8,625 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W | Actin, alpha skeletal muscle | protein | 375 | 40% helix, 17% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 23 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.85 | 0.86 | 139 | ADP |
| 2 | 950 | 0.85 | 0.86 | 139 | ADP |
| 3 | 937 | 0.85 | 0.86 | 125 | ADP |
| 4 | 950 | 0.85 | 0.86 | 135 | ADP |
| 5 | 916 | 0.85 | 0.86 | 134 | ADP |
Interfaces
43 interfaces between chains.
- U–W · 917 Ų buried · 5 hydrogen bonds · protein-protein
- S–U · 916 Ų buried · 5 hydrogen bonds · protein-protein
- Q–S · 915 Ų buried · 5 hydrogen bonds · protein-protein
- E–G · 915 Ų buried · 5 hydrogen bonds · protein-protein
- F–H · 915 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (methylation).
Compared structures
- 5MVY · Thin Filament at low calcium concentration · the same entry in another collection · chain K against K, 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 P68135
- Elsewhere: RCSB PDB 5MVY · PDBe 5MVY · UniProt P68135
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