MolNFT v1 · #123485 · protein
Cryo-EM structure of a human cytoplasmic actomyosin complex at near- atomic resolution
5JLH · Actin, cytoplasmic 2: “Cryo-EM structure of a human cytoplasmic actomyosin complex at near- atomic resolution”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.77). MolNFT v1 #123485 on GenesisL1: 3D…
- PDB
- 5JLH
- Type
- protein
- Length
- 3,884 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, cytoplasmic 2; Myosin-14,ALPHA-actinin a; Tropomyosin alpha-3 chain
- UniProt
- P63261, Q7Z406, P05095
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, cytoplasmic 2 | protein | 374 | 41% helix, 19% strand | P63261 |
| F, G | Myosin-14,ALPHA-actinin a | protein | 737 | 46% helix, 15% strand | Q7Z406, P05095 |
| H, I, J, K | Tropomyosin alpha-3 chain | protein | 135 | 99% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
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 | 859 | 0.77 | 0.80 | 95 | empty |
| 2 | 947 | 0.77 | 0.79 | 61 | empty |
| 3 | 970 | 0.76 | 0.79 | 61 | empty |
| 4 | 987 | 0.76 | 0.78 | 65 | empty |
| 5 | 217 | 0.75 | 0.90 | 47 | ADP, MG |
Interfaces
22 interfaces between chains.
- D–G · 1441 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 1438 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 1369 Ų buried · 0 hydrogen bonds · protein-protein
- J–K · 1367 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 1186 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5JLH · Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution · the same entry in another collection · chain K against K, TM-score 1.00
- P63261 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 2 (P63261) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 P63261
- Every structure of UniProt Q7Z406
- Every structure of UniProt P05095
- Elsewhere: RCSB PDB 5JLH · PDBe 5JLH · UniProt P63261 · UniProt Q7Z406 · UniProt P05095
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