MolNFT v1 · #62619 · protein
Crystal structure of monomeric actin bound to cytochalasin D
3EKU · Actin-5C: “Crystal structure of monomeric actin bound to cytochalasin D”. X-ray diffraction, 3 ligands (ATP, CY9, CA), 2 pockets (best druggability 0.76). MolNFT v1 #62619 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3EKU
- Type
- protein
- Length
- 362 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-5C
- UniProt
- P10987
- Ligands
- ATP, CY9, CA
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin-5C | protein | 362 | 44% helix, 20% strand | P10987 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- CY9 · (3S,3aR,4S,6S,6aR,7E,10S,12R,13E,15R,15aR)-3-benzyl-6,12-dihydroxy-4,10,12-trimethyl-5-methylidene-1,11-dioxo-2,3,3a,4,5,6,6a,9,10,11,12,15-dodecahydro-1H-cycloundeca[d]isoindol-15-yl acetate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.76 | 0.85 | 55 | ATP, CA |
| 2 | 188 | 0.52 | 0.77 | 26 | CY9 |
Compared structures
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 P10987
- Elsewhere: RCSB PDB 3EKU · PDBe 3EKU · UniProt P10987
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