MolNFT v1 · #71181 · protein
Crystal structure of actin in complex with lobophorolide
3M6G · Actin, alpha skeletal muscle: “Crystal structure of actin in complex with lobophorolide”. X-ray diffraction, 4 ligands (ATP, LO3, CA), 5 pockets (best druggability 0.73). MolNFT v1 #71181 on GenesisL1: 3D structure, binding sites…
- PDB
- 3M6G
- Type
- protein
- Length
- 710 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ATP, LO3, CA, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 353 | 47% helix, 20% strand | P68135 |
| B | Actin, alpha skeletal muscle | protein | 357 | 47% helix, 20% strand | P68135 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- LO3 · (1S,3S,4S,5S,7R,8S,9R,12E,14E,16R,17R,19R)-16-hydroxy-9-{(1S,2S,3S)-2-hydroxy-5-[(2S,4R,6S)-4-methoxy-6-methyltetrahydro-2H-pyran-2-yl]-1,3-dimethylpentyl}-3,5,7,17-tetramethoxy-8,14-dimethyl-11H-spiro[10,23-dioxabicyclo[17.3.1]tricosa-12,14,20-triene-4,2'-oxiran]-11-one · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.73 | 0.84 | 50 | MG, ATP |
| 2 | 413 | 0.71 | 0.83 | 56 | MG, ATP |
| 3 | 477 | 0.59 | 0.74 | 47 | empty |
| 4 | 103 | 0.39 | 0.75 | 24 | empty |
| 5 | 50 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 79 Ų buried · 0 hydrogen bonds · protein-protein
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 P68135
- Elsewhere: RCSB PDB 3M6G · PDBe 3M6G · UniProt P68135
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