Research workbench
Crystal structure of NAD+-Ia(E380S)-actin complex
Analyse Crystal structure of NAD+-Ia(E380S)-actin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H0Y
- Type
- protein
- Length
- 771 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Clostridium perfringens; Oryctolagus cuniculus
- Molecule
- Iota toxin component Ia; Actin, alpha skeletal muscle
- EC
- 2.4.2.31
- UniProt
- Q46220, P68135
- Ligands
- NAD, ATP, LAR, CA, PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.94 · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iota toxin component Ia (EC 2.4.2.31) | protein | 413 | 38% helix, 28% strand | Q46220 |
| B | Actin, alpha skeletal muscle | protein | 358 | 44% helix, 19% strand | P68135 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- LAR · Latrunculin A · ligand · chains B
- CA · Calcium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 52 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.78 | 0.81 | 76 | NAD, EDO |
| 2 | 383 | 0.75 | 0.86 | 52 | CA, ATP, LAR, EDO |
| 3 | 435 | 0.64 | 0.77 | 51 | EDO |
| 4 | 271 | 0.57 | 0.78 | 36 | EDO |
| 5 | 212 | 0.54 | 0.77 | 32 | EDO |
Interfaces
1 interface between chains.
- A–B · 777 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
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 Q46220
- Every structure of UniProt P68135
- Elsewhere: RCSB PDB 4H0Y · PDBe 4H0Y · UniProt Q46220 · UniProt P68135
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