Research workbench
Crystal structure of N-wasp vc domain in complex with skeletal actin
Analyse Crystal structure of N-wasp vc domain in complex with skeletal actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VCP
- Type
- protein
- Length
- 780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Neural wiskott-aldrich syndrome protein
- UniProt
- P68135, O00401
- Ligands
- ATP, CA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin, alpha skeletal muscle | protein | 371 | 42% helix, 20% strand | P68135 |
| D, E | Neural wiskott-aldrich syndrome protein | protein | 19 | 47% helix, 5% strand | O00401 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.72 | 0.84 | 49 | ATP, CA |
| 2 | 361 | 0.70 | 0.83 | 43 | ATP, CA |
| 3 | 364 | 0.61 | 0.77 | 41 | empty |
| 4 | 55 | 0.31 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 968 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 870 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 835 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2VCP · Crystal structure of N-Wasp VC domain in complex with skeletal actin · the same entry in another collection · chain A against A, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain A against A, TM-score 0.97
- O00401 · AlphaFold monomer V2.0 prediction for neural wiskott-aldrich syndrome protein (O00401) · a predicted model of the same protein · chain D against A, TM-score 0.41
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
- Every structure of UniProt O00401
- Elsewhere: RCSB PDB 2VCP · PDBe 2VCP · UniProt P68135 · UniProt O00401
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