Research workbench
Ternary complex of the WH2 domain of wip with actin-DNase I
Analyse Ternary complex of the WH2 domain of wip with actin-DNase I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A41
- Type
- protein
- Length
- 664 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Deoxyribonuclease-1; Wiskott-aldrich syndrome protein…
- EC
- 3.1.21.1
- UniProt
- P68135, P00639, O43516
- Ligands
- ATP, NAG, BMA, CA, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 372 | 43% helix, 20% strand | P68135 |
| B | Deoxyribonuclease-1 (EC 3.1.21.1) | protein | 260 | 30% helix, 28% strand | P00639 |
| C | Wiskott-aldrich syndrome protein interacting protein | protein | 32 | 31% helix, 9% strand | O43516 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- FMT · Formic acid · additive · chains 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 | 576 | 0.79 | 0.85 | 62 | CA, ATP |
| 2 | 142 | 0.60 | 0.84 | 27 | empty |
| 3 | 188 | 0.51 | 0.77 | 25 | empty |
| 4 | 50 | 0.27 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1641 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 973 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 127 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, methylation).
Compared structures
- 2A41 · Ternary complex of the WH2 Domain of WIP with Actin-DNAse I · the same entry in another collection · chain A against A, TM-score 1.00
- P00639 · AlphaFold monomer V2.0 prediction for deoxyribonuclease-1 (P00639) · a predicted model of the same protein · chain B against A, TM-score 0.98
- 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
- O43516 · AlphaFold monomer V2.0 prediction for WAS/WASL-interacting protein family member 1… · a predicted model of the same protein · chain C against A, TM-score 0.44
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 P00639
- Every structure of UniProt O43516
- Elsewhere: RCSB PDB 2A41 · PDBe 2A41 · UniProt P68135 · UniProt P00639 · UniProt O43516
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