MolNFT v1 · #30605 · protein
Ternary complex of the WH2 domain of wave with actin-DNase I
2A40 · Actin, alpha skeletal muscle: “Ternary complex of the WH2 domain of wave with actin-DNase I”. X-ray diffraction, 4 ligands (ATP, NAG, CA), 9 pockets (best druggability 0.74). MolNFT v1 #30605 on GenesisL1: 3D structure, binding…
- PDB
- 2A40
- Type
- protein
- Length
- 1,288 residues
- Chains
- 6
- 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
- Ligands
- ATP, NAG, CA, MG
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Actin, alpha skeletal muscle | protein | 362 | 46% helix, 22% strand | P68135 |
| B, E | Deoxyribonuclease-1 (EC 3.1.21.1) | protein | 260 | 30% helix, 28% strand | P00639 |
| C, F | Wiskott-aldrich syndrome protein family member 2 | protein | 22 | 50% helix, 5% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, E
- CA · Calcium ion · metal · 4 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 2 copies · chains B, E
- GOL · Glycerol · additive · 2 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.74 | 0.82 | 60 | CA, ATP |
| 2 | 517 | 0.74 | 0.82 | 57 | CA, ATP |
| 3 | 557 | 0.67 | 0.77 | 53 | GOL |
| 4 | 399 | 0.66 | 0.80 | 46 | empty |
| 5 | 140 | 0.48 | 0.78 | 27 | empty |
Interfaces
7 interfaces between chains.
- D–E · 943 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 937 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 852 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 847 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 358 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, methylation).
Compared structures
- 2A40 · Ternary complex of the WH2 domain of WAVE with Actin-DNAse I · the same entry in another collection · chain F against F, 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 D against A, TM-score 0.97
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
- Elsewhere: RCSB PDB 2A40 · PDBe 2A40 · UniProt P68135 · UniProt P00639
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