Research workbench
Structures of actin-bound WH2 domains of spire and the implication for filament nucleation
Analyse Structures of actin-bound WH2 domains of spire and the implication for filament… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MN6
- Type
- protein
- Length
- 1,137 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-5C; Protein spire
- UniProt
- P10987, Q9U1K1
- Ligands
- ATP, CA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, K | Actin-5C | protein | 360 | 43% helix, 21% strand | P10987 |
| X, Y, Z | Protein spire | protein | 19 | 47% helix, 5% strand | Q9U1K1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, F, K
- CA · Calcium ion · metal · 3 copies · chains A, F, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.76 | 0.84 | 55 | CA, ATP |
| 2 | 536 | 0.76 | 0.83 | 59 | CA, ATP |
| 3 | 452 | 0.76 | 0.85 | 53 | CA, ATP |
| 4 | 297 | 0.69 | 0.83 | 37 | empty |
| 5 | 285 | 0.69 | 0.83 | 36 | empty |
Interfaces
8 interfaces between chains.
- A–X · 463 Ų buried · 4 hydrogen bonds · protein-protein
- K–Z · 461 Ų buried · 4 hydrogen bonds · protein-protein
- F–Y · 455 Ų buried · 4 hydrogen bonds · protein-protein
- A–K · 110 Ų buried · 1 hydrogen bond · protein-protein
- A–F · 105 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3MN6 · Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation · the same entry in another collection · chain Z against Z, TM-score 1.00
- P10987 · AlphaFold monomer V2.0 prediction for actin-5C (P10987) · a predicted model of the same protein · chain K against A, TM-score 0.98
- Q9U1K1 · AlphaFold monomer V2.0 prediction for protein spire (Q9U1K1) · a predicted model of the same protein · chain X against A, TM-score 0.34
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 P10987
- Every structure of UniProt Q9U1K1
- Elsewhere: RCSB PDB 3MN6 · PDBe 3MN6 · UniProt P10987 · UniProt Q9U1K1
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