Research workbench
Mechanisms of crippling actin-dependent phagocytosis by yopo
Analyse Mechanisms of crippling actin-dependent phagocytosis by yopo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CI6
- Type
- protein
- Length
- 934 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin; Protein kinase yopo
- UniProt
- G3CKA6, Q93KQ6
- Ligands
- ATP, CA
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin | protein | 358 | 44% helix, 21% strand | G3CKA6 |
| B | Protein kinase yopo | protein | 576 | 56% helix, 10% strand | Q93KQ6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.77 | 0.83 | 77 | ATP, CA |
| 2 | 1110 | 0.75 | 0.77 | 139 | empty |
| 3 | 344 | 0.64 | 0.80 | 48 | empty |
| 4 | 152 | 0.42 | 0.74 | 23 | empty |
| 5 | 96 | 0.42 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2173 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 4CI6 · Mechanisms of crippling actin-dependent phagocytosis by YopO · the same entry in another collection · chain A against A, TM-score 1.00
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 G3CKA6
- Every structure of UniProt Q93KQ6
- Elsewhere: RCSB PDB 4CI6 · PDBe 4CI6 · UniProt G3CKA6 · UniProt Q93KQ6
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