Research workbench
The yersinia yopo - actin complex with mgadp
Analyse The yersinia yopo - actin complex with mgadp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CE3
- Type
- protein
- Length
- 1,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin; Protein kinase yopo
- UniProt
- G3CKA6, Q93KQ6
- Ligands
- ATP, ADP, CA, MG
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Actin | protein | 358 | 46% helix, 21% strand | G3CKA6 |
| B, D | Protein kinase yopo | protein | 598 | 57% helix, 11% strand | Q93KQ6 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.77 | 0.79 | 132 | ATP, CA |
| 2 | 372 | 0.76 | 0.86 | 53 | ATP, CA |
| 3 | 785 | 0.72 | 0.78 | 100 | empty |
| 4 | 821 | 0.72 | 0.77 | 100 | empty |
| 5 | 535 | 0.68 | 0.78 | 66 | ADP, MG |
Interfaces
2 interfaces between chains.
- A–B · 2242 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2226 Ų buried · 42 hydrogen bonds · protein-protein
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 5CE3 · PDBe 5CE3 · UniProt G3CKA6 · UniProt Q93KQ6
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