Research workbench
Pandda analysis group deposition -- crystal structure of KALIRIN/RAC1 in complex with Z56880342
Analyse Pandda analysis group deposition -- crystal structure of KALIRIN/RAC1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QQD
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related C3 botulinum toxin substrate 1; Kalirin
- EC
- 2.7.11.1
- UniProt
- P63000, O60229
- Ligands
- JGA
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related C3 botulinum toxin substrate 1 | protein | 177 | 38% helix, 22% strand | P63000 |
| B | Kalirin (EC 2.7.11.1) | protein | 179 | 79% helix, 0% strand | O60229 |
Ligands and binding sites
- JGA · N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.55 | 0.79 | 32 | empty |
| 2 | 154 | 0.47 | 0.76 | 25 | JGA |
| 3 | 50 | 0.24 | 0.72 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1229 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5QQD · PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with… · 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 P63000
- Every structure of UniProt O60229
- Elsewhere: RCSB PDB 5QQD · PDBe 5QQD · UniProt P63000 · UniProt O60229
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