Research workbench
Aurora-a kinase domain in complex with vnar-D01 (crystal form 1)
Analyse Aurora-a kinase domain in complex with vnar-D01 (crystal form 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L8L
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aurora kinase a; New antigen receptor variable domain
- EC
- 2.7.11.1
- UniProt
- O14965, Q8JJ25
- Ligands
- ADP, SO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aurora kinase a (EC 2.7.11.1) | protein | 264 | 40% helix, 20% strand | O14965 |
| B | New antigen receptor variable domain | protein | 109 | 6% helix, 51% strand | Q8JJ25 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
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 | 544 | 0.68 | 0.78 | 44 | ADP |
| 2 | 110 | 0.46 | 0.79 | 22 | SO4 |
| 3 | 83 | 0.33 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 997 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
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 O14965
- Every structure of UniProt Q8JJ25
- Elsewhere: RCSB PDB 5L8L · PDBe 5L8L · UniProt O14965 · UniProt Q8JJ25
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