Research workbench
Crystal structure of vpso (VC0937) kinase domain
Analyse Crystal structure of vpso (VC0937) kinase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U1Q
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vpso
- UniProt
- A0A2S1ZT94
- Ligands
- PTR
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vpso | protein | 208 | 40% helix, 16% strand | A0A2S1ZT94 |
| B | Vpso | protein | 203 | 38% helix, 18% strand | A0A2S1ZT94 |
Ligands and binding sites
- PTR · O-phosphotyrosine · ligand · 2 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.41 | 0.73 | 31 | PTR |
| 2 | 62 | 0.32 | 0.76 | 14 | empty |
| 3 | 61 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 901 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6U1Q · Crystal Structure of VpsO (VC0937) Kinase domain · the same entry in another collection · chain B against B, 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 A0A2S1ZT94
- Elsewhere: RCSB PDB 6U1Q · PDBe 6U1Q · UniProt A0A2S1ZT94
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