Research workbench
Kinesin-like protein KAR3 and Spindle pole body-associated protein VIK1
Analyse Kinesin-like protein KAR3 and Spindle pole body-associated protein VIK1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ETP
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KAR3; Spindle pole body-associated protein VIK1
- UniProt
- P17119, Q12045
- Ligands
- ADP, EBC, MG
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin-like protein KAR3 | protein | 379 | 43% helix, 24% strand | P17119 |
| B | Spindle pole body-associated protein VIK1 | protein | 287 | 43% helix, 24% strand | Q12045 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- EBC · N,N'-ethane-1,2-diylbis(2-iodoacetamide) · ligand · chains B
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 6 copies · chains A, B
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 | 376 | 0.60 | 0.76 | 34 | empty |
| 2 | 132 | 0.53 | 0.81 | 16 | empty |
| 3 | 128 | 0.51 | 0.80 | 31 | GOL |
| 4 | 76 | 0.44 | 0.81 | 17 | empty |
| 5 | 126 | 0.43 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1608 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ETP · C-terminal motor and motor homology domain of Kar3Vik1 fused to a synthetic heterodimeric… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12045 · AlphaFold monomer V2.0 prediction for spindle pole body-associated protein VIK1 (Q12045) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P17119 · AlphaFold monomer V2.0 prediction for kinesin-like protein KAR3 (P17119) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P17119
- Every structure of UniProt Q12045
- Elsewhere: RCSB PDB 4ETP · PDBe 4ETP · UniProt P17119 · UniProt Q12045
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