Research workbench
Crystal structure of the KIF5C motor domain without any nucleotide
Analyse Crystal structure of the KIF5C motor domain without any nucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WRD
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin heavy chain isoform 5C
- UniProt
- P28738
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin heavy chain isoform 5C | protein | 310 | 34% helix, 29% strand | P28738 |
| B | Kinesin heavy chain isoform 5C | protein | 324 | 31% helix, 27% strand | P28738 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.62 | 0.83 | 34 | empty |
| 2 | 353 | 0.57 | 0.76 | 50 | SO4 |
| 3 | 88 | 0.53 | 0.85 | 17 | empty |
| 4 | 142 | 0.50 | 0.80 | 26 | empty |
| 5 | 100 | 0.39 | 0.77 | 22 | SO4 |
Interfaces
1 interface between chains.
- A–B · 889 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3WRD · Crystal Structure of the KIF5C Motor Domain Without Any Nucleotide · the same entry in another collection · chain A against A, TM-score 1.00
- P28738 · AlphaFold monomer V2.0 prediction for kinesin heavy chain isoform 5C (P28738) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P28738
- Elsewhere: RCSB PDB 3WRD · PDBe 3WRD · UniProt P28738
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