MolNFT v1 · #137921 · protein
The structure of kinesin-14 wild-type ncd-ADP dimer
5W3D · Protein claret segregational: “The structure of kinesin-14 wild-type ncd-ADP dimer”. X-ray diffraction, 2 ligands (ADP, MG), 13 pockets (best druggability 0.59). MolNFT v1 #137921 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5W3D
- Type
- protein
- Length
- 667 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein claret segregational
- UniProt
- P20480
- Ligands
- ADP, MG
- Pockets
- 13 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein claret segregational | protein | 354 | 43% helix, 25% strand | P20480 |
| B | Protein claret segregational | protein | 313 | 43% helix, 23% strand | P20480 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.59 | 0.85 | 20 | empty |
| 2 | 138 | 0.55 | 0.81 | 28 | empty |
| 3 | 124 | 0.54 | 0.82 | 20 | empty |
| 4 | 137 | 0.48 | 0.79 | 19 | empty |
| 5 | 173 | 0.47 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1722 Ų buried · 12 hydrogen bonds · protein-protein
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 P20480
- Elsewhere: RCSB PDB 5W3D · PDBe 5W3D · UniProt P20480
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