MolNFT v1 · #58539 · protein
Crystal structure of the motor domain of human kinesin family member 3B in complex with ADP
3B6U · Kinesin-like protein KIF3B: “Crystal structure of the motor domain of human kinesin family member 3B in complex with ADP”. X-ray diffraction, 3 ligands (ADP, MG, UNX), 12 pockets (best druggability 0.65). MolNFT v1 #58539 on…
- PDB
- 3B6U
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF3B
- UniProt
- O15066
- Ligands
- ADP, MG, UNX
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin-like protein KIF3B | protein | 323 | 33% helix, 29% strand | O15066 |
| B | Kinesin-like protein KIF3B | protein | 343 | 32% helix, 29% strand | O15066 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.65 | 0.80 | 36 | empty |
| 2 | 370 | 0.63 | 0.79 | 31 | empty |
| 3 | 267 | 0.59 | 0.79 | 33 | empty |
| 4 | 107 | 0.46 | 0.79 | 30 | MG |
| 5 | 106 | 0.43 | 0.78 | 22 | UNX |
Interfaces
1 interface between chains.
- A–B · 924 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3B6U · Crystal structure of the motor domain of human kinesin family member 3B in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O15066 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF3B (O15066) · a predicted model of the same protein · chain B 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 O15066
- Elsewhere: RCSB PDB 3B6U · PDBe 3B6U · UniProt O15066
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