Research workbench
Crystal structure of the motor domain of human kinesin family member 3B in complex with ADP
Analyse Crystal structure of the motor domain of human kinesin family member 3B in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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