MolNFT v1 · #64712 · protein
Crystal structure of the motor domain of kinesin KIF13B bound with ADP
3GBJ · KIF13B protein: “Crystal structure of the motor domain of kinesin KIF13B bound with ADP”. X-ray diffraction, 3 ligands (ADP, MG, UNX), 8 pockets (best druggability 0.60). MolNFT v1 #64712 on GenesisL1: 3D structure, binding sites…
- PDB
- 3GBJ
- Type
- protein
- Length
- 894 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KIF13B protein
- UniProt
- A0JLQ2
- Ligands
- ADP, MG, UNX
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KIF13B protein | protein | 302 | 35% helix, 31% strand | A0JLQ2 |
| B | KIF13B protein | protein | 298 | 34% helix, 30% strand | A0JLQ2 |
| C | KIF13B protein | protein | 294 | 35% helix, 31% strand | A0JLQ2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- UNX · Unknown atom or ion · ion · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.60 | 0.76 | 40 | empty |
| 2 | 299 | 0.52 | 0.74 | 39 | empty |
| 3 | 124 | 0.51 | 0.80 | 24 | empty |
| 4 | 154 | 0.50 | 0.78 | 25 | empty |
| 5 | 104 | 0.44 | 0.78 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 691 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3GBJ · Crystal structure of the motor domain of kinesin KIF13B bound with ADP · the same entry in another collection · chain A against A, TM-score 1.00
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 A0JLQ2
- Elsewhere: RCSB PDB 3GBJ · PDBe 3GBJ · UniProt A0JLQ2
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