Research workbench
Crystal structure of kinesin-3 KIF13B motor domain in amppnp form
Analyse Crystal structure of kinesin-3 KIF13B motor domain in amppnp form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZBR
- Type
- protein
- Length
- 983 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin family member 13B
- UniProt
- A0A0G2K8Z9
- Ligands
- ANP, MG, PO4
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Kinesin family member 13B | protein | 330 | 34% helix, 31% strand | A0A0G2K8Z9 |
| A | Kinesin family member 13B | protein | 329 | 32% helix, 30% strand | A0A0G2K8Z9 |
| C | Kinesin family member 13B | protein | 324 | 33% helix, 30% strand | A0A0G2K8Z9 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains B, A, C
- MG · Magnesium ion · metal · 5 copies · chains B, A, C
- PO4 · Phosphate ion · ion · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.69 | 0.90 | 28 | empty |
| 2 | 250 | 0.66 | 0.83 | 37 | empty |
| 3 | 427 | 0.64 | 0.78 | 43 | empty |
| 4 | 160 | 0.61 | 0.84 | 27 | empty |
| 5 | 310 | 0.52 | 0.74 | 43 | empty |
Interfaces
3 interfaces between chains.
- B–A · 574 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZBR · Crystal Structure of Kinesin-3 KIF13B motor domain in AMPPNP form · the same entry in another collection · chain B against B, 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 A0A0G2K8Z9
- Elsewhere: RCSB PDB 5ZBR · PDBe 5ZBR · UniProt A0A0G2K8Z9
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