Research workbench
Human monomeric kinesin (1BG2) and bovine tubulin (1JFF) docked into the 9-ångström cryo-EM MAP of nucleotide-free kinesin complexed to the microtubule
Analyse Human monomeric kinesin (1BG2) and bovine tubulin (1JFF) docked into the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P4N
- Type
- protein
- Length
- 1,161 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin heavy chain; Tubulin alpha chain; Tubulin beta chain
- Ligands
- ADP, GTP, GDP, TA1, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Kinesin heavy chain | protein | 323 | 32% helix, 28% strand | — |
| A | Tubulin alpha chain | protein | 412 | 44% helix, 14% strand | — |
| B | Tubulin beta chain | protein | 426 | 44% helix, 14% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains K
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains K, A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.83 | 0.97 | 40 | MG, GTP |
| 2 | 1147 | 0.77 | 0.80 | 101 | empty |
| 3 | 69 | 0.72 | 0.97 | 24 | empty |
| 4 | 51 | 0.66 | 0.95 | 21 | empty |
| 5 | 208 | 0.59 | 0.81 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1886 Ų buried · 29 hydrogen bonds · protein-protein
- K–A · 1042 Ų buried · 54 hydrogen bonds · protein-protein
- K–B · 633 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 2P4N · Human Monomeric Kinesin (1BG2) and Bovine Tubulin (1JFF) Docked into the 9-Angstrom… · the same entry in another collection · chain K against K, 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
- Elsewhere: RCSB PDB 2P4N · PDBe 2P4N
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