Research workbench
Microtubule-bound MKLP2 motor domain in the presence of ADP
Analyse Microtubule-bound MKLP2 motor domain in the presence of ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ND2
- Type
- protein
- Length
- 1,118 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF20A; Tubulin alpha chain; Tubulin beta-2B chain
- UniProt
- P97329, F2Z4C1, Q6B856
- Ligands
- ADP, GTP, GDP, TA1, MG
- Pockets
- 13 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Kinesin-like protein KIF20A | protein | 280 | 37% helix, 30% strand | P97329 |
| A | Tubulin alpha chain | protein | 412 | 43% helix, 17% strand | F2Z4C1 |
| B | Tubulin beta-2B chain | protein | 426 | 46% helix, 18% strand | Q6B856 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains C
- 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 C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.81 | 0.96 | 39 | GTP, MG |
| 2 | 1114 | 0.81 | 0.82 | 95 | empty |
| 3 | 247 | 0.69 | 0.84 | 38 | empty |
| 4 | 70 | 0.67 | 0.93 | 26 | empty |
| 5 | 55 | 0.58 | 0.91 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1969 Ų buried · 35 hydrogen bonds · protein-protein
- C–B · 502 Ų buried · 4 hydrogen bonds · protein-protein
- C–A · 313 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 P97329
- Every structure of UniProt F2Z4C1
- Every structure of UniProt Q6B856
- Elsewhere: RCSB PDB 5ND2 · PDBe 5ND2 · UniProt P97329 · UniProt F2Z4C1 · UniProt Q6B856
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.