Research workbench
Microtubule-bound MKLP2 motor domain in the with no nucleotide
Analyse Microtubule-bound MKLP2 motor domain in the with no nucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ND3
- Type
- protein
- Length
- 1,134 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
- GTP, GDP, TA1, MG
- Pockets
- 19 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Kinesin-like protein KIF20A | protein | 296 | 34% helix, 29% strand | P97329 |
| A | Tubulin alpha chain | protein | 412 | 43% helix, 16% strand | F2Z4C1 |
| B | Tubulin beta-2B chain | protein | 426 | 45% helix, 17% strand | Q6B856 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.86 | 0.87 | 102 | empty |
| 2 | 202 | 0.82 | 0.96 | 47 | GTP, MG |
| 3 | 295 | 0.77 | 0.89 | 71 | empty |
| 4 | 80 | 0.64 | 0.91 | 17 | empty |
| 5 | 165 | 0.61 | 0.83 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1810 Ų buried · 28 hydrogen bonds · protein-protein
- C–B · 817 Ų buried · 13 hydrogen bonds · protein-protein
- C–A · 632 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5ND3 · Microtubule-bound MKLP2 motor domain in the with no nucleotide · the same entry in another collection · chain A against A, TM-score 1.00
- P97329 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF20A (P97329) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 5ND3 · PDBe 5ND3 · UniProt P97329 · UniProt F2Z4C1 · UniProt Q6B856
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