MolNFT v1 · #127997 · protein
Microtubule-bound MKLP2 motor domain in the presence of ADP.ALFX
5ND4 · Kinesin-like protein KIF20A: “Microtubule-bound MKLP2 motor domain in the presence of ADP.ALFX”. Electron microscopy, 6 ligands (ADP, ALF, GTP), 19 pockets (best druggability 0.89). MolNFT v1 #127997 on GenesisL1: 3D structure…
- PDB
- 5ND4
- Type
- protein
- Length
- 1,175 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, ALF, GTP, GDP, TA1, MG
- Pockets
- 19 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Kinesin-like protein KIF20A | protein | 337 | 34% helix, 27% strand | P97329 |
| A | Tubulin alpha chain | protein | 412 | 42% helix, 14% strand | F2Z4C1 |
| B | Tubulin beta-2B chain | protein | 426 | 44% helix, 16% strand | Q6B856 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains C
- ALF · Tetrafluoroaluminate ion · 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, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.89 | 0.90 | 106 | empty |
| 2 | 212 | 0.81 | 0.95 | 40 | GTP, MG |
| 3 | 93 | 0.68 | 0.92 | 24 | empty |
| 4 | 534 | 0.66 | 0.77 | 48 | empty |
| 5 | 114 | 0.64 | 0.88 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1899 Ų buried · 21 hydrogen bonds · protein-protein
- C–A · 876 Ų buried · 6 hydrogen bonds · protein-protein
- C–B · 785 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5ND4 · Microtubule-bound MKLP2 motor domain in the presence of ADP.AlFx · the same entry in another collection · chain C against C, 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 0.94
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 5ND4 · PDBe 5ND4 · UniProt P97329 · UniProt F2Z4C1 · UniProt Q6B856
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