MolNFT v1 · #61137 · protein
Drosophila nod (3DC4) and bovine tubulin (1JFF) docked into the 11- ångström cryo-EM MAP of nucleotide-free nod complexed to the microtubule
3DCO · Kinesin-like protein nod: “Drosophila nod (3DC4) and bovine tubulin (1JFF) docked into the 11- ångström cryo-EM MAP of nucleotide-free…”. Electron microscopy, 6 ligands (ADP, GTP, GDP), 17 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 3DCO
- Type
- protein
- Length
- 1,129 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein nod; Bovine alpha tubulin; Bovine beta tubulin
- UniProt
- P18105
- Ligands
- ADP, GTP, GDP, TA1, MG, ZN
- Pockets
- 17 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Kinesin-like protein nod | protein | 291 | 33% helix, 24% strand | P18105 |
| A | Bovine alpha tubulin | protein | 412 | 44% helix, 14% strand | — |
| B | Bovine beta tubulin | protein | 426 | 44% helix, 14% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains N
- 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 N, A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.84 | 0.97 | 39 | MG, GTP |
| 2 | 683 | 0.76 | 0.81 | 66 | empty |
| 3 | 74 | 0.73 | 0.96 | 25 | empty |
| 4 | 227 | 0.58 | 0.80 | 26 | empty |
| 5 | 352 | 0.57 | 0.75 | 41 | TA1 |
Interfaces
3 interfaces between chains.
- A–B · 1883 Ų buried · 29 hydrogen bonds · protein-protein
- N–A · 804 Ų buried · 23 hydrogen bonds · protein-protein
- N–B · 675 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3DCO · Drosophila NOD (3DC4) and Bovine Tubulin (1JFF) Docked into the 11-Angstrom Cryo-EM Map… · the same entry in another collection · chain N against N, TM-score 1.00
- P18105 · AlphaFold monomer V2.0 prediction for kinesin-like protein nod (P18105) · a predicted model of the same protein · chain N against A, TM-score 0.96
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 P18105
- Elsewhere: RCSB PDB 3DCO · PDBe 3DCO · UniProt P18105
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