Research workbench
Human NDC80 bonsai decorated microtubule
Analyse Human NDC80 bonsai decorated microtubule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IZ0
- Type
- protein
- Length
- 1,508 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha tubulin, chain a from pdb 1JFF; Beta tubulin, chain B from pdb 1JFF; NDC80-SPC25…
- UniProt
- Q05DQ6, Q9HBM1, B1AQT4, C9JGC4
- Ligands
- GTP, GDP, TA1, ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha tubulin, chain a from pdb 1JFF | protein | 412 | 44% helix, 14% strand | — |
| B | Beta tubulin, chain B from pdb 1JFF | protein | 426 | 44% helix, 14% strand | — |
| C, E | NDC80-SPC25 chimera protein, chain B from pdb 2VE7 (NDC80 bonsai) | protein | 182 | 53% helix, 1% strand | Q05DQ6, Q9HBM1 |
| D, F | NUF2-SPC24 chimera protein, chain D from pdb 2VE7 (NDC80 bonsai) | protein | 153 | 68% helix, 0% strand | B1AQT4, C9JGC4 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- ZN · Zinc ion · metal · chains A
- MG · Magnesium 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.83 | 0.96 | 41 | MG, GTP |
| 2 | 1082 | 0.76 | 0.78 | 107 | empty |
| 3 | 66 | 0.72 | 0.97 | 24 | empty |
| 4 | 990 | 0.71 | 0.75 | 84 | empty |
| 5 | 537 | 0.66 | 0.77 | 47 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2599 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 2597 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1878 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 324 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 253 Ų buried · 5 hydrogen bonds · protein-protein
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 Q05DQ6
- Every structure of UniProt Q9HBM1
- Every structure of UniProt B1AQT4
- Every structure of UniProt C9JGC4
- Elsewhere: RCSB PDB 3IZ0 · PDBe 3IZ0 · UniProt Q05DQ6 · UniProt Q9HBM1 · UniProt B1AQT4 · UniProt C9JGC4
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