MolNFT v1 · #143461 · protein
KLP10A-amppnp in complex with curved tubulin and a microtubule
6B0C · Tubulin alpha-1B chain: “KLP10A-amppnp in complex with curved tubulin and a microtubule”. Electron microscopy, 5 ligands (GTP, GDP, TA1), 20 pockets (best druggability 0.87). MolNFT v1 #143461 on GenesisL1: 3D structure, binding…
- PDB
- 6B0C
- Type
- protein
- Length
- 2,070 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Kinesin-like protein KLP10A
- UniProt
- Q2XVP4, F2Z5B2, Q960Z0
- Ligands
- GTP, GDP, TA1, ANP, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 439 | 36% helix, 12% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 425 | 35% helix, 15% strand | F2Z5B2 |
| C | Tubulin alpha-1B chain | protein | 441 | 39% helix, 15% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 429 | 44% helix, 19% strand | F2Z5B2 |
| K | Kinesin-like protein KLP10A | protein | 336 | 29% helix, 28% strand | Q960Z0 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- TA1 · Taxol · ligand · chains D
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains K
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.87 | 0.91 | 93 | empty |
| 2 | 241 | 0.83 | 0.95 | 42 | GTP, MG |
| 3 | 215 | 0.78 | 0.92 | 30 | GTP, MG |
| 4 | 61 | 0.73 | 0.98 | 25 | empty |
| 5 | 93 | 0.72 | 0.94 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2003 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1438 Ų buried · 6 hydrogen bonds · protein-protein
- A–K · 1020 Ų buried · 10 hydrogen bonds · protein-protein
- B–K · 828 Ų buried · 8 hydrogen bonds · protein-protein
- D–K · 627 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6B0C · KLP10A-AMPPNP in complex with curved tubulin and a microtubule · the same entry in another collection · chain B against B, TM-score 1.00
- Q960Z0 · AlphaFold monomer V2.0 prediction for kinesin-like protein KLP10A (Q960Z0) · a predicted model of the same protein · chain K 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 Q2XVP4
- Every structure of UniProt F2Z5B2
- Every structure of UniProt Q960Z0
- Elsewhere: RCSB PDB 6B0C · PDBe 6B0C · UniProt Q2XVP4 · UniProt F2Z5B2 · UniProt Q960Z0
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