Research workbench
Nucleotide-free kinesin motor domain complexed with gmpcpp-microtubule
Analyse Nucleotide-free kinesin motor domain complexed with gmpcpp-microtubule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J6H
- Type
- protein
- Length
- 1,113 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1A chain; Tubulin beta chain; Kinesin heavy chain isoform 5C
- UniProt
- P02550, P02554, P28738
- Ligands
- GTP, G2P, MG, SO4
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1A chain | protein | 410 | 44% helix, 12% strand | P02550 |
| B | Tubulin beta chain | protein | 426 | 41% helix, 15% strand | P02554 |
| K | Kinesin heavy chain isoform 5C | protein | 277 | 32% helix, 23% strand | P28738 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.80 | 0.83 | 75 | MG, GTP |
| 2 | 73 | 0.73 | 0.97 | 23 | empty |
| 3 | 708 | 0.73 | 0.79 | 67 | empty |
| 4 | 221 | 0.72 | 0.88 | 43 | empty |
| 5 | 281 | 0.59 | 0.79 | 38 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1195 Ų buried · 13 hydrogen bonds · protein-protein
- B–K · 528 Ų buried · 21 hydrogen bonds · protein-protein
- A–K · 128 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent (covalent ligand).
Compared structures
- 3J6H · Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule · the same entry in another collection · chain A against A, TM-score 1.00
- P02550 · AlphaFold monomer V2.0 prediction for tubulin alpha-1A chain (P02550) · a predicted model of the same protein · chain A against A, TM-score 0.88
- P28738 · AlphaFold monomer V2.0 prediction for kinesin heavy chain isoform 5C (P28738) · a predicted model of the same protein · chain K against A, TM-score 0.86
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 P02550
- Every structure of UniProt P02554
- Every structure of UniProt P28738
- Elsewhere: RCSB PDB 3J6H · PDBe 3J6H · UniProt P02550 · UniProt P02554 · UniProt P28738
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