Research workbench
Crystal structure of human kinesin EG5 in complex with (S)-dimethylenastron
Analyse Crystal structure of human kinesin EG5 in complex with (S)-dimethylenastron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X7D
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF11
- UniProt
- P52732
- Ligands
- ADP, EGB, MG
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin-like protein KIF11 | protein | 335 | 34% helix, 30% strand | P52732 |
| B | Kinesin-like protein KIF11 | protein | 334 | 33% helix, 29% strand | P52732 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- EGB · (4S)-4-(3-hydroxyphenyl)-7,7-dimethyl-2-thioxo-2,3,4,6,7,8-hexahydroquinazolin-5(1H)-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.69 | 0.74 | 79 | empty |
| 2 | 361 | 0.62 | 0.78 | 32 | empty |
| 3 | 223 | 0.61 | 0.81 | 30 | MG, EGB |
| 4 | 333 | 0.60 | 0.78 | 30 | empty |
| 5 | 154 | 0.59 | 0.83 | 26 | EGB |
Interfaces
1 interface between chains.
- A–B · 253 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2X7D · Crystal structure of human kinesin Eg5 in complex with (S)-dimethylenastron · the same entry in another collection · chain A against A, TM-score 1.00
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 P52732
- Elsewhere: RCSB PDB 2X7D · PDBe 2X7D · UniProt P52732
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