Research workbench
Crystal structure of the mitotic kinesin EG5 in complex with mg-ADP and N-(3-aminopropyl)-N-((3-benzyl-5-chloro-4-oxo-3,4- DIHYDROPYRROLO[2,1-F][1,2,4]TRIAZIN-2-YL)(CYCLOPROPYL)METHYL)-4- methylbenzamide
Analyse Crystal structure of the mitotic kinesin EG5 in complex with mg-ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GM1
- Type
- protein
- Length
- 1,293 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-related motor protein EG5
- UniProt
- P52732
- Ligands
- 2AZ, ADP, MG
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin-related motor protein EG5 | protein | 327 | 35% helix, 28% strand | P52732 |
| B | Kinesin-related motor protein EG5 | protein | 320 | 35% helix, 28% strand | P52732 |
| D | Kinesin-related motor protein EG5 | protein | 324 | 35% helix, 29% strand | P52732 |
| E | Kinesin-related motor protein EG5 | protein | 322 | 36% helix, 28% strand | P52732 |
Ligands and binding sites
- 2AZ · N-(3-aminopropyl)-N-[(R)-(3-benzyl-5-chloro-4-oxo-3,4-dihydropyrrolo[2,1-f][1,2,4]triazin-2-yl)(cyclopropyl)methyl]-4-methylbenzamide · ligand · 4 copies · chains A, B, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, E, B, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.67 | 0.83 | 26 | 2AZ |
| 2 | 419 | 0.67 | 0.80 | 70 | MG, ADP |
| 3 | 266 | 0.67 | 0.83 | 27 | 2AZ |
| 4 | 267 | 0.67 | 0.83 | 27 | 2AZ |
| 5 | 261 | 0.66 | 0.83 | 28 | 2AZ |
Interfaces
4 interfaces between chains.
- A–B · 789 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 740 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 530 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2GM1 · Crystal structure of the mitotic kinesin eg5 in complex with mg-adp and… · 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 2GM1 · PDBe 2GM1 · UniProt P52732
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