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Crystal structure of ksp in complex with ADP and thiophene containing inhibitor 15
Analyse Crystal structure of ksp in complex with ADP and thiophene containing inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PG2
- Type
- protein
- Length
- 662 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF11
- UniProt
- P52732
- Ligands
- ADP, K01, MG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kinesin-like protein KIF11 | protein | 331 | 34% helix, 29% strand | P52732 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- K01 · N,N-diethyl-2-[(2-thienylcarbonyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.81 | 0.82 | 128 | MG, ADP, K01 |
| 2 | 312 | 0.60 | 0.78 | 30 | empty |
| 3 | 292 | 0.59 | 0.78 | 30 | empty |
| 4 | 138 | 0.42 | 0.75 | 29 | empty |
| 5 | 98 | 0.34 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 925 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2PG2 · Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 15 · the same entry in another collection · chain B against B, 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 2PG2 · PDBe 2PG2 · UniProt P52732
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