Research workbench
Crystal structure of yeast CDC4/SKP1 in complex with an allosteric inhibitor scf-I2
Analyse Crystal structure of yeast CDC4/SKP1 in complex with an allosteric inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MKS
- Type
- protein
- Length
- 1,155 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Suppressor of kinetochore protein 1; Cell division control protein 4
- UniProt
- P52286, P07834
- Ligands
- C1C, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Suppressor of kinetochore protein 1 | protein | 134 | 51% helix, 10% strand | P52286 |
| B | Cell division control protein 4 | protein | 444 | 16% helix, 46% strand | P07834 |
| C | Suppressor of kinetochore protein 1 | protein | 132 | 54% helix, 11% strand | P52286 |
| D | Cell division control protein 4 | protein | 445 | 17% helix, 45% strand | P07834 |
Ligands and binding sites
- C1C · 1,1'-binaphthalene-2,2'-dicarboxylic acid · ligand · chains D
- SO4 · Sulfate ion · ion · 11 copies · chains B, D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.81 | 0.82 | 73 | SO4 |
| 2 | 604 | 0.75 | 0.82 | 48 | GOL |
| 3 | 440 | 0.71 | 0.81 | 39 | empty |
| 4 | 158 | 0.48 | 0.77 | 20 | empty |
| 5 | 191 | 0.44 | 0.74 | 27 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1431 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1373 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 459 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3MKS · Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2 · the same entry in another collection · chain D against D, TM-score 1.00
- P07834 · AlphaFold monomer V2.0 prediction for cell division control protein 4 (P07834) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P52286 · AlphaFold monomer V2.0 prediction for suppressor of kinetochore protein 1 (P52286) · a predicted model of the same protein · chain A 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 P52286
- Every structure of UniProt P07834
- Elsewhere: RCSB PDB 3MKS · PDBe 3MKS · UniProt P52286 · UniProt P07834
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