Research workbench
The crystal structure of CDK2 cyclin a in complex with a substrate peptide derived from cdc modified with a gamma-linked ATP analogue
Analyse The crystal structure of CDK2 cyclin a in complex with a substrate peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CCH
- Type
- protein
- Length
- 1,134 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2; Cell division control protein 6 homolog
- EC
- 2.7.1.-
- UniProt
- P24941, P20248, Q99741
- Ligands
- ATP, SO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.-) | protein | 297 | 34% helix, 18% strand | P24941 |
| B | Cyclin A2 | protein | 260 | 68% helix, 0% strand | P20248 |
| D | Cyclin A2 | protein | 256 | 69% helix, 0% strand | P20248 |
| E, F | Cell division control protein 6 homolog | protein | 12 | 0% helix, 0% strand | Q99741 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.81 | 0.98 | 24 | empty |
| 2 | 113 | 0.80 | 0.99 | 23 | empty |
| 3 | 886 | 0.79 | 0.81 | 117 | empty |
| 4 | 434 | 0.69 | 0.80 | 53 | ATP |
| 5 | 489 | 0.67 | 0.78 | 58 | ATP |
Interfaces
7 interfaces between chains.
- A–B · 1734 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1573 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 714 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 703 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 472 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2CCH · The crystal structure of CDK2 cyclin A in complex with a substrate peptide derived from… · the same entry in another collection · chain F against F, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain D against A, TM-score 1.00
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain C against A, TM-score 0.92
- Q99741 · AlphaFold monomer V2.0 prediction for cell division control protein 6 homolog (Q99741) · a predicted model of the same protein · chain E against A, TM-score 0.32
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 P24941
- Every structure of UniProt P20248
- Every structure of UniProt Q99741
- Elsewhere: RCSB PDB 2CCH · PDBe 2CCH · UniProt P24941 · UniProt P20248 · UniProt Q99741
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