Research workbench
CDK2/CYCLIN a in complex with an 11-residue recruitment peptide from P107
Analyse CDK2/CYCLIN a in complex with an 11-residue recruitment peptide from P107 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H28
- Type
- protein
- Length
- 1,128 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2; Retinoblastoma-like protein 1
- UniProt
- P24941, P20248, P28749
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 | protein | 297 | 32% helix, 19% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 66% helix, 0% strand | P20248 |
| E | Retinoblastoma-like protein 1 | protein | 10 | 0% helix, 0% strand | P28749 |
| F | Retinoblastoma-like protein 1 | protein | 8 | 0% helix, 0% strand | P28749 |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.81 | 0.99 | 24 | empty |
| 2 | 98 | 0.78 | 0.98 | 24 | empty |
| 3 | 929 | 0.77 | 0.79 | 96 | empty |
| 4 | 269 | 0.68 | 0.83 | 33 | empty |
| 5 | 329 | 0.66 | 0.81 | 45 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1809 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1776 Ų buried · 24 hydrogen bonds · protein-protein
- B–E · 698 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 664 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 474 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1H28 · CDK2/CyclinA in complex with an 11-residue recruitment peptide from p107 · 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 B 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 A against A, TM-score 0.91
- P28749 · AlphaFold monomer V2.0 prediction for retinoblastoma-like protein 1 (P28749) · a predicted model of the same protein · chain F 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 P28749
- Elsewhere: RCSB PDB 1H28 · PDBe 1H28 · UniProt P24941 · UniProt P20248 · UniProt P28749
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