MolNFT v1 · #19527 · protein
Phosphorylated CDK2-cyclyin a-substrate peptide complex
1QMZ · Cell division protein kinase 2: “Phosphorylated CDK2-cyclyin a-substrate peptide complex”. X-ray diffraction, 2 ligands (ATP, MG), 15 pockets (best druggability 0.81). MolNFT v1 #19527 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1QMZ
- Type
- protein
- Length
- 1,124 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; G2/MITOTIC-specific cyclin a; Substrate peptide
- EC
- 2.7.1.-
- UniProt
- P24941, P20248
- Ligands
- ATP, MG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.-) | protein | 297 | 35% helix, 16% strand | P24941 |
| B, D | G2/MITOTIC-specific cyclin a | protein | 258 | 69% helix, 0% strand | P20248 |
| E, F | Substrate peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, E, C, F
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.81 | 0.99 | 22 | empty |
| 2 | 114 | 0.81 | 0.99 | 24 | empty |
| 3 | 991 | 0.78 | 0.80 | 107 | empty |
| 4 | 374 | 0.76 | 0.86 | 49 | ATP, MG |
| 5 | 421 | 0.75 | 0.85 | 54 | ATP, MG |
Interfaces
9 interfaces between chains.
- A–B · 1736 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1731 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 500 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 495 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 438 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1QMZ · Phosphorylated CDK2-cyclyin a-substrate peptide complex · 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 0.91
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
- Elsewhere: RCSB PDB 1QMZ · PDBe 1QMZ · UniProt P24941 · UniProt P20248
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