MolNFT v1 · #94683 · protein
Structure of PCDK2/CYCLINA bound to ADP and 2 magnesium ions
4I3Z · Cyclin-dependent kinase 2: “Structure of PCDK2/CYCLINA bound to ADP and 2 magnesium ions”. X-ray diffraction, 3 ligands (ADP, MG, CL), 12 pockets (best druggability 0.81). MolNFT v1 #94683 on GenesisL1: 3D structure, binding sites…
- PDB
- 4I3Z
- Type
- protein
- Length
- 1,106 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P51943
- Ligands
- ADP, MG, CL
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 296 | 34% helix, 17% strand | P24941 |
| B, D | Cyclin-A2 | protein | 257 | 68% helix, 0% strand | P51943 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.81 | 0.98 | 23 | empty |
| 2 | 120 | 0.81 | 0.99 | 22 | empty |
| 3 | 458 | 0.70 | 0.81 | 48 | ADP, MG |
| 4 | 449 | 0.68 | 0.80 | 48 | ADP, MG |
| 5 | 253 | 0.62 | 0.81 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1606 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1593 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 363 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4I3Z · Structure of pCDK2/CyclinA bound to ADP and 2 Magnesium ions · the same entry in another collection · chain C against C, TM-score 1.00
- P51943 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P51943) · 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 0.92
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 P51943
- Elsewhere: RCSB PDB 4I3Z · PDBe 4I3Z · UniProt P24941 · UniProt P51943
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