MolNFT v1 · #159872 · protein
Crystal structure of the cyclin a-CDK2-ORC1 complex
6P3W · Cyclin-dependent kinase 2: “Crystal structure of the cyclin a-CDK2-ORC1 complex”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.81). MolNFT v1 #159872 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6P3W
- Type
- protein
- Length
- 1,118 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2; ORC1 peptide
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 298 | 35% helix, 18% strand | P24941 |
| B | Cyclin-A2 | protein | 257 | 67% helix, 0% strand | P20248 |
| E | ORC1 peptide | protein | 7 | 0% helix, 0% strand | — |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 296 | 35% helix, 18% strand | P24941 |
| D | Cyclin-A2 | protein | 256 | 66% helix, 0% strand | P20248 |
| F | ORC1 peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 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 | 140 | 0.81 | 0.98 | 24 | empty |
| 2 | 136 | 0.78 | 0.95 | 25 | empty |
| 3 | 649 | 0.73 | 0.79 | 64 | PO4 |
| 4 | 236 | 0.68 | 0.84 | 27 | empty |
| 5 | 308 | 0.65 | 0.81 | 35 | PO4 |
Interfaces
6 interfaces between chains.
- A–B · 1599 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1462 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 555 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 432 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 405 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6P3W · Crystal structure of the Cyclin A-CDK2-ORC1 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 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 P20248
- Elsewhere: RCSB PDB 6P3W · PDBe 6P3W · UniProt P24941 · UniProt P20248
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