Research workbench
Structure of phopsho-CDK2-cyclin a in complex with an ATP-competitive inhibitor
Analyse Structure of phopsho-CDK2-cyclin a in complex with an ATP-competitive inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LMK
- Type
- protein
- Length
- 1,078 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, P20248
- Ligands
- 6ZK, MG
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 297 | 34% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 258 | 67% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 266 | 35% helix, 19% strand | P24941 |
| D | Cyclin-A2 | protein | 257 | 65% helix, 0% strand | P20248 |
Ligands and binding sites
- 6ZK · 4-[4-[3-bromanyl-7-(pyridin-3-ylmethylamino)pyrazolo[1, 5-a]pyrimidin-5-yl]phenyl]benzamide · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains B
- SGM · Monothioglycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.81 | 0.99 | 22 | empty |
| 2 | 126 | 0.80 | 0.98 | 24 | empty |
| 3 | 739 | 0.79 | 0.83 | 79 | empty |
| 4 | 221 | 0.69 | 0.86 | 24 | 6ZK |
| 5 | 209 | 0.66 | 0.84 | 26 | 6ZK |
Interfaces
5 interfaces between chains.
- C–D · 1697 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1655 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 554 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 495 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 128 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (phosphorylation, additive adduct).
Compared structures
- 5LMK · Structure of phopsho-CDK2-cyclin A in complex with an ATP-competitive inhibitor · the same entry in another collection · chain D against D, 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
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 5LMK · PDBe 5LMK · UniProt P24941 · UniProt P20248
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