MolNFT v1 · #110948 · protein
CDK1/CYCLINB1/CKS2 apo
4YC3 · Cyclin-dependent kinase 1: “CDK1/CYCLINB1/CKS2 apo”. X-ray diffraction, 11 pockets (best druggability 0.82). MolNFT v1 #110948 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YC3
- Type
- protein
- Length
- 632 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 1; G2/MITOTIC-specific cyclin-B1; Cyclin-dependent kinases…
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P06493, P14635, P33552
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 1 (EC 2.7.11.22, 2.7.11.23) | protein | 295 | 35% helix, 18% strand | P06493 |
| B | G2/MITOTIC-specific cyclin-B1 | protein | 265 | 68% helix, 0% strand | P14635 |
| C | Cyclin-dependent kinases regulatory subunit 2 | protein | 72 | 15% helix, 32% strand | P33552 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.82 | 0.96 | 25 | empty |
| 2 | 296 | 0.65 | 0.80 | 23 | MPD |
| 3 | 320 | 0.61 | 0.78 | 42 | empty |
| 4 | 90 | 0.45 | 0.80 | 15 | empty |
| 5 | 195 | 0.44 | 0.74 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1415 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 760 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4YC3 · CDK1/CyclinB1/CKS2 Apo · the same entry in another collection · chain A against A, TM-score 1.00
- P14635 · AlphaFold monomer V2.0 prediction for G2/MITOTIC-specific cyclin-B1 (P14635) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P33552 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinases regulatory subunit 2… · a predicted model of the same protein · chain C against A, TM-score 0.97
- P06493 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 1 (P06493) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P06493
- Every structure of UniProt P14635
- Every structure of UniProt P33552
- Elsewhere: RCSB PDB 4YC3 · PDBe 4YC3 · UniProt P06493 · UniProt P14635 · UniProt P33552
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.