Research workbench
Crystal structure of murine gamma herpesvirus cyclin complexed to human cyclin dependent kinase 2
Analyse Crystal structure of murine gamma herpesvirus cyclin complexed to human cyclin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F5Q
- Type
- protein
- Length
- 1,079 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin dependent kinase 2; Gamma herpesvirus cyclin
- EC
- 2.7.1.-
- UniProt
- P24941, P89883
- Ligands
- CL
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin dependent kinase 2 (EC 2.7.1.-) | protein | 296 | 32% helix, 14% strand | P24941 |
| B | Gamma herpesvirus cyclin | protein | 247 | 72% helix, 0% strand | P89883 |
| C | Cyclin dependent kinase 2 (EC 2.7.1.-) | protein | 288 | 32% helix, 14% strand | P24941 |
| D | Gamma herpesvirus cyclin | protein | 248 | 74% helix, 0% strand | P89883 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.75 | 0.99 | 21 | empty |
| 2 | 56 | 0.72 | 0.99 | 23 | empty |
| 3 | 393 | 0.66 | 0.79 | 41 | empty |
| 4 | 519 | 0.64 | 0.76 | 81 | empty |
| 5 | 275 | 0.61 | 0.79 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1318 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1285 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 480 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 250 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1F5Q · Crystal structure of murine gamma herpesvirus cyclin complexed to human cyclin dependent… · the same entry in another collection · chain A 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 P89883
- Elsewhere: RCSB PDB 1F5Q · PDBe 1F5Q · UniProt P24941 · UniProt P89883
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