Research workbench
Crystal structure of SUN1-speedy a-CDK2
Analyse Crystal structure of SUN1-speedy a-CDK2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E34
- Type
- protein
- Length
- 459 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Speedy protein a; Sun domain-containing protein 1
- EC
- 2.7.11.22
- UniProt
- P24941, Q5MJ70, O94901
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 298 | 33% helix, 15% strand | P24941 |
| B | Speedy protein a | protein | 142 | 67% helix, 3% strand | Q5MJ70 |
| C | Sun domain-containing protein 1 | protein | 19 | 0% helix, 21% strand | O94901 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.69 | 0.86 | 26 | empty |
| 2 | 95 | 0.40 | 0.77 | 18 | empty |
| 3 | 50 | 0.34 | 0.80 | 14 | empty |
| 4 | 64 | 0.32 | 0.75 | 15 | empty |
| 5 | 63 | 0.28 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1549 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1136 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 366 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7E34 · Crystal structure of SUN1-Speedy A-CDK2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5MJ70 · AlphaFold monomer V2.0 prediction for speedy protein a (Q5MJ70) · a predicted model of the same protein · chain B against A, TM-score 0.98
- 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
- O94901 · AlphaFold monomer V2.0 prediction for sun domain-containing protein 1 (O94901) · a predicted model of the same protein · chain C against A, TM-score 0.25
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 Q5MJ70
- Every structure of UniProt O94901
- Elsewhere: RCSB PDB 7E34 · PDBe 7E34 · UniProt P24941 · UniProt Q5MJ70 · UniProt O94901
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