Research workbench
Structural and thermodynamic consequences of cyclization of peptide ligands for the recruitment site of cyclin a
Analyse Structural and thermodynamic consequences of cyclization of peptide ligands for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WMA
- Type
- protein
- Length
- 1,084 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin-A2; Cyclic rklfn-NH2
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 297 | 36% helix, 15% strand | P24941 |
| B, D | Cyclin-A2 | protein | 258 | 67% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 266 | 24% helix, 20% strand | P24941 |
| E | Cyclic rklfn-NH2 | protein | 5 | 0% helix, 0% strand | — |
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.80 | 0.99 | 24 | empty |
| 2 | 108 | 0.80 | 0.99 | 22 | empty |
| 3 | 785 | 0.75 | 0.79 | 74 | empty |
| 4 | 174 | 0.66 | 0.86 | 22 | empty |
| 5 | 326 | 0.62 | 0.79 | 38 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1876 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1763 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 510 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 498 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 402 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 isopeptide (phosphorylation, isopeptide).
Compared structures
- 2WMA · Structural and thermodynamic consequences of cyclization of peptide ligands for the… · the same entry in another collection · chain E against E, 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 2WMA · PDBe 2WMA · UniProt P24941 · UniProt P20248
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