Research workbench
Cyclin a binding groove inhibitor H-arg-arg-leu-asn-(P-F-phe)-NH2
Analyse Cyclin a binding groove inhibitor H-arg-arg-leu-asn-(P-F-phe)-NH2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OL2
- Type
- protein
- Length
- 1,118 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2; Arg-arg-leu-asn-pff-NH2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- NH2
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 34% helix, 16% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 65% helix, 0% strand | P20248 |
| E, F | Arg-arg-leu-asn-pff-NH2 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 2 copies · chains B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.80 | 0.98 | 22 | empty |
| 2 | 110 | 0.79 | 0.98 | 21 | empty |
| 3 | 1170 | 0.75 | 0.77 | 99 | empty |
| 4 | 209 | 0.67 | 0.85 | 31 | empty |
| 5 | 517 | 0.66 | 0.77 | 46 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1770 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1738 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 567 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 433 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1OL2 · Cyclin A binding groove inhibitor H-Arg-Arg-Leu-Asn-(p-F-Phe)-NH2 · 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 0.99
- 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 0.92
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 1OL2 · PDBe 1OL2 · UniProt P24941 · UniProt P20248
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.