Research workbench
PCSK9(DELTACRD) in complex with cyclic peptide 35
Analyse PCSK9(DELTACRD) in complex with cyclic peptide 35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S5H
- Type
- protein
- Length
- 330 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pro-peptide from proprotein convertase SUBTILISIN/KEXIN type 9; Proprotein convertase…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- 8DN, MPT, DHL, 89N
- Pockets
- 1 · best druggability 0.24
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pro-peptide from proprotein convertase SUBTILISIN/KEXIN type 9 | protein | 92 | 30% helix, 41% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 230 | 33% helix, 26% strand | Q8NBP7 |
| C | Z03-Z02-dnp-dal-phe-ftr-pro-thr-0A1-3WX-Z04-Z05 | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- 8DN · 1-(3,5-dimethylphenyl)-4-methyl-1H-1,2,3-triazole · ligand · chains C
- MPT · Beta-mercaptopropionic acid · ligand · chains B, C
- DHL · 2-amino-ethanethiol · ligand · chains B, C
- 89N · (2E)-but-2-ene-1,4-diol · ligand · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.24 | 0.72 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1317 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 418 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent, 4 modified, 3 disulfide, 1 d-amino (covalent ligand, nonstandard, disulfide, D-amino acid).
Compared structures
- 7S5H · PCSK9(deltaCRD) in complex with cyclic peptide 35 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8NBP7
- Elsewhere: RCSB PDB 7S5H · PDBe 7S5H · UniProt Q8NBP7
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