Research workbench
Short PCSK9 delta-P' complex with peptide PEP3
Analyse Short PCSK9 delta-P' complex with peptide PEP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VLL
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- ACE, CA, NH2
- Pockets
- 2 · best druggability 0.27
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 355 | 30% helix, 29% strand | Q8NBP7 |
| Y | Cys-phe-ile-pro-TRP-asn-leu-gln-arg-ile-gly-leu-leu-cys | protein | 14 | 36% helix, 0% strand | — |
| Z | ACE-thr-val-phe-thr-ser-TRP-glu-glu-tyr-leu-asp-TRP-val- NH2 | protein | 13 | 54% helix, 8% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, Z
- CA · Calcium ion · metal · chains A
- NH2 · Amino group · ion · chains Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.27 | 0.73 | 17 | empty |
| 2 | 58 | 0.25 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–Y · 525 Ų buried · 7 hydrogen bonds · protein-protein
- A–Z · 355 Ų buried · 4 hydrogen bonds · protein-protein
- Y–Z · 115 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5VLL · Short PCSK9 delta-P' complex with peptide Pep3 · 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 5VLL · PDBe 5VLL · UniProt Q8NBP7
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