Research workbench
PCSK9(DELTACRD) in complex with cyclic peptide 77
Analyse PCSK9(DELTACRD) in complex with cyclic peptide 77 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XIE
- Type
- protein
- Length
- 379 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; Peptide 77
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- B74
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 92 | 29% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 277 | 30% helix, 25% strand | Q8NBP7 |
| I | Peptide 77 | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
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 | 56 | 0.26 | 0.73 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1331 Ų buried · 27 hydrogen bonds · protein-protein
- B–I · 505 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 3 disulfide, 2 covalent, 1 d-amino (nonstandard, disulfide, covalent ligand, D-amino acid).
Compared structures
- 6XIE · PCSK9(deltaCRD) in complex with cyclic peptide 77 · 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 6XIE · PDBe 6XIE · UniProt Q8NBP7
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