Research workbench
PCSK9(DELTACRD) in complex with phage-derived inhibitory peptide 2-8
Analyse PCSK9(DELTACRD) in complex with phage-derived inhibitory peptide 2-8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NMX
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; Peptide 2-8
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- ACE, NH2
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 | protein | 92 | 30% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 278 | 29% helix, 25% strand | Q8NBP7 |
| Z | Peptide 2-8 | protein | 13 | 54% helix, 8% strand | — |
Ligands and binding sites
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 | 69 | 0.31 | 0.75 | 18 | empty |
| 2 | 60 | 0.26 | 0.72 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1341 Ų buried · 28 hydrogen bonds · protein-protein
- B–Z · 414 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4NMX · PCSK9(deltaCRD) in complex with phage-derived inhibitory peptide 2-8 · the same entry in another collection · chain B against B, 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 4NMX · PDBe 4NMX · UniProt Q8NBP7
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