MolNFT v1 · #49625 · protein
The crystal structure of PCSK9 at 1.9 ångströms resolution reveals structural homology to resistin within the C-terminal domain
2QTW · Proprotein convertase SUBTILISIN/KEXIN type 9 propeptide: “The crystal structure of PCSK9 at 1.9 ångströms resolution reveals structural homology to resistin within the…”. X-ray diffraction, 2 ligands (NAG, CA), 5 pockets (best…
- PDB
- 2QTW
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9 propeptide; Proprotein convertase…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- NAG, CA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 propeptide (EC 3.4.21.-) | protein | 92 | 30% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 486 | 17% helix, 39% strand | Q8NBP7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.73 | 0.82 | 56 | CA |
| 2 | 400 | 0.69 | 0.81 | 49 | empty |
| 3 | 167 | 0.44 | 0.74 | 35 | empty |
| 4 | 51 | 0.40 | 0.82 | 16 | empty |
| 5 | 67 | 0.34 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1381 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2QTW · The Crystal Structure of PCSK9 at 1.9 Angstroms Resolution Reveals structural homology to… · 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 2QTW · PDBe 2QTW · UniProt Q8NBP7
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