Research workbench
PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl- WNLK(HR)IGLLR - NH2
Analyse PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U2F
- Type
- protein
- Length
- 1,026 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; Organo-peptide PCSK9 inhibitor; 7G7 heavy…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7, Q569X1, A0A0U5BC76
- Ligands
- PQG, CA
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 582 | 18% helix, 38% strand | Q8NBP7 |
| B | Organo-peptide PCSK9 inhibitor | protein | 10 | 40% helix, 0% strand | — |
| H | 7G7 heavy chain | protein | 220 | 5% helix, 53% strand | Q569X1 |
| L | 7G7 light chain | protein | 214 | 7% helix, 49% strand | A0A0U5BC76 |
Ligands and binding sites
- PQG · Cis-1-amino-4-phenylcyclohexane-1-carboxylic acid · ligand · chains A, B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.74 | 0.80 | 75 | empty |
| 2 | 273 | 0.71 | 0.86 | 38 | empty |
| 3 | 596 | 0.64 | 0.75 | 64 | empty |
| 4 | 364 | 0.64 | 0.79 | 44 | empty |
| 5 | 295 | 0.52 | 0.74 | 33 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1951 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 879 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 337 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 6U2F · PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)IGLLR - NH2 · 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
- Every structure of UniProt Q569X1
- Every structure of UniProt A0A0U5BC76
- Elsewhere: RCSB PDB 6U2F · PDBe 6U2F · UniProt Q8NBP7 · UniProt Q569X1 · UniProt A0A0U5BC76
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