MolNFT v1 · #54581 · protein
The crystal structure of PCSK9 in complex with 1D05 Fab
2XTJ · Proprotein convertase SUBTILISIN/KEXIN type 9: “The crystal structure of PCSK9 in complex with 1D05 Fab”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.57). MolNFT v1 #54581 on GenesisL1: 3D structure, binding…
- PDB
- 2XTJ
- Type
- protein
- Length
- 782 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; Fab from a human monoclonal antibody…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- CA
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 242 | 30% helix, 26% strand | Q8NBP7 |
| B | Fab from a human monoclonal antibody, 1D05 | protein | 107 | 3% helix, 50% strand | — |
| C | Fab from a human monoclonal antibody, 1D05 | protein | 105 | 10% helix, 52% strand | — |
| D | Fab from a human monoclonal antibody, 1D05 | protein | 131 | 5% helix, 52% strand | — |
| E | Fab from a human monoclonal antibody, 1D05 | protein | 105 | 9% helix, 50% strand | — |
| P | Proprotein convertase subtilisin-kexin type 9 (EC 3.4.21.-) | protein | 92 | 28% helix, 39% strand | Q8NBP7 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.57 | 0.74 | 49 | empty |
| 2 | 204 | 0.52 | 0.77 | 32 | empty |
| 3 | 136 | 0.41 | 0.74 | 29 | empty |
| 4 | 85 | 0.38 | 0.77 | 18 | empty |
| 5 | 91 | 0.38 | 0.76 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–P · 1261 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 1056 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 814 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 752 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 412 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 2XTJ · The crystal structure of PCSK9 in complex with 1D05 Fab · 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 2XTJ · PDBe 2XTJ · UniProt Q8NBP7
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