Research workbench
Crystal structure of human activated protein C (apc) complexed with ppack
Analyse Crystal structure of human activated protein C (apc) complexed with ppack in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F6U
- Type
- protein
- Length
- 338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin K-dependent protein C heavy chain; Vitamin K-dependent protein C light chain
- EC
- 3.4.21.69
- UniProt
- P04070
- Ligands
- 0G6, NA, CA
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Vitamin K-dependent protein C heavy chain (EC 3.4.21.69) | protein | 240 | 12% helix, 36% strand | P04070 |
| L | Vitamin K-dependent protein C light chain (EC 3.4.21.69) | protein | 98 | 4% helix, 24% strand | P04070 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains H
- NA · Sodium ion · metal · chains H
- CA · Calcium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.44 | 0.77 | 20 | empty |
| 2 | 77 | 0.36 | 0.77 | 21 | 0G6 |
| 3 | 83 | 0.33 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- H–L · 904 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 3F6U · Crystal structure of human Activated Protein C (APC) complexed with PPACK · the same entry in another collection · chain H against H, TM-score 1.00
- P04070 · AlphaFold monomer V2.0 prediction for vitamin K-dependent protein C (P04070) · a predicted model of the same protein · chain H against A, TM-score 0.95
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 P04070
- Elsewhere: RCSB PDB 3F6U · PDBe 3F6U · UniProt P04070
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