MolNFT v1 · #63180 · protein
Crystal structure of protein Z complexed with protein Z-dependent inhibitor
3F1S · Protein Z-dependent protease inhibitor: “Crystal structure of protein Z complexed with protein Z-dependent inhibitor”. X-ray diffraction, 2 ligands (NAG, CL), 8 pockets (best druggability 0.70). MolNFT v1 #63180 on GenesisL1: 3D…
- PDB
- 3F1S
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein Z-dependent protease inhibitor; Vitamin K-dependent protein Z
- UniProt
- Q9UK55, P22891
- Ligands
- NAG, CL
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein Z-dependent protease inhibitor | protein | 385 | 31% helix, 31% strand | Q9UK55 |
| B | Vitamin K-dependent protein Z | protein | 259 | 15% helix, 33% strand | P22891 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A, B
- FLC · Citrate anion · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.70 | 0.79 | 67 | empty |
| 2 | 158 | 0.53 | 0.80 | 29 | empty |
| 3 | 80 | 0.49 | 0.83 | 25 | EDO |
| 4 | 68 | 0.47 | 0.83 | 19 | empty |
| 5 | 90 | 0.44 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1337 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3F1S · Crystal structure of Protein Z complexed with protein Z-dependent inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UK55 · AlphaFold monomer V2.0 prediction for protein Z-dependent protease inhibitor (Q9UK55) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P22891 · AlphaFold monomer V2.0 prediction for vitamin K-dependent protein Z (P22891) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9UK55
- Every structure of UniProt P22891
- Elsewhere: RCSB PDB 3F1S · PDBe 3F1S · UniProt Q9UK55 · UniProt P22891
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