Research workbench
X-ray structure of protein Z-protein Z inhibitor complex
Analyse X-ray structure of protein Z-protein Z inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H5C
- Type
- protein
- Length
- 696 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, BGC
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein Z-dependent protease inhibitor | protein | 384 | 30% helix, 29% strand | Q9UK55 |
| B | Vitamin K-dependent protein Z | protein | 312 | 10% helix, 28% strand | P22891 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.77 | 0.91 | 32 | empty |
| 2 | 203 | 0.63 | 0.83 | 25 | empty |
| 3 | 143 | 0.60 | 0.84 | 24 | empty |
| 4 | 129 | 0.56 | 0.82 | 17 | empty |
| 5 | 133 | 0.53 | 0.81 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1311 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 7 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 3H5C · X-Ray Structure of Protein Z-Protein Z Inhibitor Complex · 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 0.96
- 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 0.96
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 3H5C · PDBe 3H5C · UniProt Q9UK55 · UniProt P22891
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