Research workbench
Importance of MG2+ in the CA2+-dependent folding of the gamma- carboxyglutamic acid domains of vitamin K-dependent clotting and anticlotting proteins
Analyse Importance of MG2+ in the CA2+-dependent folding of the gamma- carboxyglutamic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JTC
- Type
- protein
- Length
- 411 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endothelial protein C receptor; Vitamin K-dependent protein C
- EC
- 3.4.21.69
- UniProt
- Q9UNN8, P04070
- Ligands
- PTY, NAG, CA, MG
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endothelial protein C receptor | protein | 172 | 35% helix, 38% strand | Q9UNN8 |
| B | Endothelial protein C receptor | protein | 173 | 36% helix, 37% strand | Q9UNN8 |
| C, D | Vitamin K-dependent protein C (EC 3.4.21.69) | protein | 33 | 52% helix, 0% strand | P04070 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- CA · Calcium ion · metal · 10 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.82 | 0.88 | 60 | PTY |
| 2 | 539 | 0.82 | 0.87 | 63 | PTY |
Interfaces
3 interfaces between chains.
- B–D · 492 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 489 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 46 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 modified, 6 glycan, 4 disulfide (carboxylation, N-glycosylation, disulfide).
Compared structures
- 3JTC · Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UNN8 · AlphaFold monomer V2.0 prediction for endothelial protein C receptor (Q9UNN8) · a predicted model of the same protein · chain A against A, 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 C against A, TM-score 0.84
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 Q9UNN8
- Every structure of UniProt P04070
- Elsewhere: RCSB PDB 3JTC · PDBe 3JTC · UniProt Q9UNN8 · UniProt P04070
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