Research workbench
MG2+ is required for optimal folding of the gamma-carboxyglutamic acid (gla) domains of vitamin K-dependent clotting factors at physiological CA2+
Analyse MG2+ is required for optimal folding of the gamma-carboxyglutamic acid (gla)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TH3
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII light chain; Coagulation factor VII heavy chain; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- 0GE, FUC, BGC, CA, CL
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII light chain (EC 3.4.21.21) | protein | 96 | 7% helix, 23% strand | P08709 |
| H | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 254 | 14% helix, 36% strand | P08709 |
| T | Tissue factor | protein | 154 | 11% helix, 40% strand | P13726 |
Ligands and binding sites
- 0GE · N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-alpha-glutamyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]glycinamide · ligand · chains H
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- BGC · beta-D-glucopyranose · sugar · chains L
- CA · Calcium ion · metal · 2 copies · chains L, H
- CL · Chloride ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.67 | 0.82 | 48 | empty |
| 2 | 92 | 0.48 | 0.81 | 17 | empty |
| 3 | 154 | 0.47 | 0.77 | 23 | empty |
| 4 | 139 | 0.46 | 0.77 | 21 | empty |
| 5 | 145 | 0.45 | 0.77 | 34 | 0GE |
Interfaces
3 interfaces between chains.
- L–H · 1008 Ų buried · 13 hydrogen bonds · protein-protein
- L–T · 968 Ų buried · 13 hydrogen bonds · protein-protein
- H–T · 649 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, O-glycosylation).
Compared structures
- 3TH3 · Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of… · the same entry in another collection · chain T against T, TM-score 1.00
- P13726 · AlphaFold monomer V2.0 prediction for tissue factor (P13726) · a predicted model of the same protein · chain T against A, TM-score 0.98
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain H against A, TM-score 0.97
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 P08709
- Every structure of UniProt P13726
- Elsewhere: RCSB PDB 3TH3 · PDBe 3TH3 · UniProt P08709 · UniProt P13726
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