MolNFT v1 · #94942 · protein
Rubidium sites in blood coagulation factor viia
4IBL: “Rubidium sites in blood coagulation factor viia”. X-ray diffraction, 7 ligands (BEN, BGC, FUC), 9 pockets (best druggability 0.60). MolNFT v1 #94942 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4IBL
- Type
- protein
- Length
- 592 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- BEN, BGC, FUC, RB, CA, MG, CL
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 140 | 27% helix, 22% strand | P08709 |
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 254 | 15% helix, 37% strand | P08709 |
| T | Tissue factor | protein | 198 | 8% helix, 51% strand | P13726 |
Ligands and binding sites
- BEN · Benzamidine · ligand · chains H
- BGC · beta-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- RB · Rubidium ion · metal · 6 copies · chains L, H
- CA · Calcium ion · metal · 4 copies · chains L, H
- MG · Magnesium ion · metal · 3 copies · chains L
- CL · Chloride ion · ion · 4 copies · chains H, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.60 | 0.82 | 25 | CL |
| 2 | 51 | 0.54 | 0.89 | 16 | empty |
| 3 | 192 | 0.52 | 0.78 | 26 | empty |
| 4 | 95 | 0.49 | 0.81 | 18 | empty |
| 5 | 130 | 0.46 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- L–T · 1436 Ų buried · 20 hydrogen bonds · protein-protein
- L–H · 1036 Ų buried · 16 hydrogen bonds · protein-protein
- H–T · 634 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 modified, 2 glycan (disulfide, carboxylation, O-glycosylation).
Compared structures
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 4IBL · PDBe 4IBL · UniProt P08709 · UniProt P13726
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