Research workbench
Crystal structure of dfpr-VIIA/STF
Analyse Crystal structure of dfpr-VIIA/STF in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FIR
- Type
- protein
- Length
- 587 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 (ec 3.4.21.21)…
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- 0G7, GLC, FUC, CA, MG, ZN, NA, CL
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII light chain (EC 3.4.21.21) | protein | 142 | 25% helix, 17% strand | P08709 |
| H | Coagulation factor VII heavy chain (ec 3.4.21.21) | protein | 254 | 12% helix, 37% strand | P08709 |
| T | Tissue factor | protein | 191 | 10% helix, 47% strand | P13726 |
Ligands and binding sites
- 0G7 · D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide · ligand · chains H
- GLC · alpha-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- CA · Calcium ion · metal · 6 copies · chains L, H
- MG · Magnesium ion · metal · 3 copies · chains L
- ZN · Zinc ion · metal · 2 copies · chains H
- NA · Sodium ion · metal · chains H
- CL · Chloride ion · ion · 3 copies · chains H, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.59 | 0.81 | 31 | empty |
| 2 | 175 | 0.52 | 0.78 | 25 | empty |
| 3 | 53 | 0.51 | 0.87 | 17 | empty |
| 4 | 78 | 0.48 | 0.83 | 17 | empty |
| 5 | 134 | 0.48 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–T · 1335 Ų buried · 14 hydrogen bonds · protein-protein
- L–H · 1019 Ų buried · 15 hydrogen bonds · protein-protein
- H–T · 617 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 modified, 1 covalent (disulfide, carboxylation, covalent ligand).
Compared structures
- 2FIR · Crystal structure of DFPR-VIIa/sTF · the same entry in another collection · chain L against L, 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 2FIR · PDBe 2FIR · UniProt P08709 · UniProt P13726
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