Research workbench
Crystal structure of factor VII.STF complexed with PD0297121
Analyse Crystal structure of factor VII.STF complexed with PD0297121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C4F
- Type
- protein
- Length
- 584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII precursor; Tissue factor precursor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- GIL, GLC, FUC, NAG, CA
- Pockets
- 10 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Coagulation factor VII precursor (EC 3.4.21.21) | protein | 254 | 12% helix, 37% strand | P08709 |
| L | Coagulation factor VII precursor (EC 3.4.21.21) | protein | 139 | 29% helix, 19% strand | P08709 |
| T | Tissue factor precursor | protein | 75 | 5% helix, 57% strand | P13726 |
| U | Tissue factor precursor | protein | 116 | 10% helix, 46% strand | P13726 |
Ligands and binding sites
- GIL · 2-{[6-{3-[amino(imino)methyl]phenoxy}-4-(diisopropylamino)-3,5-difluoropyridin-2-yl]oxy}-5-[(isobutylamino)carbonyl]ben zoic acid · ligand · chains H
- GLC · alpha-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, U
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains U
- CA · Calcium ion · metal · 5 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.52 | 0.77 | 29 | empty |
| 2 | 170 | 0.49 | 0.77 | 22 | empty |
| 3 | 104 | 0.49 | 0.81 | 24 | empty |
| 4 | 71 | 0.45 | 0.82 | 17 | empty |
| 5 | 91 | 0.45 | 0.80 | 21 | empty |
Interfaces
6 interfaces between chains.
- T–U · 1250 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 1034 Ų buried · 16 hydrogen bonds · protein-protein
- L–U · 875 Ų buried · 6 hydrogen bonds · protein-protein
- L–T · 637 Ų buried · 10 hydrogen bonds · protein-protein
- H–T · 352 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 modified, 1 glycan (disulfide, carboxylation, N-glycosylation).
Compared structures
- 2C4F · crystal structure of factor VII.stf complexed with pd0297121 · the same entry in another collection · chain U against U, 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 0.99
- 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 2C4F · PDBe 2C4F · UniProt P08709 · UniProt P13726
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