Research workbench
Crystal structure of a fviia-trypsin chimera (st) in complex with soluble tissue factor
Analyse Crystal structure of a fviia-trypsin chimera (st) in complex with soluble… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZMA
- Type
- protein
- Length
- 586 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
- 0Z6, BGC, FUC, CA
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 141 | 30% helix, 18% strand | P08709 |
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 247 | 12% helix, 36% strand | P08709 |
| T | Tissue factor | protein | 198 | 9% helix, 46% strand | P13726 |
Ligands and binding sites
- 0Z6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide · ligand · chains H
- BGC · beta-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- CA · Calcium ion · metal · 8 copies · chains L, H
- CAC · Cacodylate ion · additive · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.57 | 0.81 | 32 | empty |
| 2 | 261 | 0.56 | 0.77 | 42 | empty |
| 3 | 140 | 0.51 | 0.80 | 23 | empty |
| 4 | 103 | 0.47 | 0.80 | 20 | empty |
| 5 | 79 | 0.45 | 0.82 | 20 | 0Z6 |
Interfaces
3 interfaces between chains.
- L–T · 1251 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1000 Ų buried · 11 hydrogen bonds · protein-protein
- H–T · 624 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 modified, 4 covalent, 2 glycan (disulfide, carboxylation, covalent ligand, O-glycosylation, additive adduct).
Compared structures
- 4ZMA · Crystal Structure of a FVIIa-Trypsin Chimera (ST) in Complex with Soluble Tissue Factor · 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 0.98
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 4ZMA · PDBe 4ZMA · UniProt P08709 · UniProt P13726
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