MolNFT v1 · #111950 · protein
Crystal structure of a fviia-trypsin chimera (yt) in complex with soluble tissue factor
4Z6A · Coagulation factor VII: “Crystal structure of a fviia-trypsin chimera (yt) in complex with soluble tissue factor”. X-ray diffraction, 4 ligands (0Z6, BGC, FUC), 7 pockets (best druggability 0.57). MolNFT v1 #111950 on GenesisL1: 3D…
- PDB
- 4Z6A
- Type
- protein
- Length
- 544 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
- 7 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 94 | 13% helix, 23% strand | P08709 |
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 249 | 12% helix, 37% strand | P08709 |
| T | Tissue factor | protein | 201 | 8% helix, 50% 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 · chains H
- CIT · Citric acid · additive · chains T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.57 | 0.80 | 31 | empty |
| 2 | 121 | 0.50 | 0.80 | 25 | empty |
| 3 | 109 | 0.44 | 0.78 | 29 | 0Z6 |
| 4 | 112 | 0.44 | 0.78 | 24 | empty |
| 5 | 135 | 0.43 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1034 Ų buried · 13 hydrogen bonds · protein-protein
- L–T · 928 Ų buried · 13 hydrogen bonds · protein-protein
- H–T · 627 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 3 covalent, 1 glycan (disulfide, covalent ligand, O-glycosylation).
Compared structures
- 4Z6A · Crystal Structure of a FVIIa-Trypsin Chimera (YT) 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 4Z6A · PDBe 4Z6A · UniProt P08709 · UniProt P13726
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