MolNFT v1 · #56737 · protein
Human factor viia-tissue factor complexed with benzylsulfonamide-D- ile-gln-P-aminobenzamidine
2ZP0 · Factor VII light chain: “Human factor viia-tissue factor complexed with benzylsulfonamide-D- ile-gln-P-aminobenzamidine”. X-ray diffraction, 4 ligands (PI0, BGC, FUC), 8 pockets (best druggability 0.63). MolNFT v1 #56737 on…
- PDB
- 2ZP0
- Type
- protein
- Length
- 587 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor VII light chain; Factor VII heavy chain; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- PI0, BGC, FUC, CA
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Factor VII light chain (EC 3.4.21.21) | protein | 142 | 26% helix, 18% strand | P08709 |
| H | Factor VII heavy chain (EC 3.4.21.21) | protein | 254 | 15% helix, 36% strand | P08709 |
| T | Tissue factor | protein | 191 | 8% helix, 50% strand | P13726 |
Ligands and binding sites
- PI0 · (2S)-N-[(4-carbamimidoylphenyl)methyl]-2-[[(2R,3R)-3-methyl-2-(phenylmethylsulfonylamino)pentanoyl]amino]pentanediamide · ligand · chains H
- BGC · beta-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- CA · Calcium ion · metal · 9 copies · chains L, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.63 | 0.78 | 48 | empty |
| 2 | 191 | 0.57 | 0.81 | 34 | PI0 |
| 3 | 120 | 0.48 | 0.79 | 23 | empty |
| 4 | 111 | 0.47 | 0.80 | 23 | empty |
| 5 | 151 | 0.45 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–T · 1431 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1014 Ų buried · 15 hydrogen bonds · protein-protein
- H–T · 590 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 modified, 2 glycan (disulfide, carboxylation, O-glycosylation).
Compared structures
- 2ZP0 · Human factor viia-tissue factor complexed with… · 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 0.99
- 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 2ZP0 · PDBe 2ZP0 · UniProt P08709 · UniProt P13726
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