MolNFT v1 · #4676 · protein
Crystal structure of the complex between the peptide exosite inhibitor E-76 and coagulation factor viia
1DVA · Des-gla factor viia (heavy chain): “Crystal structure of the complex between the peptide exosite inhibitor E-76 and coagulation factor viia”. X-ray diffraction, 8 ligands (ACE, 0Z6, FUC), 10 pockets (best druggability 0.75). MolNFT…
- PDB
- 1DVA
- Type
- protein
- Length
- 744 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Des-gla factor viia (heavy chain); Des-gla factor viia (light chain); Peptide E-76
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- ACE, 0Z6, FUC, BGC, GAL, GLC, FUL, CA
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, I | Des-gla factor viia (heavy chain) (EC 3.4.21.21) | protein | 254 | 13% helix, 33% strand | P08709 |
| L, M | Des-gla factor viia (light chain) (EC 3.4.21.21) | protein | 101 | 8% helix, 31% strand | P08709 |
| X, Y | Peptide E-76 | protein | 17 | 24% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains X, Y
- 0Z6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide · ligand · 2 copies · chains H, I
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains L, M
- BGC · beta-D-glucopyranose · sugar · chains L
- GAL · beta-D-galactopyranose · sugar · chains L, M
- GLC · alpha-D-glucopyranose · sugar · chains M
- FUL · beta-L-fucopyranose · sugar · chains M
- CA · Calcium ion · metal · 4 copies · chains H, L, I, M
- CAC · Cacodylate ion · additive · 2 copies · chains H, I
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 | 1181 | 0.75 | 0.78 | 86 | empty |
| 2 | 691 | 0.71 | 0.78 | 67 | empty |
| 3 | 64 | 0.56 | 0.88 | 17 | CAC |
| 4 | 122 | 0.41 | 0.75 | 23 | 0Z6 |
| 5 | 101 | 0.40 | 0.76 | 24 | 0Z6 |
Interfaces
8 interfaces between chains.
- H–L · 953 Ų buried · 13 hydrogen bonds · protein-protein
- I–M · 945 Ų buried · 12 hydrogen bonds · protein-protein
- H–X · 633 Ų buried · 10 hydrogen bonds · protein-protein
- I–Y · 628 Ų buried · 10 hydrogen bonds · protein-protein
- L–I · 329 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 6 covalent, 4 glycan (disulfide, covalent ligand, O-glycosylation).
Compared structures
- 1DVA · Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and… · the same entry in another collection · chain Y against Y, TM-score 1.00
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain I against A, TM-score 0.95
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
- Elsewhere: RCSB PDB 1DVA · PDBe 1DVA · UniProt P08709
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