Research workbench
Crystal structure of factor viia in complex with N-[[4-(aminomethyl)- 2-(2-amino-2-OXOETHOXY)PHENYL]METHYL]-2-(4-hydroxyphenyl)-2- METHOXYACETAMIDE;HYDROCHLORIDE
Analyse Crystal structure of factor viia in complex with N-[[4-(aminomethyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5PAK
- Type
- protein
- Length
- 307 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII light chain; Coagulation factor VII heavy chain
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- 7YP, CA, SO4
- Pockets
- 4 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VII light chain (EC 3.4.21.21) | protein | 57 | 18% helix, 28% strand | P08709 |
| C | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 250 | 15% helix, 37% strand | P08709 |
Ligands and binding sites
- 7YP · (2~{S})-~{N}-[[4-(aminomethyl)-2-(2-azanyl-2-oxidanylidene-ethoxy)phenyl]methyl]-2-(4-hydroxyphenyl)-2-methoxy-ethanami de · ligand · chains C
- CA · Calcium ion · metal · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.43 | 0.75 | 33 | 7YP |
| 2 | 56 | 0.41 | 0.81 | 20 | empty |
| 3 | 130 | 0.41 | 0.75 | 19 | empty |
| 4 | 59 | 0.41 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 1040 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain C 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
- Elsewhere: RCSB PDB 5PAK · PDBe 5PAK · UniProt P08709
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