MolNFT v1 · #130343 · protein
Crystal structure of factor viia in complex with N-(2-amino-1H- benzimidazol-5-yl)-2-[3-[(2-amino-2-oxoethyl)-methylsulfonylamino]-5- CHLOROPHENYL]ACETAMIDE;2,2,2-trifluoroacetic acid
5PAF · Coagulation factor VII light chain: “Crystal structure of factor viia in complex with N-(2-amino-1H…”. X-ray diffraction, 4 ligands (7LR, CA, SO4), 3 pockets (best druggability 0.42). MolNFT v1 #130343 on GenesisL1: 3D structure…
- PDB
- 5PAF
- Type
- protein
- Length
- 308 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
- 7LR, CA, SO4, CL
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VII light chain (EC 3.4.21.21) | protein | 58 | 19% helix, 28% strand | P08709 |
| B | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 250 | 14% helix, 38% strand | P08709 |
Ligands and binding sites
- 7LR · N-(2-amino-1H-benzimidazol-5-yl)-2-[3-[(2-amino-2-oxoethyl)-methylsulfonylamino]-5-chlorophenyl]acetamide · ligand · chains B
- CA · Calcium ion · metal · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
- TFA · trifluoroacetic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.42 | 0.76 | 32 | SO4, 7LR |
| 2 | 65 | 0.41 | 0.80 | 15 | GOL |
| 3 | 122 | 0.40 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1033 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 5PAF · PDBe 5PAF · UniProt P08709
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