MolNFT v1 · #130342 · protein
Crystal structure of factor viia in complex with (2S)-2-hydroxy-N-[[3- [5-hydroxy-4-(1H-PYRROLO[3,2-C]PYRIDIN-2-YL)PYRAZOL-1- YL]PHENYL]METHYL]PROPANAMIDE
5PAE · Coagulation factor VII light chain: “Crystal structure of factor viia in complex with (2S)-2-hydroxy-N-[[3…”. X-ray diffraction, 3 ligands (7YA, CA, SO4), 2 pockets (best druggability 0.50). MolNFT v1 #130342 on GenesisL1: 3D…
- PDB
- 5PAE
- Type
- protein
- Length
- 303 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
- 7YA, CA, SO4
- Pockets
- 2 · best druggability 0.50
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 | 56 | 16% helix, 29% strand | P08709 |
| B | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 247 | 14% helix, 38% strand | P08709 |
Ligands and binding sites
- 7YA · (2S)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]propanamide · ligand · chains B
- CA · Calcium ion · metal · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.50 | 0.77 | 38 | 7YA |
| 2 | 132 | 0.43 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1051 Ų buried · 16 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 B 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 5PAE · PDBe 5PAE · UniProt P08709
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