MolNFT v1 · #164121 · protein
Synthetic mimic of an epcr-binding PFEMP1 bound to epcr
6SNY · Synthetic epcr binding protein: “Synthetic mimic of an epcr-binding PFEMP1 bound to epcr”. X-ray diffraction, 3 ligands (PTY, NAG, MAN), 7 pockets (best druggability 0.82). MolNFT v1 #164121 on GenesisL1: 3D structure, binding sites…
- PDB
- 6SNY
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synthetic epcr binding protein; Endothelial protein C receptor
- UniProt
- Q9UNN8
- Ligands
- PTY, NAG, MAN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Synthetic epcr binding protein | protein | 107 | 84% helix, 0% strand | — |
| B, C | Endothelial protein C receptor | protein | 169 | 34% helix, 38% strand | Q9UNN8 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 2 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains B, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.82 | 0.86 | 70 | PTY |
| 2 | 568 | 0.80 | 0.85 | 62 | PTY |
| 3 | 256 | 0.63 | 0.81 | 30 | empty |
| 4 | 216 | 0.51 | 0.76 | 30 | empty |
| 5 | 82 | 0.49 | 0.82 | 20 | empty |
Interfaces
2 interfaces between chains.
- B–C · 747 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 663 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 3 disulfide (N-glycosylation, 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 Q9UNN8
- Elsewhere: RCSB PDB 6SNY · PDBe 6SNY · UniProt Q9UNN8
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