Research workbench
X-ray structure of soluble epcr in P212121 space group
Analyse X-ray structure of soluble epcr in P212121 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OKS
- Type
- protein
- Length
- 671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endothelial protein C receptor
- UniProt
- Q9UNN8
- Ligands
- PTY, NAG, FUC, BMA, MAN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endothelial protein C receptor | protein | 168 | 39% helix, 38% strand | Q9UNN8 |
| B | Endothelial protein C receptor | protein | 167 | 37% helix, 38% strand | Q9UNN8 |
| C | Endothelial protein C receptor | protein | 166 | 39% helix, 37% strand | Q9UNN8 |
| D | Endothelial protein C receptor | protein | 170 | 36% helix, 39% strand | Q9UNN8 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, C, D
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.83 | 0.84 | 101 | NAG, PTY |
| 2 | 462 | 0.82 | 0.88 | 52 | PTY |
| 3 | 641 | 0.80 | 0.85 | 65 | PTY |
| 4 | 545 | 0.79 | 0.85 | 62 | PTY |
| 5 | 185 | 0.53 | 0.78 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 720 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 500 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 393 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 207 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 4 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 7OKS · PDBe 7OKS · UniProt Q9UNN8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.