Research workbench
The cidra domain from IT4VAR07 PFEMP1 bound to endothelial protein C receptor
Analyse The cidra domain from IT4VAR07 PFEMP1 bound to endothelial protein C receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V3E
- Type
- protein
- Length
- 359 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IT4VAR07 cidra; Endothelial protein C receptor
- UniProt
- Q9UNN8
- Ligands
- PTY, NAG, MAN
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IT4VAR07 cidra | protein | 192 | 56% helix, 9% strand | — |
| B | Endothelial protein C receptor | protein | 167 | 37% helix, 38% strand | Q9UNN8 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.83 | 0.88 | 59 | PTY |
| 2 | 131 | 0.74 | 0.93 | 24 | empty |
| 3 | 66 | 0.32 | 0.75 | 12 | empty |
| 4 | 57 | 0.26 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1001 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4V3E · The CIDRa domain from IT4var07 PfEMP1 bound to endothelial protein C receptor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UNN8 · AlphaFold monomer V2.0 prediction for endothelial protein C receptor (Q9UNN8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 4V3E · PDBe 4V3E · UniProt Q9UNN8
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