Research workbench
The cidra domain from HB3VAR03 PFEMP1 bound to endothelial protein C receptor
Analyse The cidra domain from HB3VAR03 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
- 4V3D
- Type
- protein
- Length
- 733 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HB3VAR03 cidra domain; Endothelial protein C receptor
- UniProt
- Q9UNN8
- Ligands
- PTY, NAG, MAN
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HB3VAR03 cidra domain | protein | 210 | 55% helix, 14% strand | — |
| B | Endothelial protein C receptor | protein | 169 | 36% helix, 38% strand | Q9UNN8 |
| C | HB3VAR03 cidra domain | protein | 186 | 59% helix, 10% strand | — |
| D | Endothelial protein C receptor | protein | 168 | 35% helix, 38% strand | Q9UNN8 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains B, D, C
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.81 | 0.86 | 66 | PTY |
| 2 | 607 | 0.81 | 0.86 | 69 | PTY |
| 3 | 128 | 0.73 | 0.93 | 24 | empty |
| 4 | 102 | 0.73 | 0.94 | 25 | empty |
| 5 | 268 | 0.54 | 0.76 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1045 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1038 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 408 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4V3D · The CIDRa domain from HB3var03 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 D against A, TM-score 1.00
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 4V3D · PDBe 4V3D · UniProt Q9UNN8
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