Research workbench
The cidra domain from MCVAR1 PFEMP1 bound to CD36
Analyse The cidra domain from MCVAR1 PFEMP1 bound to CD36 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LGD
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet glycoprotein 4; PFEMP1 variant 1 of strain mc
- UniProt
- P16671, Q25733
- Ligands
- PLM, NAG, MAN
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet glycoprotein 4 | protein | 400 | 24% helix, 34% strand | P16671 |
| B | PFEMP1 variant 1 of strain mc | protein | 151 | 68% helix, 0% strand | Q25733 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- GOL · Glycerol · additive · 5 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.87 | 0.88 | 134 | PLM |
| 2 | 102 | 0.43 | 0.78 | 14 | NAG |
| 3 | 59 | 0.40 | 0.81 | 16 | empty |
| 4 | 50 | 0.39 | 0.81 | 12 | TRS |
| 5 | 81 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 708 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 6 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 P16671
- Every structure of UniProt Q25733
- Elsewhere: RCSB PDB 5LGD · PDBe 5LGD · UniProt P16671 · UniProt Q25733
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