5LGD
The CIDRa domain from MCvar1 PfEMP1 bound to CD36
- PDB DOI: https://doi.org/10.2210/pdb5LGD/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens, Plasmodium falciparum
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2016-07-06 Released: 2016-08-31 
- Funding Organization(s): Wellcome Trust
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.07 Å
- R-Value Free: 0.253 
- R-Value Work: 0.212 
- R-Value Observed: 0.214 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Platelet glycoprotein 4 | 472 | Homo sapiens | Mutation(s): 0  Gene Names: CD36, GP3B, GP4 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P16671 (Homo sapiens) Explore P16671  Go to UniProtKB:  P16671 | |||||
PHAROS:  P16671 GTEx:  ENSG00000135218  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P16671 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PfEMP1 variant 1 of strain MC | 179 | Plasmodium falciparum | Mutation(s): 0  Gene Names: MCvar-1 PfEMP1 | ||
UniProt | |||||
Find proteins for Q25733 (Plasmodium falciparum) Explore Q25733  Go to UniProtKB:  Q25733 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q25733 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PLM Query on PLM | L [auth A], M [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
NAG Query on NAG | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
TRS Query on TRS | R [auth A], T [auth B] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O | |||
GOL Query on GOL | N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.07 Å
- R-Value Free: 0.253 
- R-Value Work: 0.212 
- R-Value Observed: 0.214 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 129.826 | α = 90 |
b = 40.726 | β = 114.85 |
c = 138.836 | γ = 90 |
Software Name | Purpose |
---|---|
BUSTER | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-08-31  Deposition Author(s): Hsieh, F.L., Higgins, M.K.
Funding Organization | Location | Grant Number |
---|---|---|
Wellcome Trust | United Kingdom | 101020/Z/13/Z |
Revision History (Full details and data files)
- Version 1.0: 2016-08-31
Type: Initial release - Version 1.1: 2016-10-05
Changes: Database references - Version 1.2: 2019-10-16
Changes: Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary