3Q25

Crystal structure of human alpha-synuclein (1-19) fused to maltose binding protein (MBP)

PDB DOI: https://doi.org/10.2210/pdb3Q25/pdb

Classification: SUGAR BINDING PROTEIN, PROTEIN FIBRIL
Organism(s): Escherichia coli, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-19 Released: 2011-06-01
Deposition Author(s): Zhao, M., Sawaya, M.R., Cascio, D., Eisenberg, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.196
R-Value Work: 0.170
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 44.55 kDa
Atom Count: 3,392
Modelled Residue Count: 388
Deposited Residue Count: 390
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein/alpha-synuclein chimeric protein	A	390	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Find proteins for P37840 (Homo sapiens) Explore P37840 Go to UniProtKB: P37840
PHAROS: P37840 GTEx: ENSG00000145335
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P37840P0AEX9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A]	M [auth A] N [auth A] O [auth A] P [auth A] Q [auth A] M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.196
R-Value Work: 0.170
R-Value Observed: 0.171
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.47	α = 90
b = 77.47	β = 90
c = 172.64	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-08-02
Changes: Refinement description, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3Q25

Crystal structure of human alpha-synuclein (1-19) fused to maltose binding protein (MBP)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)