4DXG

Crystal structure of Staphylococcal Superantigen-Like protein 4 complexed with sialyl Lewis X

PDB DOI: https://doi.org/10.2210/pdb4DXG/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus str. Newman
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-02-27 Released: 2012-09-19
Deposition Author(s): Hermans, S.J., Baker, H.M., Langley, R.J., Baker, E.N., Fraser, J.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.254
R-Value Work: 0.185
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 24.59 kDa
Atom Count: 1,723
Modelled Residue Count: 194
Deposited Residue Count: 204
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal enterotoxin-like toxin	A	204	Staphylococcus aureus subsp. aureus str. Newman	Mutation(s): 0 Gene Names: NWMN_0391, ssl4nm
UniProt
Find proteins for A0A0H3K6A3 (Staphylococcus aureus (strain Newman)) Explore A0A0H3K6A3 Go to UniProtKB: A0A0H3K6A3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3K6A3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose	B	4		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G07675NG GlyCosmos: G07675NG GlyGen: G07675NG

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIN Query on PIN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) C₈ H₁₈ N₂ O₆ S₂ IHPYMWDTONKSCO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900122 Query on PRD_900122	B	Sialyl-Lewis X antigen, alpha anomer	Oligosaccharide / Antigen		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.254
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.88	α = 90
b = 78.88	β = 90
c = 97.701	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-19
Type: Initial release
Version 1.1: 2014-03-12
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

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4DXG

Crystal structure of Staphylococcal Superantigen-Like protein 4 complexed with sialyl Lewis X

Entity ID: 1

UniProt

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Sequence Annotations

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Entity ID: 2