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- PDB-9ral: E-selectin complexed with glycomimetic ligand MZ2139 -

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Basic information

Entry
Database: PDB / ID: 9ral
TitleE-selectin complexed with glycomimetic ligand MZ2139
ComponentsE-selectin
KeywordsCELL ADHESION / selectin / glycomimetic
Function / homology
Function and homology information


actin filament-based process / positive regulation of leukocyte tethering or rolling / sialic acid binding / leukocyte migration involved in inflammatory response / oligosaccharide binding / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterophilic cell-cell adhesion / leukocyte cell-cell adhesion / cortical cytoskeleton ...actin filament-based process / positive regulation of leukocyte tethering or rolling / sialic acid binding / leukocyte migration involved in inflammatory response / oligosaccharide binding / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterophilic cell-cell adhesion / leukocyte cell-cell adhesion / cortical cytoskeleton / positive regulation of receptor internalization / response to tumor necrosis factor / phospholipase binding / clathrin-coated pit / response to cytokine / response to interleukin-1 / Cell surface interactions at the vascular wall / calcium-mediated signaling / caveola / transmembrane signaling receptor activity / regulation of inflammatory response / response to lipopolysaccharide / phospholipase C-activating G protein-coupled receptor signaling pathway / membrane raft / inflammatory response / external side of plasma membrane / perinuclear region of cytoplasm / : / metal ion binding / plasma membrane
Similarity search - Function
Selectin superfamily / Selectin, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Lectin C-type domain ...Selectin superfamily / Selectin, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / EGF-like domain / C-type lectin fold / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJakob, R.P. / Ernst, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: E-selectin complexed with glycomimetic ligand MZ2139
Authors: Jakob, R.P. / Ernst, B.
History
DepositionMay 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E-selectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,44510
Polymers31,3061
Non-polymers2,1399
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.410, 73.190, 52.310
Angle α, β, γ (deg.)90.00, 94.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E-selectin / CD62 antigen-like family member E / Endothelial leukocyte adhesion molecule 1 / ELAM-1 / Leukocyte- ...CD62 antigen-like family member E / Endothelial leukocyte adhesion molecule 1 / ELAM-1 / Leukocyte-endothelial cell adhesion molecule 2 / LECAM2


Mass: 31305.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SELE, ELAM1 / Cell line (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16581
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1JDV / (2~{R},7~{a}~{R},8~{R},10~{R},11~{S},11~{a}~{S})-10-(hydroxymethyl)-8-[(1~{R},2~{R},3~{S})-3-methyl-2-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-cyclohexyl]oxy-11-oxidanyl-2,3,4,5,6,7~{a},8,10,11,11~{a}-decahydropyrano[3,4-b][1,4]dioxonine-2-carboxylic acid


Mass: 550.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42O13 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M CaCl2, 0.1 M Mops pH 6.2, 11-14% PEG8000, after microseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46.56 Å / Num. obs: 13733 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 51.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1357 / CC1/2: 0.7 / Rpim(I) all: 0.44 / % possible all: 97.1

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Processing

Software
NameClassification
PDB_EXTRACTdata extraction
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.56 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2673 --
Rwork0.2515 --
obs-13662 98.7 %
Refinement stepCycle: LAST / Resolution: 2.4→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 137 60 2362

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