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- PDB-9ram: E-selectin complexed with glycomimetic ligand MZ2257 -

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Basic information

Entry
Database: PDB / ID: 9ram
TitleE-selectin complexed with glycomimetic ligand MZ2257
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: 2.6 Å
AuthorsJakob, R.P. / Ernst, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: E-selectin complexed with glycomimetic ligand MZ2257
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

Downloads & links

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Assembly

Deposited unit
A: E-selectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,43110
Polymers31,3061
Non-polymers2,1259
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.960, 72.300, 52.350
Angle α, β, γ (deg.)90.00, 94.51, 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: obtained synthetically / 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
#4: Chemical ChemComp-A1JDU / (2~{R},6~{a}~{R},7~{R},9~{R},10~{S},10~{a}~{S})-9-(hydroxymethyl)-7-[(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-10-oxidanyl-3,4,5,6~{a},7,9,10,10~{a}-octahydro-2~{H}-pyrano[3,4-b][1,4]dioxocine-2-carboxylic acid


Mass: 536.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O13 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
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, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45.84 Å / Num. obs: 10469 / % possible obs: 98.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 70.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.052 / Net I/σ(I): 10.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 2.02 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 1015 / CC1/2: 0.39 / Rpim(I) all: 1.11 / % possible all: 96.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.84 Å / Cor.coef. Fo:Fc: 0.9151 / Cor.coef. Fo:Fc free: 0.9327 / SU R Cruickshank DPI: 0.263 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.829 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.274
RfactorNum. reflection% reflectionSelection details
Rfree0.224 472 4.51 %RANDOM
Rwork0.224 ---
obs0.2239 10464 98.52 %-
Displacement parametersBiso mean: 99.28 Å2
Baniso -1Baniso -2Baniso -3
1--23.8921 Å20 Å2-7.3825 Å2
2--0.7597 Å20 Å2
3---23.1324 Å2
Refine analyzeLuzzati coordinate error obs: 0.62 Å
Refinement stepCycle: 1 / Resolution: 2.6→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 136 39 2345
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012375HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.343244HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d816SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it2375HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion19.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion334SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2677SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3283 129 4.41 %
Rwork0.2814 2794 -
all0.2834 2923 -
obs--98.52 %
Refinement TLS params.Method: refined / Origin x: -11.5271 Å / Origin y: -7.9654 Å / Origin z: 4.1009 Å
111213212223313233
T-0.1581 Å2-0.0149 Å20.0562 Å2--0.2304 Å20.0714 Å2---0.3007 Å2
L0.3705 °20.5614 °2-1.129 °2-1.401 °2-2.333 °2--7.7198 °2
S0.0627 Å °0.0666 Å °-0.1154 Å °0.0758 Å °0.0214 Å °0.0321 Å °-0.6038 Å °-0.7476 Å °-0.0841 Å °
Refinement TLS groupSelection details: { A|* }

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