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- PDB-9hgy: E-selectin complexed with glycomimetic ligand BW1030 -

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Basic information

Entry
Database: PDB / ID: 9hgy
TitleE-selectin complexed with glycomimetic ligand BW1030
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 / oligosaccharide binding / leukocyte migration involved in inflammatory response / 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 / oligosaccharide binding / leukocyte migration involved in inflammatory response / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterophilic cell-cell adhesion / leukocyte cell-cell adhesion / cortical cytoskeleton / response to tumor necrosis factor / positive regulation of receptor internalization / 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 / extracellular space / 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: 2.5 Å
AuthorsJakob, R.P. / Ernst, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: E-selectin complexed with glycomimetic ligand BW1030
Authors: Jakob, R.P. / Ernst, B.
History
DepositionNov 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: 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)33,58011
Polymers31,3061
Non-polymers2,27410
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint16 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.080, 72.910, 52.340
Angle α, β, γ (deg.)90.00, 94.34, 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
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-A1IUU / (2~{S})-3-cyclohexyl-1-(3-ethylazetidin-1-yl)-2-[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(1~{R},2~{R})-2-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxycyclohexyl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-propan-1-one


Mass: 645.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H55NO12 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
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: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.5→57.3 Å / Num. obs: 11958 / % possible obs: 98.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 58.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.054 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.75 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2934 / CC1/2: 0.69 / Rpim(I) all: 0.58 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20.05 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9129 / SU R Cruickshank DPI: 0.552 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.549 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.298
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 578 4.84 %RANDOM
Rwork0.2205 ---
obs0.2228 11944 98.21 %-
Displacement parametersBiso mean: 73.02 Å2
Baniso -1Baniso -2Baniso -3
1--9.3783 Å20 Å2-2.1149 Å2
2---4.0547 Å20 Å2
3---13.433 Å2
Refine analyzeLuzzati coordinate error obs: 0.513 Å
Refinement stepCycle: 1 / Resolution: 2.5→20.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 145 68 2389
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012396HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.233282HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d821SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes340HARMONIC5
X-RAY DIFFRACTIONt_it2396HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion18.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion341SEMIHARMONIC5
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_contact2691SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.74 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2955 128 4.53 %
Rwork0.2596 2697 -
all0.2612 2825 -
obs--98.21 %
Refinement TLS params.Method: refined / Origin x: -11.6431 Å / Origin y: -8.176 Å / Origin z: 4.6601 Å
111213212223313233
T0.0539 Å2-0.0338 Å20.0002 Å2--0.1666 Å20.0498 Å2---0.2727 Å2
L0.3197 °20.4254 °2-0.7827 °2-1.1078 °2-2.121 °2--4.5952 °2
S0.0111 Å °0.067 Å °-0.0884 Å °0.0354 Å °0.0283 Å °-0.0125 Å °-0.3075 Å °-0.2372 Å °-0.0394 Å °
Refinement TLS groupSelection details: { A|* }

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