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- PDB-9hgx: E-selectin complexed with glycomimetic ligand BW1025 -

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Basic information

Entry
Database: PDB / ID: 9hgx
TitleE-selectin complexed with glycomimetic ligand BW1025
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 / response to cytokine / clathrin-coated pit / 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: 2.75 Å
AuthorsJakob, R.P. / Ernst, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: E-selectin complexed with glycomimetic ligand BW1025
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)33,62011
Polymers31,3061
Non-polymers2,31410
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint17 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.030, 73.220, 52.360
Angle α, β, γ (deg.)90.00, 93.59, 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-A1IUT / (2~{S})-1-(2-azaspiro[3.5]nonan-2-yl)-3-cyclohexyl-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: 685.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H59NO12 / 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.: 75 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
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: 2.75→57.49 Å / Num. obs: 9186 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 60 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.109 / Net I/σ(I): 5.8
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1474 / CC1/2: 0.586 / Rpim(I) all: 0.75 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→57.49 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.8744 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.35
RfactorNum. reflection% reflectionSelection details
Rfree0.252 454 4.94 %RANDOM
Rwork0.2005 ---
obs0.2031 9186 99.65 %-
Displacement parametersBiso mean: 77.03 Å2
Baniso -1Baniso -2Baniso -3
1--16.5209 Å20 Å20.3693 Å2
2---0.3461 Å20 Å2
3---16.867 Å2
Refine analyzeLuzzati coordinate error obs: 0.461 Å
Refinement stepCycle: 1 / Resolution: 2.75→57.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 148 76 2400
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012400HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.253289HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d820SINUSOIDAL2
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_it2400HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion18.56
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_contact2669SEMIHARMONIC4
LS refinement shellResolution: 2.75→3.07 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3169 130 5.04 %
Rwork0.2429 2450 -
all0.2466 2580 -
obs--99.65 %
Refinement TLS params.Method: refined / Origin x: -11.5915 Å / Origin y: -8.2132 Å / Origin z: 4.7667 Å
111213212223313233
T0.1495 Å2-0.0168 Å20.0303 Å2--0.1528 Å20.0508 Å2---0.195 Å2
L0.2153 °20.4335 °2-0.605 °2-1.46 °2-2.5324 °2--4.9815 °2
S-0.004 Å °0.067 Å °-0.0893 Å °0.049 Å °0.0248 Å °-0.0121 Å °-0.3998 Å °-0.1987 Å °-0.0208 Å °
Refinement TLS groupSelection details: { A|* }

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