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- PDB-8r5l: E-selectin complexed with glycomimetic ligand BW850 -

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Basic information

Entry
Database: PDB / ID: 8r5l
TitleE-selectin complexed with glycomimetic ligand BW850
ComponentsE-selectin
KeywordsCELL ADHESION / sickle cell / vaso-occlusive crisis (VOC) / rivipansel / sickle cell disease (SCD)
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 via plasma membrane cell adhesion molecules / 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 via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cortical cytoskeleton / phospholipase binding / positive regulation of receptor internalization / response to tumor necrosis factor / 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 / phospholipase C-activating G protein-coupled receptor signaling pathway / response to lipopolysaccharide / inflammatory response / membrane raft / 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: 2.2 Å
AuthorsJakob, R.P. / Ernst, B. / Maier, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Analogues of the pan-selectin antagonist rivipansel (GMI-1070).
Authors: Wagner, B. / Smiesko, M. / Jakob, R.P. / Muhlethaler, T. / Cramer, J. / Maier, T. / Rabbani, S. / Schwardt, O. / Ernst, B.
History
DepositionNov 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: 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)34,19510
Polymers31,3061
Non-polymers2,8899
Water97354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint23 kcal/mol
Surface area18080 Å2
Unit cell
Length a, b, c (Å)93.100, 72.810, 52.530
Angle α, β, γ (deg.)90.00, 94.11, 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-Y6T / (2~{S})-3-cyclohexyl-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(1~{R},2~{R},3~{S},5~{R})-3-ethyl-2-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-[3-[1-[3-oxidanylidene-3-[(3,6,8-trisulfonaphthalen-1-yl)amino]propyl]-1,2,3-triazol-4-yl]propylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-5-oxidanyl-3-(phenylcarbonyloxy)oxan-4-yl]oxy-propanoic acid


Mass: 1300.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H73N5O25S3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 56.63 %
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: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.2→46.43 Å / Num. obs: 17529 / % possible obs: 98.3 % / Redundancy: 8.7 % / Biso Wilson estimate: 63 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.055 / Rrim(I) all: 0.099 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1701 / CC1/2: 0.742 / Rpim(I) all: 0.721 / Rrim(I) all: 1.48 / % possible all: 95.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.43 Å / Cor.coef. Fo:Fc: 0.9401 / Cor.coef. Fo:Fc free: 0.9398 / SU R Cruickshank DPI: 0.294 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 853 5.11 %RANDOM
Rwork0.2201 ---
obs0.2213 16685 93.53 %-
Displacement parametersBiso mean: 85.74 Å2
Baniso -1Baniso -2Baniso -3
1--17.2857 Å20 Å2-10.3867 Å2
2--7.8636 Å20 Å2
3---9.4221 Å2
Refine analyzeLuzzati coordinate error obs: 0.7 Å
Refinement stepCycle: 1 / Resolution: 2.2→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 187 55 2412
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012506HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.323511HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d828SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes350HARMONIC5
X-RAY DIFFRACTIONt_it2506HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion19.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion342SEMIHARMONIC5
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_contact2678SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.5951 112 4.99 %
Rwork0.4609 2133 -
all0.4677 2245 -
obs--93.53 %
Refinement TLS params.Method: refined / Origin x: -11.5166 Å / Origin y: -7.8564 Å / Origin z: 4.0817 Å
111213212223313233
T0.1047 Å2-0.0154 Å2-0.0753 Å2-0.07 Å20.0434 Å2---0.2171 Å2
L0.3505 °20.3202 °2-0.5775 °2-0.7082 °2-1.4796 °2--3.8172 °2
S0.0692 Å °0.0592 Å °-0.0822 Å °0.0073 Å °-0.0361 Å °-0.0181 Å °-0.2871 Å °-0.2605 Å °-0.0331 Å °
Refinement TLS groupSelection details: { A|* }

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