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- PDB-6xfq: Structure of a novel antithrombotic agent Agkisacucetin in comple... -

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Basic information

Entry
Database: PDB / ID: 6xfq
TitleStructure of a novel antithrombotic agent Agkisacucetin in complex with the platelet glycoprotein Ib receptor
Components
  • Platelet glycoprotein Ib alpha chain
  • Snaclec agglucetin subunit alpha-1
  • Snaclec agglucetin subunit beta-2
KeywordsSTRUCTURAL PROTEIN / complex / GPIb
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / regulation of blood coagulation / Platelet Aggregation (Plug Formation) / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / release of sequestered calcium ion into cytosol / extracellular matrix / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / platelet activation / cell morphogenesis / blood coagulation / toxin activity / cell surface receptor signaling pathway / cell adhesion / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Lectin C-type domain ...Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / 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 / C-type lectin fold / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Platelet glycoprotein Ib alpha chain / Snaclec agglucetin subunit beta-2 / Snaclec agglucetin subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Deinagkistrodon acutus (Chinese moccasin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsWang, J. / Gao, Y.X. / Ke, J.Y. / Zhu, Z.L. / Niu, L.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1632124 China
CitationJournal: To be published
Title: Structure of a novel antithrombotic agent Agkisacucetin in complex with the platelet glycoprotein Ib receptor
Authors: Wang, J. / Gao, Y.X. / Ke, J.Y. / Zhu, Z.L. / Niu, L.W.
History
DepositionJun 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Platelet glycoprotein Ib alpha chain
A: Snaclec agglucetin subunit alpha-1
B: Snaclec agglucetin subunit beta-2


Theoretical massNumber of molelcules
Total (without water)68,6043
Polymers68,6043
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-31 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.304, 86.304, 189.963
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Protein Platelet glycoprotein Ib alpha chain / Glycoprotein Ibalpha / Antigen CD42b-alpha


Mass: 34010.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GP1BA / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-DE44 / References: UniProt: P07359
#2: Protein Snaclec agglucetin subunit alpha-1 / Agkisacucetin subunit alpha


Mass: 17334.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinagkistrodon acutus (Chinese moccasin)
Production host: Komagataella pastoris (fungus) / References: UniProt: Q8JIV9
#3: Protein Snaclec agglucetin subunit beta-2 / Antithrombin 1 chain B


Mass: 17258.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinagkistrodon acutus (Chinese moccasin)
Production host: Komagataella pastoris (fungus) / References: UniProt: Q8AYA3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 15% PEG4000, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.3→58.1 Å / Num. obs: 11456 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 115.46 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.057 / Net I/σ(I): 9.8
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 8.6 % / Num. unique obs: 2290 / CC1/2: 0.918 / Rpim(I) all: 0.674 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9A, 3UBU

1p9a

3ubu


Resolution: 3.3→51.34 Å / SU ML: 0.546 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 44.5898 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3115 526 4.66 %
Rwork0.2746 10773 -
obs0.2763 11299 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 162.83 Å2
Refinement stepCycle: LAST / Resolution: 3.3→51.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 0 6 4128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944232
X-RAY DIFFRACTIONf_angle_d1.25315762
X-RAY DIFFRACTIONf_chiral_restr0.0662640
X-RAY DIFFRACTIONf_plane_restr0.0084733
X-RAY DIFFRACTIONf_dihedral_angle_d13.59031522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.630.40331220.41192613X-RAY DIFFRACTION98.63
3.63-4.160.3091130.32262643X-RAY DIFFRACTION98.57
4.16-5.240.27851390.25662671X-RAY DIFFRACTION98.98
5.24-51.340.31171520.24382846X-RAY DIFFRACTION99.37

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