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- PDB-4zh8: Factor Xa complex with GTC000006 -

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Basic information

Entry
Database: PDB / ID: 4zh8
TitleFactor Xa complex with GTC000006
Components(Coagulation factor XFactor X) x 2
KeywordsHYDROLASE / Inhibitor
Function / homology
Function and homology information


coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-4O4 / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Model detailsChains A & B are disulfide bonded together
AuthorsConvery, M.A.
CitationJournal: To Be Published
Title: Factor Xa complex with GTC000006
Authors: Convery, M.A.
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.2Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor X
B: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1784
Polymers43,6042
Non-polymers5742
Water4,882271
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-23 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.663, 72.781, 80.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coagulation factor X / Factor X / Stuart factor / Stuart-Prower factor


Mass: 28550.596 Da / Num. of mol.: 1 / Fragment: residues 235 - 488 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein Coagulation factor X / Factor X / Stuart factor / Stuart-Prower factor


Mass: 15053.597 Da / Num. of mol.: 1 / Fragment: residues 43-179 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-4O4 / 6-chloro-N-{(3S)-1-[(2S)-1-(morpholin-4-yl)-1-oxopropan-2-yl]-2-oxo-2,3-dihydro-1H-pyrrol-3-yl}-N-(2-oxobutyl)naphthalene-2-sulfonamide


Mass: 534.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28ClN3O6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16-20% PEG 6K, 50 mM Mes=NaOH pH 5.7-6.0, 5 mM CaCl2 and 50 mM NaCl
PH range: 5.7-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 29515 / % possible obs: 92.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.116 / Χ2: 1.055 / Net I/av σ(I): 9.297 / Net I/σ(I): 7.9 / Num. measured all: 97671
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-IDRejects% possible all
1.8-1.860.68319911.0781063.4
1.86-1.940.52824461.0611077.7
1.94-2.030.43626551.0921083.8
2.03-2.130.4731211.141099.7
2.13-2.270.33331571.0981099.7
2.27-2.440.23331621.0471099.7
2.44-2.690.17631811.0761099.8
2.69-3.080.12532151.0531099.8
3.08-3.880.06932420.9831099.9
3.88-300.06633450.9841098.3

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Processing

Software
NameVersionClassification
DENZO1.96.2data reduction
SCALEPACK1.96.2data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ezq

1ezq


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.538 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1568 5 %RANDOM
Rwork0.2065 ---
obs0.2089 29528 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 62.72 Å2 / Biso mean: 27.687 Å2 / Biso min: 11.81 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2---2.3 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 37 271 2534
Biso mean--30.83 34.96 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222326
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9633149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4265286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.18524.057106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2515393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8861515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211782
X-RAY DIFFRACTIONr_mcbond_it0.9821416
X-RAY DIFFRACTIONr_mcangle_it1.89442275
X-RAY DIFFRACTIONr_scbond_it2.4215909
X-RAY DIFFRACTIONr_scangle_it3.8897872
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 99 -
Rwork0.345 1984 -
all-2083 -
obs--100 %

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