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- PDB-3liw: Factor XA in complex with (R)-2-(1-ADAMANTYLCARBAMOYLAMINO)-3-(3-... -

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Basic information

Entry
Database: PDB / ID: 3liw
TitleFactor XA in complex with (R)-2-(1-ADAMANTYLCARBAMOYLAMINO)-3-(3-CARBAMIDOYL-PHENYL)-N-PHENETHYL-PROPIONIC ACID AMIDE
Components
  • Activated factor Xa heavy chain
  • Factor X light chain
KeywordsHYDROLASE / COAGULATION FACTOR INHIBITOR / FACTOR XA / Blood coagulation / Calcium / Cleavage on pair of basic residues / Disulfide bond / EGF-like domain / Gamma-carboxyglutamic acid / Glycoprotein / Hydroxylation / Polymorphism / Protease / Secreted / Serine protease / Zymogen
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 leukocyte chemotaxis / 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 ...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 leukocyte chemotaxis / 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 / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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 / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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-RUP / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMueller, M.M. / Sperl, S. / Sturzebecher, J. / Bode, W. / Moroder, L.
CitationJournal: Biol.Chem. / Year: 2003
Title: (R)-3-Amidinophenylalanine-Derived Inhibitors of Factor Xa with a Novel Active-Site Binding Mode
Authors: Mueller, M.M. / Sperl, S. / Sturzebecher, J. / Bode, W. / Moroder, L.
History
DepositionJan 25, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionApr 7, 2010ID: 1KYE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activated factor Xa heavy chain
B: Factor X light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4755
Polymers31,9072
Non-polymers5683
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-32 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.480, 72.510, 78.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Activated factor Xa heavy chain / Stuart factor / Stuart-Prower factor / Factor X heavy chain / Coagulation factor X


Mass: 26447.104 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 235-468 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein Factor X light chain / Stuart factor / Stuart-Prower factor / Coagulation factor X


Mass: 5460.055 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 128-178 / 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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-RUP / (R)-2-(3-ADAMANTAN-1-YL-UREIDO)-3-(3-CARBAMIMIDOYL-PHENYL)-N-PHENETHYL-PROPIONAMIDE


Mass: 487.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H37N5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: CACL2, PEG 6000, MES, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 2001 / Details: OSMIC
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.5421
21.54181
ReflectionResolution: 2.22→34.5 Å / Num. obs: 15847 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 14.3
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.275 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FAX

1fax


Resolution: 2.22→26.61 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1712553.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1603 10.1 %RANDOM
Rwork0.223 ---
all0.223 15846 --
obs0.223 15846 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.12 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---4.61 Å20 Å2
3---4.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.22→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 38 123 2386
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.22→2.36 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 265 10.4 %
Rwork0.261 2288 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3INH.PARAMINH.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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