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- PDB-1hcg: STRUCTURE OF HUMAN DES(1-45) FACTOR XA AT 2.2 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1hcg
TitleSTRUCTURE OF HUMAN DES(1-45) FACTOR XA AT 2.2 ANGSTROMS RESOLUTION
Components(BLOOD COAGULATION FACTOR XA) x 2
KeywordsCOAGULATION FACTOR
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 / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / 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 / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / 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 / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / 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 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsTulinsky, A. / Padmanabhan, K.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Structure of human des(1-45) factor Xa at 2.2 A resolution.
Authors: Padmanabhan, K. / Padmanabhan, K.P. / Tulinsky, A. / Park, C.H. / Bode, W. / Huber, R. / Blankenship, D.T. / Cardin, A.D. / Kisiel, W.
#1: Journal: Biochemistry / Year: 1992
Title: Three-Dimensional Structure of the Apo Form of the N-Terminal Egf-Like Module of Blood Coagulation Factor X as Determined by NMR Spectroscopy and Simulated Folding
Authors: Ullner, M. / Selander, M. / Persson, E. / Stenflo, J. / Drakenberg, T. / Teleman, O.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin
Authors: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. / Westbrook, M. / Maraganore, J.M.
#3: Journal: J.Mol.Biol. / Year: 1981
Title: Comparative Model-Building of the Mammalian Serine Proteases
Authors: Greer, J.
History
DepositionMay 5, 1993Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 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
A: BLOOD COAGULATION FACTOR XA
B: BLOOD COAGULATION FACTOR XA


Theoretical massNumber of molelcules
Total (without water)32,7052
Polymers32,7052
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-8 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.660, 93.660, 119.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: RESIDUES LEU A 247 AND GLN B 10 HAVE RAMACHANDRAN ANGLES OUTSIDE THE ALLOWED REGION. THESE RESIDUES ARE VERY WELL-DEFINED IN THE ELECTRON DENSITY.

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Components

#1: Protein BLOOD COAGULATION FACTOR XA


Mass: 27201.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00742
#2: Protein BLOOD COAGULATION FACTOR XA


Mass: 5504.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00742
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.24 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.2 Mammonium sulfate1dropprecipitant
30.1 MHEPES1dropprecipitant
42.0 Msodium potassium phosphate1dropprecipitant
51.9 Mprecipitant1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 17121 / % possible obs: 61.5 % / Observed criterion σ(F): 2 / Num. measured all: 53755 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.5 Å / % possible obs: 38 %

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→7 Å / σ(F): 4
Details: SOME OF THE WATERS WHICH ARE MORE THAN 4 ANGSTROMS FROM THE PROTEIN MAY BE PART OF THE FLEXIBLY DISORDERED N-TERMINAL EGF-LIKE DOMAIN. RESIDUES LEU A 247 AND GLN B 10 HAVE RAMACHANDRAN ...Details: SOME OF THE WATERS WHICH ARE MORE THAN 4 ANGSTROMS FROM THE PROTEIN MAY BE PART OF THE FLEXIBLY DISORDERED N-TERMINAL EGF-LIKE DOMAIN. RESIDUES LEU A 247 AND GLN B 10 HAVE RAMACHANDRAN ANGLES OUTSIDE THE ALLOWED REGION. THESE RESIDUES ARE VERY WELL-DEFINED IN THE ELECTRON DENSITY.
RfactorNum. reflection
obs0.168 16286
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 0 207 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0550.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0670.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.21.5
X-RAY DIFFRACTIONp_mcangle_it2.12
X-RAY DIFFRACTIONp_scbond_it2.62.5
X-RAY DIFFRACTIONp_scangle_it3.83
X-RAY DIFFRACTIONp_plane_restr0.0270.03
X-RAY DIFFRACTIONp_chiral_restr0.1990.15
X-RAY DIFFRACTIONp_singtor_nbd0.240.6
X-RAY DIFFRACTIONp_multtor_nbd0.310.6
X-RAY DIFFRACTIONp_xhyhbond_nbd0.320.6
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor43
X-RAY DIFFRACTIONp_staggered_tor2520
X-RAY DIFFRACTIONp_orthonormal_tor2725
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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