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- PDB-1fxy: COAGULATION FACTOR XA-TRYPSIN CHIMERA INHIBITED WITH D-PHE-PRO-AR... -

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Basic information

Entry
Database: PDB / ID: 1fxy
TitleCOAGULATION FACTOR XA-TRYPSIN CHIMERA INHIBITED WITH D-PHE-PRO-ARG-CHLOROMETHYLKETONE
ComponentsCOAGULATION FACTOR XA-TRYPSIN CHIMERA
Keywordshydrolase/hydrolase inhibitor / CHIMERA / PROTEASE / CHLOROMETHYLKETONE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Uptake of dietary cobalamins into enterocytes / Activation of Matrix Metalloproteinases / trypsin / extracellular matrix disassembly / digestion / collagen-containing extracellular matrix / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space ...Uptake of dietary cobalamins into enterocytes / Activation of Matrix Metalloproteinases / trypsin / extracellular matrix disassembly / digestion / collagen-containing extracellular matrix / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
: / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / 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 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
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.15 Å
AuthorsHopfner, K.P. / Kopetzki, E. / Kresse, G.-B. / Huber, R. / Bode, W. / Engh, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: New enzyme lineages by subdomain shuffling.
Authors: Hopfner, K.P. / Kopetzki, E. / Kresse, G.B. / Bode, W. / Huber, R. / Engh, R.A.
History
DepositionApr 22, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: COAGULATION FACTOR XA-TRYPSIN CHIMERA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1232
Polymers24,6691
Non-polymers4541
Water1,47782
1
A: COAGULATION FACTOR XA-TRYPSIN CHIMERA
hetero molecules

A: COAGULATION FACTOR XA-TRYPSIN CHIMERA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2464
Polymers49,3382
Non-polymers9082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)65.510, 48.920, 75.540
Angle α, β, γ (deg.)90.00, 111.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein COAGULATION FACTOR XA-TRYPSIN CHIMERA


Mass: 24668.814 Da / Num. of mol.: 1 / Mutation: Q20Y, E21N, C27V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): UT5600 / References: UniProt: P07477
#2: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57
Sequence detailsRESIDUES ARE NUMBERED ACCORDING TO THE CHYMOTRYPSIN NUMBERING SYSTEM. THE MOLECULE IS A CHIMERIC ...RESIDUES ARE NUMBERED ACCORDING TO THE CHYMOTRYPSIN NUMBERING SYSTEM. THE MOLECULE IS A CHIMERIC CONSTRUCT COMPOSED OF RESIDUES 16 - 121 FROM HUMAN COAGULATION FACTOR XA AND RESIDUES 122 - 246 FROM HUMAN TRYPSIN I. THE N-TERMINAL 15 RESIDUES WERE CLEAVED OFF PROTEOLYTICALLY.

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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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growpH: 7.8
Details: PROTEIN WAS CRYSTALLIZED FROM 15% PEG 6K, 100 MM HEPES, PH 7.8.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlenzyme1drop
2100 mMHEPES1reservoir
315 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.15 Å
Reflection
*PLUS
Lowest resolution: 8 Å / Num. obs: 10714 / % possible obs: 89.3 % / Rmerge(I) obs: 0.072 / Num. measured all: 28062
Reflection shell
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 2.25 Å / % possible obs: 91.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
X-PLOR3.8model building
X-PLOR3.8refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.8phasing
RefinementResolution: 2.15→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 -10 %RANDOM
Rwork0.18 ---
obs0.18 10714 90.9 %-
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 30 82 1842
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.237
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185 / Rfactor Rfree: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.2

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