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- PDB-5mho: FXIIIa in complex with the inhibitor ZED2369 -

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Basic information

Entry
Database: PDB / ID: 5mho
TitleFXIIIa in complex with the inhibitor ZED2369
Components
  • Coagulation factor XIII A chain
  • inhibitor ZED2369
KeywordsHYDROLASE / factor XIII / inhibition / transglutaminase
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / Interleukin-4 and Interleukin-13 signaling ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / blood microparticle / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. ...Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Transglutaminase-like superfamily / Papain-like cysteine peptidase superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Coagulation factor XIII A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.92 Å
AuthorsStieler, M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
BMBFFKZ0316030 Germany
Citation
Journal: To Be Published
Title: FXIIIa in complex with the inhibitor ZED2369
Authors: Stieler, M. / Heine, A. / Klebe, G.
#1: Journal: Angew Chem Int Ed Engl. / Year: 2013
Title: Structure of active coagulation factor XIII triggered by calcium binding: basis for the design of next-generation anticoagulants.
Authors: Stieler, M. / Weber, J. / Hils, M. / Kolb, P. / Heine, A. / Buechold, C. / Pasternack, R. / Klebe, G.
History
DepositionNov 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor XIII A chain
B: Coagulation factor XIII A chain
G: inhibitor ZED2369
H: inhibitor ZED2369
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,04313
Polymers170,5154
Non-polymers5299
Water1,928107
1
A: Coagulation factor XIII A chain
G: inhibitor ZED2369
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4746
Polymers85,2572
Non-polymers2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coagulation factor XIII A chain
H: inhibitor ZED2369
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5707
Polymers85,2572
Non-polymers3125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.555, 80.508, 102.904
Angle α, β, γ (deg.)88.20, 76.91, 82.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Coagulation factor XIII A chain / Coagulation factor XIIIa / Protein-glutamine gamma-glutamyltransferase A chain / Transglutaminase A chain


Mass: 84206.039 Da / Num. of mol.: 2 / Mutation: T649I, Q651E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F13A1, F13A / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase
#2: Protein/peptide inhibitor ZED2369


Mass: 1051.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 170 mM ammonium sulfate, 85 mM sodium cacodylate, 25.5 % PEG8000, 15 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.92→48.11 Å / Num. obs: 37113 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rsym value: 0.087 / Net I/σ(I): 10.7
Reflection shellResolution: 2.92→3.09 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementStarting model: 4KTY

4kty


Resolution: 2.92→17.706 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.58
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1775 4.87 %Random selection
Rwork0.2173 ---
obs0.2189 36458 95.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.92→17.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10450 0 93 107 10650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410834
X-RAY DIFFRACTIONf_angle_d0.67414741
X-RAY DIFFRACTIONf_dihedral_angle_d13.2966371
X-RAY DIFFRACTIONf_chiral_restr0.0451638
X-RAY DIFFRACTIONf_plane_restr0.0031961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9172-2.99570.37681240.33332611X-RAY DIFFRACTION93
2.9957-3.08340.32151600.31422648X-RAY DIFFRACTION96
3.0834-3.18240.32311290.28862671X-RAY DIFFRACTION96
3.1824-3.29540.33351320.27352670X-RAY DIFFRACTION96
3.2954-3.42650.32291480.26092655X-RAY DIFFRACTION96
3.4265-3.58120.2549990.23182722X-RAY DIFFRACTION96
3.5812-3.76830.26351210.21792712X-RAY DIFFRACTION96
3.7683-4.00180.21931320.20142660X-RAY DIFFRACTION96
4.0018-4.30670.21411430.19142681X-RAY DIFFRACTION97
4.3067-4.73260.20991740.16742682X-RAY DIFFRACTION97
4.7326-5.40030.23981290.17912715X-RAY DIFFRACTION97
5.4003-6.74080.25411460.20892692X-RAY DIFFRACTION97
6.7408-17.7060.17581380.18172564X-RAY DIFFRACTION93

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