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- PDB-5mhn: FXIIIa in complex with the inhibitor ZED2360 -

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Basic information

Entry
Database: PDB / ID: 5mhn
TitleFXIIIa in complex with the inhibitor ZED2360
Components
  • Coagulation factor XIII A chain
  • inhibitor ZED2360
KeywordsTRANSFERASE / 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 / FOURIER SYNTHESIS / Resolution: 2.48 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 Mi0621
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

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XIII A chain
B: Coagulation factor XIII A chain
H: inhibitor ZED2360
I: inhibitor ZED2360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,59418
Polymers170,5974
Non-polymers99714
Water3,477193
1
A: Coagulation factor XIII A chain
H: inhibitor ZED2360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7959
Polymers85,2982
Non-polymers4977
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coagulation factor XIII A chain
I: inhibitor ZED2360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7999
Polymers85,2982
Non-polymers5017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.608, 80.513, 103.108
Angle α, β, γ (deg.)87.98, 77.01, 82.26
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABHI

#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 ZED2360


Mass: 1092.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 207 molecules

#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.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
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: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.48→48.12 Å / Num. obs: 60898 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rsym value: 0.068 / Net I/σ(I): 9.83
Reflection shellResolution: 2.48→2.63 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4KTY

4kty


Resolution: 2.48→48.12 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.97
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3042 5 %Random selection
Rwork0.1796 ---
obs0.1825 60829 97.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.48→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10749 0 49 193 10991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111087
X-RAY DIFFRACTIONf_angle_d1.0615069
X-RAY DIFFRACTIONf_dihedral_angle_d13.0416512
X-RAY DIFFRACTIONf_chiral_restr0.0581672
X-RAY DIFFRACTIONf_plane_restr0.0061987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4777-2.51650.36911320.2912537X-RAY DIFFRACTION93
2.5165-2.55770.31151390.27232636X-RAY DIFFRACTION98
2.5577-2.60180.34571370.25692612X-RAY DIFFRACTION97
2.6018-2.64910.31291360.2552592X-RAY DIFFRACTION97
2.6491-2.70010.30561390.2522641X-RAY DIFFRACTION97
2.7001-2.75520.30451360.23812563X-RAY DIFFRACTION97
2.7552-2.81510.34331380.23422633X-RAY DIFFRACTION97
2.8151-2.88060.27991390.21432632X-RAY DIFFRACTION98
2.8806-2.95260.28621400.2122652X-RAY DIFFRACTION98
2.9526-3.03240.29411370.21292598X-RAY DIFFRACTION97
3.0324-3.12160.26361400.20512665X-RAY DIFFRACTION98
3.1216-3.22240.29271390.19872635X-RAY DIFFRACTION98
3.2224-3.33750.23771390.19772649X-RAY DIFFRACTION98
3.3375-3.47110.23871370.18422607X-RAY DIFFRACTION97
3.4711-3.6290.23571400.16582653X-RAY DIFFRACTION98
3.629-3.82030.22481410.15832675X-RAY DIFFRACTION99
3.8203-4.05950.22531390.15382641X-RAY DIFFRACTION98
4.0595-4.37270.17641410.14172679X-RAY DIFFRACTION98
4.3727-4.81240.17931380.12812621X-RAY DIFFRACTION97
4.8124-5.50790.19131360.14012611X-RAY DIFFRACTION98
5.5079-6.93610.22961400.17022668X-RAY DIFFRACTION98
6.9361-48.13310.19441390.16532587X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78710.27670.9030.9040.20014.13630.16910.057-0.0188-0.4166-0.05630.34160.0872-0.1512-0.10290.48180.0378-0.15330.2865-0.02840.45731.322758.4751-30.3113
21.0636-0.0250.58082.99261.83152.4398-0.0577-0.04770.00960.0628-0.0308-0.0102-0.0562-0.03460.10080.26990.0130.00060.2772-0.00420.296644.164769.5268-3.555
32.086-0.17040.75941.63960.28061.8597-0.0296-0.10070.07540.37190.0606-0.49810.13650.2722-0.03190.45150.0043-0.10420.3017-0.02890.413559.265859.45133.3493
44.0983-1.0758-0.41481.14610.46740.859-0.2461-0.21170.06830.14310.1226-0.35650.00560.1130.14430.46040.0185-0.11750.34940.01780.587966.778235.9977-1.1966
54.00191.15750.61085.1826-0.36964.8276-0.48570.38160.1798-0.43370.52770.1072-0.2775-0.3196-0.07620.4901-0.01010.0020.40820.00240.26738.629715.5949-12.2294
60.95780.2380.63161.021-0.16323.35240.11720.01990.00850.0949-0.10660.20590.1076-0.1583-0.00860.38490.0143-0.01590.2875-0.04780.376837.540719.642119.6179
71.0342-0.43110.35031.52790.34741.13810.0139-0.21630.08470.6821-0.0367-0.27670.1992-0.01770.02490.8843-0.083-0.15730.35170.00110.391858.845821.821350.9629
82.8224-0.40510.47530.56850.42730.8560.0424-0.1085-0.3570.4390.0561-0.3032-0.02640.0689-0.06330.9475-0.0377-0.33460.38990.03550.761972.0508-6.551648.9166
94.042-0.1509-0.23154.2586-0.82233.4003-0.16690.34410.0517-0.09570.2022-0.21730.0233-0.2956-0.0460.7629-0.0409-0.1290.34860.00520.387244.5248-26.593635.2565
105.82571.58751.12052.10261.35543.042-0.34330.18680.19380.4970.31820.0091-0.4006-0.25150.03440.86020.011-0.18660.37820.06780.483639.3089-20.563937.3138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 15:192)
2X-RAY DIFFRACTION2(chain A and resid 193:318)
3X-RAY DIFFRACTION3(chain A and resid 319:497)
4X-RAY DIFFRACTION4(chain A and resid 498:628)
5X-RAY DIFFRACTION5(chain A and resid 629:725)
6X-RAY DIFFRACTION6(chain B and resid 15:189)
7X-RAY DIFFRACTION7(chain B and resid 190:516)
8X-RAY DIFFRACTION8(chain B and resid 517:629)
9X-RAY DIFFRACTION9(chain B and resid 630:691)
10X-RAY DIFFRACTION10(chain B and resid 692:725)

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