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- PDB-5mhm: FXIIIa in complex with the inhibitor ZED1630 -

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Basic information

Entry
Database: PDB / ID: 5mhm
TitleFXIIIa in complex with the inhibitor ZED1630
Components
  • Coagulation factor XIII A chain
  • inhibitor ZED1630
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: 2.12 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 / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / 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 / _entity_src_gen.gene_src_common_name / _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

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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 ZED1630
O: inhibitor ZED1630
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,62723
Polymers170,2824
Non-polymers1,34419
Water15,151841
1
A: Coagulation factor XIII A chain
H: inhibitor ZED1630
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,85712
Polymers85,1412
Non-polymers71610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coagulation factor XIII A chain
O: inhibitor ZED1630
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,76911
Polymers85,1412
Non-polymers6289
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.912, 80.715, 103.190
Angle α, β, γ (deg.)88.44, 76.60, 81.79
Int Tables number1
Space group name H-MP1

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Components

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

#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 ZED1630


Mass: 935.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 860 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 841 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.12→25 Å / Num. obs: 97508 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rsym value: 0.083 / Net I/σ(I): 10.5
Reflection shellResolution: 2.12→2.17 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 2 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementResolution: 2.12→24.88 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.07
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4899 5.03 %Random selection
Rwork0.17 ---
obs0.172 97449 96.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10788 0 69 841 11698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911209
X-RAY DIFFRACTIONf_angle_d1.04315216
X-RAY DIFFRACTIONf_dihedral_angle_d12.8076633
X-RAY DIFFRACTIONf_chiral_restr0.0571681
X-RAY DIFFRACTIONf_plane_restr0.0052005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1175-2.14160.32841290.2452790X-RAY DIFFRACTION88
2.1416-2.16680.26931620.23293007X-RAY DIFFRACTION94
2.1668-2.19320.26741670.23123096X-RAY DIFFRACTION95
2.1932-2.22090.24721600.22542981X-RAY DIFFRACTION95
2.2209-2.25010.26591770.20893077X-RAY DIFFRACTION96
2.2501-2.28090.28351710.20873036X-RAY DIFFRACTION96
2.2809-2.31350.24441800.20063069X-RAY DIFFRACTION97
2.3135-2.3480.25961400.20193134X-RAY DIFFRACTION97
2.348-2.38470.27511690.20173057X-RAY DIFFRACTION97
2.3847-2.42370.27681760.20433064X-RAY DIFFRACTION97
2.4237-2.46550.28441670.20553097X-RAY DIFFRACTION97
2.4655-2.51030.2841660.19273100X-RAY DIFFRACTION97
2.5103-2.55850.25511680.1923106X-RAY DIFFRACTION97
2.5585-2.61070.26461690.1833081X-RAY DIFFRACTION97
2.6107-2.66740.25191620.18023101X-RAY DIFFRACTION97
2.6674-2.72940.26331420.17883135X-RAY DIFFRACTION97
2.7294-2.79750.22221500.1773105X-RAY DIFFRACTION97
2.7975-2.87310.19751710.16923154X-RAY DIFFRACTION98
2.8731-2.95750.18551720.16473060X-RAY DIFFRACTION98
2.9575-3.05280.22331630.16383090X-RAY DIFFRACTION98
3.0528-3.16170.21161730.16373166X-RAY DIFFRACTION98
3.1617-3.2880.20811450.16233109X-RAY DIFFRACTION98
3.288-3.43730.18261440.1523116X-RAY DIFFRACTION98
3.4373-3.6180.15831590.14213138X-RAY DIFFRACTION98
3.618-3.84390.17061630.14643159X-RAY DIFFRACTION98
3.8439-4.13940.18431710.1423107X-RAY DIFFRACTION98
4.1394-4.55370.16661660.13033069X-RAY DIFFRACTION97
4.5537-5.20740.15871750.13513138X-RAY DIFFRACTION98
5.2074-6.54090.1971890.17043106X-RAY DIFFRACTION98
6.5409-24.87690.1981530.17193102X-RAY DIFFRACTION97
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)
10.82460.01760.99020.6418-0.02153.33980.1014-0.0317-0.0173-0.0772-0.04640.13860.0637-0.1874-0.04720.16340.0017-0.01360.1313-0.01230.18431.293759.2428-30.1424
20.8413-0.12750.42211.06790.33061.5704-0.0418-0.11680.01950.1934-0.0057-0.0595-0.0194-0.13560.05230.16020.00270.00980.14190.00250.117644.979769.601-3.4403
31.4666-0.0850.54461.03580.01021.6925-0.0248-0.15850.03320.35750.0448-0.36810.12550.2269-0.02610.27060.0197-0.07630.1845-0.00340.259259.121359.03673.0636
44.0229-1.2355-0.11590.85260.15420.6528-0.1769-0.3155-0.02020.13630.1047-0.27540.01790.09110.04920.27980.0297-0.07010.20740.01460.366267.496536.0807-1.2654
55.1377-0.64751.5386.2069-0.67285.2094-0.26670.3678-0.1232-0.25520.525-0.05260.1524-0.2333-0.27310.3109-0.01850.03850.28280.00370.200939.415515.4658-12.2209
60.6639-0.03930.63590.8963-0.09583.22490.07660.0025-0.0107-0.0377-0.03480.1410.053-0.1559-0.04360.12580.00430.00740.12220.00090.177737.582519.507519.3146
70.9549-0.16550.24241.06480.14970.8488-0.0394-0.16850.05160.27250.0105-0.12320.00410.00970.0230.2697-0.0282-0.01070.15440.01040.146358.76421.874951.2508
84.56120.69820.67380.62890.61650.7333-0.0459-0.0493-0.26330.12790.0328-0.18260.0490.10120.01270.2981-0.008-0.0710.18130.04630.312971.7304-6.528549.0175
94.8207-1.2690.82625.48250.04464.2308-0.05310.3054-0.4167-0.25850.27190.16850.0534-0.4137-0.21520.2843-0.0131-0.02610.21420.03960.227645.2975-26.901735.7571
105.468-0.68872.22065.06020.26665.1313-0.1288-0.1437-0.0822-0.09530.47470.5021-0.2198-0.8504-0.33090.3208-0.0125-0.00140.29680.12170.267239.3385-20.434837.404
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 629:726)
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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