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- PDB-4kty: Fibrin-stabilizing factor with a bound ligand -

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Basic information

Entry
Database: PDB / ID: 4kty
TitleFibrin-stabilizing factor with a bound ligand
Components
  • Coagulation factor XIII A chain
  • Peptide-like ligand
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / transglutaminase / COAGULATION / TRANSFERASE / ACYLTRANSFERASE / ligand / calcium ions / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
N-[(2S)-2-({(2S)-2-[(N-acetyl-D-alpha-aspartyl)amino]-7-methoxy-7-oxoheptanoyl}amino)butanoyl]-L-norleucyl-L-leucyl-L-prolyl-L-tryptophyl-L-proline / Coagulation factor XIII A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsStieler, M. / Heine, A. / Klebe, G.
CitationJournal: 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. / Buchold, C. / Pasternack, R. / Klebe, G.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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
C: Peptide-like ligand
D: Peptide-like ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,65420
Polymers170,4884
Non-polymers1,16516
Water16,574920
1
A: Coagulation factor XIII A chain
C: Peptide-like ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,91711
Polymers85,2442
Non-polymers6739
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coagulation factor XIII A chain
D: Peptide-like ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7379
Polymers85,2442
Non-polymers4937
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.761, 80.510, 102.844
Angle α, β, γ (deg.)88.14, 76.70, 82.01
Int Tables number1
Space group name H-MP1

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Components

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

#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: T650I, Q652E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F13A, F13A1 / Plasmid: pFASTBac / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase
#2: Protein/peptide Peptide-like ligand


Type: Peptide-like / Class: Inhibitor / Mass: 1038.193 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: N-[(2S)-2-({(2S)-2-[(N-acetyl-D-alpha-aspartyl)amino]-7-methoxy-7-oxoheptanoyl}amino)butanoyl]-L-norleucyl-L-leucyl-L-prolyl-L-tryptophyl-L-proline

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Non-polymers , 4 types, 936 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.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 920 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE UNREACTED FORM OF THE PEPTIDE, CHAIN C/D HAS A DOUBLE BOND BETWEEN C23 AND C24 OF THE 1TX. UPON ...THE UNREACTED FORM OF THE PEPTIDE, CHAIN C/D HAS A DOUBLE BOND BETWEEN C23 AND C24 OF THE 1TX. UPON REACTION WITH PROTEIN, A COVALENT BOND BETWEEN C23 AND SG OF CYS 314 IS FORMED.

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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: 53.7 %
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, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2012 / Details: Mirrors
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR KMC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 119138 / Num. obs: 119138 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.084 / Net I/σ(I): 10
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 7864 / Rsym value: 0.363 / % possible all: 95.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F13

1f13


Resolution: 1.98→20.795 Å / SU ML: 0.21 / Cross valid method: R-free / σ(F): 1.96 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 5980 5.02 %random
Rwork0.1691 ---
obs0.171 119041 96.86 %-
all-119041 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→20.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10991 0 65 920 11976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111445
X-RAY DIFFRACTIONf_angle_d1.36615618
X-RAY DIFFRACTIONf_dihedral_angle_d14.7054112
X-RAY DIFFRACTIONf_chiral_restr0.0831723
X-RAY DIFFRACTIONf_plane_restr0.0052026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-1.99820.2891940.25153443X-RAY DIFFRACTION89
1.9982-2.02160.28941930.24013795X-RAY DIFFRACTION96
2.0216-2.04630.26042130.2323684X-RAY DIFFRACTION96
2.0463-2.07220.25811870.22183771X-RAY DIFFRACTION96
2.0722-2.09940.2571900.22363784X-RAY DIFFRACTION96
2.0994-2.12810.27051970.21333709X-RAY DIFFRACTION97
2.1281-2.15850.27181990.20543752X-RAY DIFFRACTION97
2.1585-2.19070.25152120.20163787X-RAY DIFFRACTION96
2.1907-2.22490.22621960.19313749X-RAY DIFFRACTION97
2.2249-2.26130.25612020.18323728X-RAY DIFFRACTION96
2.2613-2.30030.2082220.1823786X-RAY DIFFRACTION97
2.3003-2.3420.21981720.17223753X-RAY DIFFRACTION97
2.342-2.3870.22921980.18013814X-RAY DIFFRACTION97
2.387-2.43570.25632150.17883741X-RAY DIFFRACTION97
2.4357-2.48850.23181920.17763743X-RAY DIFFRACTION97
2.4885-2.54630.2382050.17073791X-RAY DIFFRACTION96
2.5463-2.60990.22512050.17223745X-RAY DIFFRACTION97
2.6099-2.68030.241830.17083809X-RAY DIFFRACTION97
2.6803-2.7590.2251880.17313809X-RAY DIFFRACTION98
2.759-2.84790.19812010.17323806X-RAY DIFFRACTION97
2.8479-2.94940.2242080.17113770X-RAY DIFFRACTION98
2.9494-3.06710.21231950.16683801X-RAY DIFFRACTION98
3.0671-3.20620.21452050.17113826X-RAY DIFFRACTION98
3.2062-3.37460.21281780.1663852X-RAY DIFFRACTION98
3.3746-3.5850.18441950.15413818X-RAY DIFFRACTION98
3.585-3.86020.16781920.14313834X-RAY DIFFRACTION99
3.8602-4.24570.15712070.1373846X-RAY DIFFRACTION98
4.2457-4.85320.15062190.12823804X-RAY DIFFRACTION99
4.8532-6.0890.1762280.15763835X-RAY DIFFRACTION99
6.089-20.79610.19151890.16913676X-RAY DIFFRACTION94
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)
10.6654-0.11220.81710.64320.10683.11470.0681-0.0345-0.0597-0.1823-0.03140.19050.089-0.2076-0.02330.1796-0.0044-0.04030.1108-0.01520.163532.245158.2715-25.6905
20.9204-0.20050.31191.87080.40971.3563-0.0754-0.07280.0350.15660.0205-0.1415-0.09130.01450.05480.125-0.0010.00640.1046-0.01390.084349.007570.4555-2.2205
31.6971-0.31560.51551.5660.17551.9678-0.0044-0.11140.03230.38390.0215-0.43760.1150.2065-0.04740.1910.0101-0.05420.1458-0.01240.196460.366359.20383.4878
44.7581-1.1969-0.08280.9490.50321.2691-0.1461-0.0664-0.14830.08730.1822-0.306-0.03870.1394-0.04090.22020.0285-0.07880.18170.0160.331470.90438.25940.1238
54.33960.7086-0.8670.551-0.13760.1903-0.069-0.7228-0.64330.09880.1215-0.0706-0.0460.0416-0.08830.28020.0434-0.09090.211-0.01510.286665.820734.87081.0296
66.714.39622.25114.17541.32891.6825-0.11230.12040.1394-0.0980.1308-0.02480.13210.0330.00940.21940.06520.00810.15350.00160.175155.540531.8549-6.4104
75.8017-0.33762.41866.1243-0.77776.639-0.33160.1447-0.1495-0.12230.5397-0.15930.0009-0.2507-0.19560.3106-0.00020.04460.2075-0.02190.134339.609515.1127-10.5389
80.7733-0.03250.96820.77850.07152.69390.1135-0.0642-0.03690.1099-0.04860.10540.1243-0.225-0.0580.1373-0.00690.02010.1046-0.01380.127438.492118.586823.3217
90.9287-0.15710.21751.43850.25170.96550.001-0.15480.04360.4466-0.0197-0.20770.01360.01190.01680.3885-0.0474-0.09140.1234-0.00060.142660.200922.649951.8291
104.3941.11421.2440.24370.22450.57050.0636-0.0514-0.27750.08930.0055-0.21290.06440.0571-0.06920.42260.0001-0.13250.17050.01490.331670.6655-7.100348.0706
115.5417-1.49631.17783.8547-0.68432.3415-0.15410.1147-0.137-0.10420.30630.3402-0.0693-0.3841-0.14120.3625-0.0278-0.06590.19970.05880.246641.1813-24.691635.878
121.15270.01720.40160.49420.32140.7364-0.0102-0.2470.01990.20150.0385-0.1950.03550.1548-0.0960.42110.106-0.17360.2717-0.27170.197860.021370.971314.0252
131.28860.19140.64370.50860.28171.94640.0547-0.2090.0160.1696-0.0197-0.13670.16310.2157-0.10130.7608-0.0565-0.1740.307-0.0560.195565.121428.11565.7359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 22:223 )A22 - 223
2X-RAY DIFFRACTION2( CHAIN A AND RESID 224:366 )A224 - 366
3X-RAY DIFFRACTION3( CHAIN A AND RESID 367:494 )A367 - 494
4X-RAY DIFFRACTION4( CHAIN A AND RESID 495:565 )A495 - 565
5X-RAY DIFFRACTION5( CHAIN A AND RESID 566:596 )A566 - 596
6X-RAY DIFFRACTION6( CHAIN A AND RESID 597:651 )A597 - 651
7X-RAY DIFFRACTION7( CHAIN A AND RESID 652:725 )A652 - 725
8X-RAY DIFFRACTION8( CHAIN B AND RESID 22:222 )B22 - 222
9X-RAY DIFFRACTION9( CHAIN B AND RESID 223:501 )B223 - 501
10X-RAY DIFFRACTION10( CHAIN B AND RESID 515:643 )B515 - 643
11X-RAY DIFFRACTION11( CHAIN B AND RESID 644:730 )B644 - 730
12X-RAY DIFFRACTION12( CHAIN C AND RESID 1:9 )C1 - 9
13X-RAY DIFFRACTION13( CHAIN D AND RESID 1:9 )D1 - 9

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