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- PDB-6tdt: Thrombin in Complex with a D-DiPhe-Pro-p-pyridine derivative -

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Basic information

Entry
Database: PDB / ID: 6tdt
TitleThrombin in Complex with a D-DiPhe-Pro-p-pyridine derivative
Components
  • (Prothrombin) x 2
  • Hirudin variant-2
KeywordsHYDROLASE / COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / BLOOD CLOTTING INHIBITOR / THROMBIN INHIBITOR / PREORGANIZATION / GLYCOSYLATION / BLOOD
Function / homology
Function and homology information


positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain ...Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / 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
Chem-LXW / PHOSPHATE ION / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsNgo, K. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
Authors: Ngo, K. / Collins-Kautz, C. / Gerstenecker, S. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionNov 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_ptnr1_PDB_ins_code / _struct_conn.pdbx_role / _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.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Prothrombin
L: Prothrombin
I: Hirudin variant-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2379
Polymers35,3683
Non-polymers8696
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-35 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.872, 71.726, 72.099
Angle α, β, γ (deg.)90.000, 100.175, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11H-75-

ARG

21H-411-

HOH

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Components

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Protein/peptide , 2 types, 2 molecules LI

#2: Protein/peptide Prothrombin / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide Hirudin variant-2


Mass: 1491.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945

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Protein / Sugars , 2 types, 2 molecules H

#1: Protein Prothrombin / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 253 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-LXW / (2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide


Mass: 428.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28N4O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Sodium dihydrogen phosphate, 350 mM NaCl, 27% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.529→43.36 Å / Num. obs: 52277 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 15.51 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.101 / Rsym value: 0.085 / Net I/σ(I): 8.6
Reflection shellResolution: 1.53→1.62 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8431 / CC1/2: 0.811 / Rrim(I) all: 0.557 / Rsym value: 0.473 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H8D

1h8d


Resolution: 1.53→43.36 Å / SU ML: 0.1526 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.4343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1769 2611 5 %
Rwork0.1596 49639 -
obs0.1605 52250 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.16 Å2
Refinement stepCycle: LAST / Resolution: 1.53→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 57 248 2646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822512
X-RAY DIFFRACTIONf_angle_d1.03073404
X-RAY DIFFRACTIONf_chiral_restr0.0657353
X-RAY DIFFRACTIONf_plane_restr0.0075461
X-RAY DIFFRACTIONf_dihedral_angle_d16.31371528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.560.28881340.2532554X-RAY DIFFRACTION97.64
1.56-1.590.24961380.22792613X-RAY DIFFRACTION99.39
1.59-1.620.2311390.2012644X-RAY DIFFRACTION99.64
1.62-1.650.18841380.1882620X-RAY DIFFRACTION99.71
1.65-1.690.21471370.17952604X-RAY DIFFRACTION99.42
1.69-1.740.20751390.17932633X-RAY DIFFRACTION99.28
1.74-1.780.19371380.1662641X-RAY DIFFRACTION99.39
1.78-1.830.19451360.16622599X-RAY DIFFRACTION99.17
1.83-1.890.17791360.16242582X-RAY DIFFRACTION97.73
1.89-1.960.2111290.16922477X-RAY DIFFRACTION93.98
1.96-2.040.17661370.14932599X-RAY DIFFRACTION99.49
2.04-2.130.16741380.1492619X-RAY DIFFRACTION98.85
2.13-2.250.17321390.14292636X-RAY DIFFRACTION99.32
2.25-2.390.15681390.14852647X-RAY DIFFRACTION99.15
2.39-2.570.17731380.14842624X-RAY DIFFRACTION99.07
2.57-2.830.18921390.15912638X-RAY DIFFRACTION99.46
2.83-3.240.18151380.16292626X-RAY DIFFRACTION99.21
3.24-4.080.1491370.1452588X-RAY DIFFRACTION96.46
4.08-43.360.15941420.15672695X-RAY DIFFRACTION99.2
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)
10.120127117991-0.0490706080187-0.006952093103960.0436111104169-0.0274533222940.03072803953350.152641570243-0.0109442192333-0.1555768831890.00674043889521-0.1978811254250.1045705240270.0231088229554-0.147100697359-0.0001455772645760.134740208230.00400400651759-0.01519177039060.155627435577-0.01791407643740.1741011459071.336806401120.5931683405517.1977119263
20.394275207671-0.1803369942460.05651050432740.0805244613765-0.01199304204860.1617852845510.1648052495850.341214058658-0.0750889266101-0.267498699645-0.153067755488-0.02832645387650.08008815910630.1061608668580.001530714713470.1959280651160.06872999523090.003174533166290.20062817618-0.02157443198240.13267264917615.1285743935-0.6937774245519.03389298775
30.940348599631-0.511178063630.2654440973390.817799500293-0.08518331684870.558266862310.1311078763520.2285428394450.0537485514419-0.14348342574-0.150799553282-0.1116777404350.06444209729650.1382208951390.002762689657360.1408493256390.05067466003280.01121502432690.1778466474380.01112249243120.1109828474918.5131931501-0.010557964568312.2999087245
40.225519089776-0.1157344967180.007274006699860.06796304446280.02867835568410.0776111483048-0.0436322189733-0.0844775807087-0.02732318907260.1640983704310.119396714195-0.03998544047920.0367866710260.1322605116229.98375951456E-50.1643769705080.0152295090603-0.02322433818610.157369579998-0.02514486500440.1500238735219.709762794174.6990116357532.1479747393
50.294985002822-0.018623657467-0.1091594425170.242800827441-0.1404116459870.1289335146060.059682384606-0.025899485324-0.228961696602-0.01005759808050.05662122914320.1209858843840.24435699321-0.05562459809070.0002227018373780.1798167951590.0039216616533-0.03454673018620.139305235773-0.01836727903610.1841673183944.01997545903-7.4629172756720.1813575587
60.0229740778170.0444345426967-0.03821946385660.0724845153426-0.06072503598040.0452863658784-0.0591385768742-0.107997963929-0.02630767641750.2390243021150.0553624013836-0.06521098162840.02193765936750.009802092678292.95839934645E-50.1861857865560.0299860804664-0.01255628365120.1505086126310.01804424383890.15552136969218.6966364417-10.643812913835.7460972299
70.24730255145-0.2220302104920.08605166557210.221932896617-0.1476790443470.1888780730230.0049586964739-0.0345022992496-0.2204201534240.0009756694697290.02093714499210.05594424499050.1699040845260.06912295511970.008227348343630.1539939739720.001153835500110.00972629648360.1049432489460.01653737952650.1826170711846.89457454229-8.7783880937927.9061799654
80.626096318743-0.110525462803-0.0409731235740.127304859628-0.1986461992670.427840539582-0.0237612244599-0.0736004068131-0.08551082299790.0418073651660.02674036582960.03875121944810.02561341328530.02522653623120.002492591398560.1232856795110.01925974569460.005530404730280.1105586451320.004836667965430.1391795681810.5285132981-0.97084822480627.3266374941
90.0896969811101-0.02434794310570.01047000997340.115356637178-0.0007847483469430.01717796228510.0557106711003-0.1311806964290.2221592218290.091739446312-0.0986454737464-0.263038439094-0.1319758897060.2464207935880.0009854578708940.129092668053-0.027674790580.004002112751470.1694562612460.02007335206190.27595173098726.83879894348.6183575759622.4067520308
100.0345982754265-0.0392925378143-0.01420158916730.04428087632780.01131482466230.02741650594640.06963301900880.06035875632030.00312922801258-0.0917328946718-0.111542924927-0.0745142493704-0.202382406315-0.02393747595029.63336953497E-50.1621529793150.03216851682190.01216738842980.1332842387820.009336793748170.1538256077025.2537779483714.828976098518.1129390124
110.1271413932120.1091855517520.02023259845380.128453890894-0.03384177719070.08752504058940.0603744946218-0.1159798040340.07908232928470.0250596924651-0.0979962025493-0.0756940972657-0.173554249524-0.100742389669-0.002484870066420.1472090221390.05944397186990.001019211902570.156790219193-0.01418814675930.174494538007-3.2563341914812.977172657120.2196272903
120.02395805672080.005681407046730.02431832437980.0156792824572-0.01227069022720.04032518079720.0965961654946-0.116553901807-0.0782052109547-0.03573455680640.03498027441210.03437076541490.0113364388691-0.2573900499564.63840714646E-50.1483628081720.03523081549560.02015693852350.1774407746570.005952059473310.176261521855-2.231199084945.8669288701630.9429204042
130.0375651899358-0.001372802773090.06286079584420.001807101154720.001654471095070.107085184614-0.25560195997-0.1148150906790.2448593912570.4282863402060.0748738720275-0.0771582671115-0.05201124844220.0588206055306-0.004113406925120.3067349806410.0742286448860.0167073534660.189335527203-0.01257200016910.2612257034782.967061753399.5394431952539.060639436
140.18804556033-0.2194831003950.01362965729810.26241743664-0.01315190408830.002106153247740.1595910407570.522108203483-0.0400891871366-0.313409351629-0.0929706146896-0.014044018701-0.166976359244-0.007359616452680.09000760595820.3884806149120.103005070520.01824794378620.491814521121-0.08140969909710.15801973387811.8620471582-1.36589043422-3.09377438097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 16 through 29 )
2X-RAY DIFFRACTION2chain 'H' and (resid 30 through 50 )
3X-RAY DIFFRACTION3chain 'H' and (resid 51 through 125 )
4X-RAY DIFFRACTION4chain 'H' and (resid 126 through 140 )
5X-RAY DIFFRACTION5chain 'H' and (resid 141 through 164 )
6X-RAY DIFFRACTION6chain 'H' and (resid 165 through 179 )
7X-RAY DIFFRACTION7chain 'H' and (resid 180 through 197 )
8X-RAY DIFFRACTION8chain 'H' and (resid 198 through 231 )
9X-RAY DIFFRACTION9chain 'H' and (resid 232 through 246 )
10X-RAY DIFFRACTION10chain 'L' and (resid 1C through 7 )
11X-RAY DIFFRACTION11chain 'L' and (resid 8 through 14B)
12X-RAY DIFFRACTION12chain 'L' and (resid 14C through 14I)
13X-RAY DIFFRACTION13chain 'L' and (resid 14J through 15 )
14X-RAY DIFFRACTION14chain 'I' and (resid 555 through 565 )

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