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- PDB-3hy7: Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex ... -

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Basic information

Entry
Database: PDB / ID: 3hy7
TitleCrystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with Marimastat
ComponentsA disintegrin and metalloproteinase with thrombospondin motifs 5
KeywordsHYDROLASE / alpha/beta structure / central five stranded beta-sheet / Cleavage on pair of basic residues / Disulfide bond / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen
Function / homology
Function and homology information


Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / pulmonary valve morphogenesis / myoblast fusion / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / extracellular matrix binding / aortic valve morphogenesis / negative regulation of cold-induced thermogenesis / endocardial cushion morphogenesis / extracellular matrix disassembly ...Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / pulmonary valve morphogenesis / myoblast fusion / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / extracellular matrix binding / aortic valve morphogenesis / negative regulation of cold-induced thermogenesis / endocardial cushion morphogenesis / extracellular matrix disassembly / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / metallopeptidase activity / integrin binding / heparin binding / peptidase activity / collagen-containing extracellular matrix / endopeptidase activity / defense response to bacterium / endoplasmic reticulum lumen / proteolysis / extracellular space / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Peptidase M12B, ADAM-TS5 / Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain / ADAM, cysteine-rich domain ...Peptidase M12B, ADAM-TS5 / Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-097 / A disintegrin and metalloproteinase with thrombospondin motifs 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsShieh, H.-S. / Williams, J.M. / Caspers, N. / Mathis, K.J. / Tortorella, M.D. / Tomasselli, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and inhibition analysis reveals the mechanism of selectivity of a series of aggrecanase inhibitors
Authors: Tortorella, M.D. / Tomasselli, A.G. / Mathis, K.J. / Schnute, M.E. / Woodard, S.S. / Munie, G. / Williams, J.M. / Caspers, N. / Wittwer, A.J. / Malfait, A.M. / Shieh, H.S.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A disintegrin and metalloproteinase with thrombospondin motifs 5
B: A disintegrin and metalloproteinase with thrombospondin motifs 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,90712
Polymers48,8732
Non-polymers1,03410
Water9,674537
1
A: A disintegrin and metalloproteinase with thrombospondin motifs 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9546
Polymers24,4371
Non-polymers5175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A disintegrin and metalloproteinase with thrombospondin motifs 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9546
Polymers24,4371
Non-polymers5175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.606, 44.464, 76.349
Angle α, β, γ (deg.)90.00, 89.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein A disintegrin and metalloproteinase with thrombospondin motifs 5 / ADAMTS-5 / ADAM-TS 5 / ADAM-TS5 / Aggrecanase-2 / ADMP-2 / A disintegrin and metalloproteinase with ...ADAMTS-5 / ADAM-TS 5 / ADAM-TS5 / Aggrecanase-2 / ADMP-2 / A disintegrin and metalloproteinase with thrombospondin motifs 11 / ADAMTS-11 / ADAM-TS 11


Mass: 24436.645 Da / Num. of mol.: 2 / Fragment: Catalytic Domain (UNP residues 262 to 480) / Mutation: L282K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS-5, ADAMTS11, ADAMTS5, ADMP2 / Plasmid: PPHA79257 / Production host: Escherichia coli (E. coli) / Strain (production host): MON208
References: UniProt: Q9UNA0, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-097 / (2S,3R)-N~4~-[(1S)-2,2-dimethyl-1-(methylcarbamoyl)propyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide / MARIMASTAT / Marimastat


Mass: 331.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H29N3O5 / Comment: antineoplastic, inhibitor*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 1.86 Å3/Da / Density % sol: 33.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 200 mM ammonium acetate, 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 39500 / Num. obs: 38276 / % possible obs: 96.9 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 19.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3239 / Rsym value: 0.35 / % possible all: 83.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3B8Z
Resolution: 1.69→26.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.511 / SU ML: 0.084 / Isotropic thermal model: Individual isotropic / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22385 1987 5.2 %RANDOM
Rwork0.17336 ---
obs0.17598 36271 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.831 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å2-0.28 Å2
2---0.8 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.69→26.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 54 537 3927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213448
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9554674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69124.026154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84215580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8981520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022568
X-RAY DIFFRACTIONr_nbd_refined0.2070.21831
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22341
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2392
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2122
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.291
X-RAY DIFFRACTIONr_mcbond_it0.7651.52188
X-RAY DIFFRACTIONr_mcangle_it1.35723434
X-RAY DIFFRACTIONr_scbond_it1.90431365
X-RAY DIFFRACTIONr_scangle_it3.0624.51240
LS refinement shellResolution: 1.693→1.737 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 110 -
Rwork0.244 2084 -
obs--77.01 %

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