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- PDB-3hy9: Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex ... -

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Basic information

Entry
Database: PDB / ID: 3hy9
TitleCrystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with an Amino-2-indanol compound
ComponentsCatalytic Domain of ADAMTS-5
KeywordsHYDROLASE / alpha/beta structure / central five stranded beta-sheet
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 / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / integrin binding / metallopeptidase activity / peptidase activity / heparin binding / endopeptidase activity / defense response to bacterium / endoplasmic reticulum lumen / proteolysis / extracellular space / extracellular region / zinc ion binding / 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 ...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-098 / A disintegrin and metalloproteinase with thrombospondin motifs 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.02 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catalytic Domain of ADAMTS-5
B: Catalytic Domain of ADAMTS-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,12412
Polymers48,8732
Non-polymers1,25010
Water8,773487
1
A: Catalytic Domain of ADAMTS-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0626
Polymers24,4371
Non-polymers6255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Catalytic Domain of ADAMTS-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0626
Polymers24,4371
Non-polymers6255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.692, 44.444, 76.458
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Catalytic Domain of ADAMTS-5


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 / 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-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-098 / (3R)-N~2~-(cyclopropylmethyl)-N~1~-hydroxy-3-(3-hydroxybenzyl)-N~4~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-L-aspartamide


Mass: 439.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H29N3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 32.85 %
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: 2.02→50 Å / Num. all: 23498 / Num. obs: 23451 / % possible obs: 99.8 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 29.1
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 7.8 / Num. unique all: 2238 / Rsym value: 0.098 / % possible all: 98.2

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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

3b8z


Resolution: 2.02→31.02 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.9 / SU B: 4.396 / SU ML: 0.127 / Isotropic thermal model: Individual Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23793 1205 5.1 %RANDOM
Rwork0.15912 ---
obs0.16321 22235 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.495 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20.16 Å2
2---1.33 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.02→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 72 487 3909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213488
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9624732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69324.103156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64815575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1541520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022668
X-RAY DIFFRACTIONr_nbd_refined0.2070.21770
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2370
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.2137
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.288
X-RAY DIFFRACTIONr_mcbond_it0.7721.52211
X-RAY DIFFRACTIONr_mcangle_it1.34923454
X-RAY DIFFRACTIONr_scbond_it1.88231400
X-RAY DIFFRACTIONr_scangle_it2.9394.51272
LS refinement shellResolution: 2.019→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 69 -
Rwork0.149 1561 -
obs--97.14 %

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