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- PDB-7ju8: X-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-y... -

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Basic information

Entry
Database: PDB / ID: 7ju8
TitleX-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-yl)pyridine
ComponentsCollagenase 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
4-(1,2,3-thiadiazol-4-yl)pyridine / FORMIC ACID / TRIETHYLENE GLYCOL / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFarrow, N.A.
CitationJournal: Acs Omega / Year: 2021
Title: Indole Inhibitors of MMP-13 for Arthritic Disorders
Authors: Taylor, S.J. / Abeywardane, A. / Liang, S. / Xiong, Z. / Proudfoot, J.R. / Farmer, B.S. / Gao, D.A. / Heim-Riether, A. / Smith-Keenan, L.L. / Muegge, I. / Yu, Y. / Zhang, Q. / Souza, D. / ...Authors: Taylor, S.J. / Abeywardane, A. / Liang, S. / Xiong, Z. / Proudfoot, J.R. / Farmer, B.S. / Gao, D.A. / Heim-Riether, A. / Smith-Keenan, L.L. / Muegge, I. / Yu, Y. / Zhang, Q. / Souza, D. / Panzenbeck, M. / Goldberg, D. / Hill-Drzewi, M. / Margarit, M. / Collins, B. / Li, J.X. / Zuvela-Jelaska, L. / Li, J. / Farrow, N.A.
History
DepositionAug 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,07025
Polymers38,4712
Non-polymers1,59923
Water6,684371
1
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,03613
Polymers19,2351
Non-polymers80012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,03412
Polymers19,2351
Non-polymers79911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.764, 35.987, 95.724
Angle α, β, γ (deg.)90.000, 130.550, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Collagenase 3 / Matrix metalloproteinase-13 / MMP-13


Mass: 19235.383 Da / Num. of mol.: 2 / Fragment: PROTEASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Production host: Escherichia coli (E. coli)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 7 types, 394 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-9DY / 4-(1,2,3-thiadiazol-4-yl)pyridine


Mass: 163.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5N3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% w/v PEG4000, 1 M ammonium formate, and 100 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2→72.74 Å / Num. obs: 24211 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 2.6
Reflection shellResolution: 2→2.08 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.1978 / Num. unique obs: 1637 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XUD

1xud


Resolution: 2→72.74 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.855 / SU B: 6.104 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 1202 5 %RANDOM
Rwork0.1978 ---
obs0.2012 22822 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.93 Å2 / Biso mean: 21.911 Å2 / Biso min: 8.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0.31 Å2
2--0.15 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 2→72.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 86 371 3108
Biso mean--43.81 33.13 -
Num. residues----333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212853
X-RAY DIFFRACTIONr_bond_other_d0.0020.022387
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.9593873
X-RAY DIFFRACTIONr_angle_other_deg0.78535595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89824.104134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86215413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.999156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02614
X-RAY DIFFRACTIONr_nbd_refined0.1880.2642
X-RAY DIFFRACTIONr_nbd_other0.1710.22466
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21379
X-RAY DIFFRACTIONr_nbtor_other0.0830.21402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2310
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.249
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 86 -
Rwork0.243 1637 -
all-1723 -
obs--99.48 %

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