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- PDB-5uwn: Matrix metalloproteinase-13 complexed with selective inhibitor co... -

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Basic information

Entry
Database: PDB / ID: 5uwn
TitleMatrix metalloproteinase-13 complexed with selective inhibitor compound 10d
ComponentsCollagenase 3
Keywordshydrolase/hydrolase inhibitor / Metalloproteinase / collagenase / MMP-13 / 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 / 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-8O7 / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTaylor, A.B. / Cao, X. / Hart, P.J.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors.
Authors: Choi, J.Y. / Fuerst, R. / Knapinska, A.M. / Taylor, A.B. / Smith, L. / Cao, X. / Hart, P.J. / Fields, G.B. / Roush, W.R.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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
C: Collagenase 3
D: Collagenase 3
E: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,51644
Polymers96,8335
Non-polymers4,68339
Water00
1
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2268
Polymers19,3671
Non-polymers8607
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2268
Polymers19,3671
Non-polymers8607
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2268
Polymers19,3671
Non-polymers8607
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,51411
Polymers19,3671
Non-polymers1,14810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3229
Polymers19,3671
Non-polymers9568
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.727, 131.727, 418.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 19366.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (UNP RESIDUES 104-274) / Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: PAK8H / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-8O7 / N-(2-aminoethyl)-4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-sulfonami de / N-(2-aminoethyl)-4'-{[(4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)sulfanyl]methyl}[1,1'-biphenyl]-4-sulfon amide


Mass: 456.581 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H24N4O3S2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4

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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: 4.88 Å3/Da / Density % sol: 74.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2→125.66 Å / Num. obs: 30172 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 60.8 Å2 / Rpim(I) all: 0.12 / Rsym value: 0.244 / Net I/σ(I): 7.6
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4397 / Rpim(I) all: 0.506 / Rsym value: 1.03 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L19

4l19


Resolution: 3.2→95.8 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.05
RfactorNum. reflection% reflection
Rfree0.2344 1998 6.62 %
Rwork0.1948 --
obs0.1974 30163 97.29 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 3.2→95.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6588 0 245 0 6833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117051
X-RAY DIFFRACTIONf_angle_d1.3479600
X-RAY DIFFRACTIONf_dihedral_angle_d15.5632458
X-RAY DIFFRACTIONf_chiral_restr0.071938
X-RAY DIFFRACTIONf_plane_restr0.011223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.28010.39421430.30482019X-RAY DIFFRACTION99
3.2801-3.36880.30681410.27941984X-RAY DIFFRACTION99
3.3688-3.46790.32331440.27352029X-RAY DIFFRACTION99
3.4679-3.57980.27861410.25071998X-RAY DIFFRACTION99
3.5798-3.70780.26921420.21281992X-RAY DIFFRACTION99
3.7078-3.85620.26781410.20082008X-RAY DIFFRACTION98
3.8562-4.03170.24081430.18062012X-RAY DIFFRACTION98
4.0317-4.24430.19981430.17232007X-RAY DIFFRACTION98
4.2443-4.51020.17811410.16291992X-RAY DIFFRACTION98
4.5102-4.85840.18921430.15722007X-RAY DIFFRACTION97
4.8584-5.34730.19981430.15532011X-RAY DIFFRACTION97
5.3473-6.1210.22541410.17822000X-RAY DIFFRACTION96
6.121-7.71130.23991440.18422021X-RAY DIFFRACTION95
7.7113-95.8420.19891480.1812085X-RAY DIFFRACTION93

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