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

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Basic information

Entry
Database: PDB / ID: 5uwl
TitleMatrix metalloproteinase-13 complexed with selective inhibitor compound (S)-17a
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 / bone morphogenesis / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / 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 / bone morphogenesis / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / 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-8OJ / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,09112
Polymers38,7332
Non-polymers1,35810
Water1,11762
1
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0987
Polymers19,3671
Non-polymers7326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9935
Polymers19,3671
Non-polymers6264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.962, 129.962, 142.076
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 19366.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (UNP RESIDUES 104-274) / Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: PKA8H / 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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-8OJ / (S)-N-(3-methyl-1-(methylamino)-1-oxobutan-2-yl)-5-(4-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)phenyl)furan-2-carboxamide


Mass: 480.579 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H28N4O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.47 Å3/Da / Density % sol: 72.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium chloride, 0.1 M Tris pH 7, 1.0 M sodium citrate

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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: 2.55→60.07 Å / Num. obs: 23277 / % possible obs: 99 % / Redundancy: 7.3 % / Biso Wilson estimate: 50.1 Å2 / Rpim(I) all: 0.047 / Rsym value: 0.124 / Net I/σ(I): 12.1
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3333 / Rpim(I) all: 0.369 / Rsym value: 0.967 / % possible all: 99.1

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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: 2.55→60.07 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.76
RfactorNum. reflection% reflection
Rfree0.2395 1999 8.59 %
Rwork0.1988 --
obs0.2023 23266 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→60.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 76 62 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012713
X-RAY DIFFRACTIONf_angle_d1.1583689
X-RAY DIFFRACTIONf_dihedral_angle_d17.171954
X-RAY DIFFRACTIONf_chiral_restr0.052366
X-RAY DIFFRACTIONf_plane_restr0.008475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.61380.3631380.31271476X-RAY DIFFRACTION99
2.6138-2.68450.36671420.30731507X-RAY DIFFRACTION99
2.6845-2.76350.33981410.27981493X-RAY DIFFRACTION99
2.7635-2.85270.30231400.27331493X-RAY DIFFRACTION99
2.8527-2.95470.33481420.25991518X-RAY DIFFRACTION99
2.9547-3.0730.30841410.26711497X-RAY DIFFRACTION99
3.073-3.21280.34671420.25761511X-RAY DIFFRACTION99
3.2128-3.38220.22161420.22111511X-RAY DIFFRACTION99
3.3822-3.59410.23521430.20921516X-RAY DIFFRACTION99
3.5941-3.87150.23361430.17241527X-RAY DIFFRACTION99
3.8715-4.2610.1841440.15861532X-RAY DIFFRACTION99
4.261-4.87740.1911460.14621540X-RAY DIFFRACTION98
4.8774-6.1440.18841450.17251553X-RAY DIFFRACTION97
6.144-60.08970.21541500.16851593X-RAY DIFFRACTION93

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