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

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Basic information

Entry
Database: PDB / ID: 5uwk
TitleMatrix metalloproteinase-13 complexed with selective inhibitor compound (S)-10a
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 / Activation of Matrix Metalloproteinases / bone mineralization / 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 / Activation of Matrix Metalloproteinases / bone mineralization / 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 / extracellular region / zinc ion binding
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / 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-8OM / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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)40,26314
Polymers38,7332
Non-polymers1,52912
Water6,557364
1
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1317
Polymers19,3671
Non-polymers7656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1317
Polymers19,3671
Non-polymers7656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.784, 57.155, 120.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4 / 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-8OM / (S)-3-methyl-2-(4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-ylsulfonamido)butanoic acid


Mass: 513.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27N3O5S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.19 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris:HCl pH 8.5, 25% PEG 3350

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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: 1.6→120.56 Å / Num. obs: 42491 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 18.2 Å2 / Rpim(I) all: 0.035 / Rsym value: 0.062 / Net I/σ(I): 15.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6124 / Rpim(I) all: 0.43 / Rsym value: 0.768 / % possible all: 100

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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: 1.6→51.646 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.1989 2000 4.71 %
Rwork0.1477 --
obs0.1501 42432 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→51.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 80 364 2992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082724
X-RAY DIFFRACTIONf_angle_d1.1013708
X-RAY DIFFRACTIONf_dihedral_angle_d16.023954
X-RAY DIFFRACTIONf_chiral_restr0.052368
X-RAY DIFFRACTIONf_plane_restr0.007476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28771420.20472855X-RAY DIFFRACTION100
1.64-1.68440.29571400.19552846X-RAY DIFFRACTION100
1.6844-1.73390.2741410.18332846X-RAY DIFFRACTION100
1.7339-1.78990.2321420.16212868X-RAY DIFFRACTION100
1.7899-1.85390.22991410.15172849X-RAY DIFFRACTION100
1.8539-1.92810.24251430.15352882X-RAY DIFFRACTION100
1.9281-2.01590.22731410.14122859X-RAY DIFFRACTION100
2.0159-2.12210.19311410.13072861X-RAY DIFFRACTION100
2.1221-2.25510.18891420.13732874X-RAY DIFFRACTION100
2.2551-2.42920.18211430.14262906X-RAY DIFFRACTION100
2.4292-2.67370.18981450.15622903X-RAY DIFFRACTION100
2.6737-3.06050.22051440.16452928X-RAY DIFFRACTION100
3.0605-3.85570.19531460.13492949X-RAY DIFFRACTION99
3.8557-51.67250.15151490.13793006X-RAY DIFFRACTION97

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