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- PDB-3elm: Crystal Structure of MMP-13 Complexed with Inhibitor 24f -

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Basic information

Entry
Database: PDB / ID: 3elm
TitleCrystal Structure of MMP-13 Complexed with Inhibitor 24f
ComponentsCollagenase 3
KeywordsHYDROLASE / metallo-enzyme / MMP-13 / carboxylate inhibitor / Calcium / Collagen degradation / Disease mutation / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen
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-24F / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsKulathila, R. / Monovich, L. / Koehn, J.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Discovery of potent, selective, and orally active carboxylic acid based inhibitors of matrix metalloproteinase-13
Authors: Monovich, L.G. / Tommasi, R.A. / Fujimoto, R.A. / Blancuzzi, V. / Clark, K. / Cornell, W.D. / Doti, R. / Doughty, J. / Fang, J. / Farley, D. / Fitt, J. / Ganu, V. / Goldberg, R. / Goldstein, ...Authors: Monovich, L.G. / Tommasi, R.A. / Fujimoto, R.A. / Blancuzzi, V. / Clark, K. / Cornell, W.D. / Doti, R. / Doughty, J. / Fang, J. / Farley, D. / Fitt, J. / Ganu, V. / Goldberg, R. / Goldstein, R. / Lavoie, S. / Kulathila, R. / Macchia, W. / Parker, D.T. / Melton, R. / O'Byrne, E. / Pastor, G. / Pellas, T. / Quadros, E. / Reel, N. / Roland, D.M. / Sakane, Y. / Singh, H. / Skiles, J. / Somers, J. / Toscano, K. / Wigg, A. / Zhou, S. / Zhu, L. / Shieh, W.C. / Xue, S. / McQuire, L.W.
History
DepositionSep 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)40,03415
Polymers38,4712
Non-polymers1,56313
Water4,306239
1
A: Collagenase 3
B: Collagenase 3
hetero molecules

A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,06830
Polymers76,9424
Non-polymers3,12726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area8840 Å2
ΔGint-157 kcal/mol
Surface area28740 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-73 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.500, 36.070, 95.180
Angle α, β, γ (deg.)90.000, 130.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 19235.383 Da / Num. of mol.: 2 / Fragment: UNP residues 104 to 274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: Pet3B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
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.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-24F / (2R)-({[5-(4-ethoxyphenyl)thiophen-2-yl]sulfonyl}amino){1-[(1-methylethoxy)carbonyl]piperidin-4-yl}ethanoic acid


Mass: 510.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H30N2O7S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 13% PEG 6K, 0.1M Tris, 1.2M NaAcetate, 2% glycerol, 15 mM CaCl2, 10 uM Zn(Ac)2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 4, 2001 / Details: multi-layer mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 26969 / % possible obs: 96.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.038 / Χ2: 0.848 / Net I/σ(I): 26.246
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2114 / Χ2: 0.84 / % possible all: 76.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
CNX2002refinement
RefinementResolution: 1.9→25.56 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 725073 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2588 10 %RANDOM
Rwork0.164 ---
obs-25975 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.97 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 54.41 Å2 / Biso mean: 19.453 Å2 / Biso min: 8.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å21.65 Å2
2---0.47 Å20 Å2
3----1.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.9→25.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2631 0 79 239 2949
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.213 355 10.4 %
Rwork0.163 3066 -
all-3421 -
obs--74.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION424F.parameter24F.topology

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