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- PDB-3i7g: MMP-13 in complex with a non zinc-chelating inhibitor -

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Basic information

Entry
Database: PDB / ID: 3i7g
TitleMMP-13 in complex with a non zinc-chelating inhibitor
ComponentsCollagenase 3
KeywordsHYDROLASE / protease / Calcium / Collagen degradation / Disease mutation / Disulfide bond / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Secreted / Zinc / Zymogen
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-732 / FORMIC ACID / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFarrow, N.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Improving potency and selectivity of a new class of non-Zn-chelating MMP-13 inhibitors.
Authors: Heim-Riether, A. / Taylor, S.J. / Liang, S. / Gao, D.A. / Xiong, Z. / Michael August, E. / Collins, B.K. / Farmer, B.T. / Haverty, K. / Hill-Drzewi, M. / Junker, H.D. / Mariana Margarit, S. ...Authors: Heim-Riether, A. / Taylor, S.J. / Liang, S. / Gao, D.A. / Xiong, Z. / Michael August, E. / Collins, B.K. / Farmer, B.T. / Haverty, K. / Hill-Drzewi, M. / Junker, H.D. / Mariana Margarit, S. / Moss, N. / Neumann, T. / Proudfoot, J.R. / Keenan, L.S. / Sekul, R. / Zhang, Q. / Li, J. / Farrow, N.A.
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,44015
Polymers38,4712
Non-polymers96913
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-144 kcal/mol
Surface area15990 Å2
MethodPISA
2
A: Collagenase 3
B: Collagenase 3
hetero molecules

A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,88030
Polymers76,9424
Non-polymers1,93826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area9830 Å2
ΔGint-301 kcal/mol
Surface area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.770, 36.100, 95.333
Angle α, β, γ (deg.)90.000, 130.770, 90.000
Int Tables number5
Space group name H-MC121

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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: UNP residues 104-274
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 , 5 types, 359 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.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-732 / 5-(4-chlorophenyl)-N-[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]furan-2-carboxamide


Mass: 374.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23ClN2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.27 Å3/Da / Density % sol: 45.71 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→50.65 Å / Num. obs: 24419 / Biso Wilson estimate: 20.95 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_6refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→33.374 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.849 / SU ML: 0.85 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1171 4.8 %
Rwork0.173 --
obs0.176 24413 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.716 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 83.34 Å2 / Biso mean: 23.951 Å2 / Biso min: 7.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.961 Å20 Å21.062 Å2
2--0.89 Å2-0 Å2
3----3.851 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 36 352 3006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012743
X-RAY DIFFRACTIONf_angle_d1.2373725
X-RAY DIFFRACTIONf_chiral_restr0.082373
X-RAY DIFFRACTIONf_plane_restr0.007485
X-RAY DIFFRACTIONf_dihedral_angle_d18.53947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.0390.2791210.1822051217268
2.039-2.1460.2371560.1742897305397
2.146-2.2810.231310.1623004313599
2.281-2.4570.2171640.1630253189100
2.457-2.7040.2521410.17330233164100
2.704-3.0950.261400.19130603200100
3.095-3.8980.2151510.1630693220100
3.898-33.3790.1981670.1673113328099

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