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- PDB-8jug: Crystal structure of human MMP-7 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 8jug
TitleCrystal structure of human MMP-7 in complex with inhibitor
Components
  • Matrilysin
  • Peptide Inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Matrilysin / Matrin / Matrix metalloproteinase-7 / Pump-1 protease / Uterine metalloproteinase / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


matrilysin / antibacterial peptide secretion / antibacterial peptide biosynthetic process / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation / membrane protein ectodomain proteolysis / collagen catabolic process / extracellular matrix disassembly ...matrilysin / antibacterial peptide secretion / antibacterial peptide biosynthetic process / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation / membrane protein ectodomain proteolysis / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / metallopeptidase activity / regulation of cell population proliferation / defense response to Gram-negative bacterium / endopeptidase activity / Extra-nuclear estrogen signaling / defense response to Gram-positive bacterium / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region
Similarity search - Function
Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase ...Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKamitani, M. / Abe-Sato, K. / Oka, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Structure-Based Optimization and Biological Evaluation of Potent and Selective MMP-7 Inhibitors for Kidney Fibrosis.
Authors: Abe-Sato, K. / Tabuse, H. / Kanazawa, H. / Kamitani, M. / Endo, M. / Tokura, S. / Wakabayashi, S. / Yahara, T. / Takeda, T. / Hitaka, K. / Gunji, E. / Kojima, N. / Oka, Y.
History
DepositionJun 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrilysin
C: Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4946
Polymers20,2832
Non-polymers2114
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-56 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.060, 76.060, 61.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Matrilysin / Matrin / Matrix metalloproteinase-7 / MMP-7 / Pump-1 protease / Uterine metalloproteinase


Mass: 19344.727 Da / Num. of mol.: 1 / Mutation: E215Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP7, MPSL1, PUMP1 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09237, matrilysin
#2: Protein/peptide Peptide Inhibitor


Mass: 938.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 10% w/v Polyethylene glycol 20000, 2% v/v 1,4-Dioxane, 100mM BICINE pH9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.3→48.05 Å / Num. obs: 42891 / % possible obs: 99.8 % / Redundancy: 12.3 % / CC1/2: 0.998 / Net I/σ(I): 9.2
Reflection shellResolution: 1.3→1.37 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6269 / CC1/2: 0.583

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→48.05 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.906 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23789 2108 4.9 %RANDOM
Rwork0.22122 ---
obs0.22208 40782 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.598 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0 Å2
2---1 Å2-0 Å2
3---2 Å2
Refinement stepCycle: 1 / Resolution: 1.3→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 4 113 1449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131449
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181299
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.7731981
X-RAY DIFFRACTIONr_angle_other_deg1.4751.6982988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6575162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17821.51566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57715200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.183157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3351.442651
X-RAY DIFFRACTIONr_mcbond_other1.3071.439650
X-RAY DIFFRACTIONr_mcangle_it1.9892.157812
X-RAY DIFFRACTIONr_mcangle_other1.9882.159813
X-RAY DIFFRACTIONr_scbond_it1.7961.666798
X-RAY DIFFRACTIONr_scbond_other1.7951.669799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7142.4271170
X-RAY DIFFRACTIONr_long_range_B_refined3.88417.1061647
X-RAY DIFFRACTIONr_long_range_B_other3.79916.8661628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.304→1.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 155 -
Rwork0.379 3000 -
obs--100 %

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