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

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Basic information

Entry
Database: PDB / ID: 7wxx
TitleCrystal structure of human MMP-7 in complex with inhibitor
Components
  • Matrilysin
  • Peptide Inhibitor
KeywordsHYDROLASE / Matrilysin / Matrin / Matrix metalloproteinase-7 / Pump-1 protease / Uterine metalloproteinase
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: 1.5 Å
AuthorsKamitani, M. / Oka, Y. / Tabuse, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of Highly Potent and Selective Matrix Metalloproteinase-7 Inhibitors by Hybridizing the S1' Subsite Binder with Short Peptides.
Authors: Tabuse, H. / Abe-Sato, K. / Kanazawa, H. / Yashiro, M. / Tamura, Y. / Kamitani, M. / Hitaka, K. / Gunji, E. / Mitani, A. / Kojima, N. / Oka, Y.
History
DepositionFeb 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: 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
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 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrilysin
B: Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3246
Polymers20,1132
Non-polymers2114
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-57 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.360, 77.360, 62.710
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: 768.222 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.: 148 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 20% w/v Polyethylene glycol 6000, 100mM MES pH6.0, 200mM Lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→54.7 Å / Num. obs: 29640 / % possible obs: 100 % / Redundancy: 11.8 % / Rrim(I) all: 0.201 / Net I/σ(I): 11.81
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 11.7 % / Num. unique obs: 4719 / CC1/2: 0.687 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOLREP11.6.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y6C

2y6c


Resolution: 1.5→54.7 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.731 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20343 1624 5.5 %RANDOM
Rwork0.17018 ---
obs0.17191 28015 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2---1.16 Å20 Å2
3---2.33 Å2
Refinement stepCycle: 1 / Resolution: 1.5→54.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 4 148 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191415
X-RAY DIFFRACTIONr_bond_other_d0.0020.021242
X-RAY DIFFRACTIONr_angle_refined_deg2.2711.9681931
X-RAY DIFFRACTIONr_angle_other_deg1.15132886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22122.95161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15915207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.397157
X-RAY DIFFRACTIONr_chiral_restr0.1350.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211600
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02314
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_it2.2582.239679
X-RAY DIFFRACTIONr_mcbond_other2.2362.233678
X-RAY DIFFRACTIONr_mcangle_it3.2573.34854
X-RAY DIFFRACTIONr_mcangle_other3.2573.346855
X-RAY DIFFRACTIONr_scbond_it3.4312.606736
X-RAY DIFFRACTIONr_scbond_other3.4292.605737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9853.7691078
X-RAY DIFFRACTIONr_long_range_B_refined7.59246.1336956
X-RAY DIFFRACTIONr_long_range_B_other7.5745.8116834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.545 150 -
Rwork0.496 2046 -
obs--99.95 %

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