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- PDB-8h78: Crystal structure of human MMP-2 catalytic domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 8h78
TitleCrystal structure of human MMP-2 catalytic domain in complex with inhibitor
ComponentsMatrix metalloproteinase-2
KeywordsHYDROLASE / Gelatinase A / Matrix metalloproteinase-2 / 72 kDa type IV collagenase
Function / homologyDIHYDROGENPHOSPHATE ION / Chem-L2U
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKamitani, M. / Takeuchi, T. / Mima, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with a Phenylbenzamide-Pentapeptide Hybrid Scaffold.
Authors: Takeuchi, T. / Nomura, Y. / Tamita, T. / Nishikawa, R. / Kakinuma, H. / Kojima, N. / Hitaka, K. / Tamura, Y. / Kamitani, M. / Mima, M. / Nozoe, A. / Hayashi, M.
History
DepositionOct 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix metalloproteinase-2
B: Matrix metalloproteinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,05115
Polymers37,6202
Non-polymers2,43113
Water55831
1
A: Matrix metalloproteinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0748
Polymers18,8101
Non-polymers1,2647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area8110 Å2
MethodPISA
2
B: Matrix metalloproteinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9777
Polymers18,8101
Non-polymers1,1676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.683, 79.683, 127.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Matrix metalloproteinase-2


Mass: 18809.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP2 / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: gelatinase A

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Non-polymers , 5 types, 44 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-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#5: Chemical ChemComp-L2U / (2~{R})-2-[[4-[(4-aminocarbonylphenyl)carbonylamino]phenyl]sulfonylamino]-5-[(2~{S},4~{S})-4-azanyl-2-[[(2~{S})-1-[[(2~{S})-1-[(5-azanyl-5-oxidanylidene-pentyl)amino]-5-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]-methyl-amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamoyl]pyrrolidin-1-yl]-5-oxidanylidene-pentanoic acid


Mass: 916.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H57N9O13S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 16 % w/v Polyethylene glycol 8,000, 20 % v/v Glycerol, 40 mM Potassium di-hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.4→21.78 Å / Num. obs: 15535 / % possible obs: 99.8 % / Redundancy: 11.5 % / CC1/2: 0.976 / Net I/σ(I): 5.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2252 / CC1/2: 0.567 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AYU

3ayu


Resolution: 2.4→21.78 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.844 / SU B: 17.224 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R: 0.58 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31892 799 5.2 %RANDOM
Rwork0.26515 ---
obs0.26794 14715 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.291 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å2-0 Å2
2--0.3 Å2-0 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 2.4→21.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 143 31 2804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132853
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172472
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.7063889
X-RAY DIFFRACTIONr_angle_other_deg1.221.6475688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4815333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47422.566152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9615377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5751513
X-RAY DIFFRACTIONr_chiral_restr0.0660.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023309
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02711
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_it3.0333.6251338
X-RAY DIFFRACTIONr_mcbond_other3.0173.621337
X-RAY DIFFRACTIONr_mcangle_it4.9235.421669
X-RAY DIFFRACTIONr_mcangle_other4.935.4241670
X-RAY DIFFRACTIONr_scbond_it2.6483.7181514
X-RAY DIFFRACTIONr_scbond_other2.6473.7191515
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2675.5312220
X-RAY DIFFRACTIONr_long_range_B_refined9.50667.04312215
X-RAY DIFFRACTIONr_long_range_B_other9.50567.06112209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 65 -
Rwork0.374 1077 -
obs--100 %

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