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- PDB-8k5y: Crystal structure of human proMMP-9 catalytic domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 8k5y
TitleCrystal structure of human proMMP-9 catalytic domain in complex with inhibitor
ComponentsMatrix metalloproteinase-9
KeywordsHYDROLASE / MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding / positive regulation of release of cytochrome c from mitochondria / Activation of Matrix Metalloproteinases / endodermal cell differentiation / response to amyloid-beta / Collagen degradation / macrophage differentiation / collagen catabolic process / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / cellular response to cadmium ion / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of apoptotic process / positive regulation of protein phosphorylation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site ...Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / 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 / Metallopeptidase, catalytic domain superfamily / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / Chem-VP6 / Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsKamitani, M. / Mima, M. / Nishikawa-Shimono, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: Discovery of novel indole derivatives as potent and selective inhibitors of proMMP-9 activation.
Authors: Nishikawa-Shimono, R. / Kuwabara, M. / Fujisaki, S. / Matsuda, D. / Endo, M. / Kamitani, M. / Futamura, A. / Nomura, Y. / Yamaguchi-Sasaki, T. / Yabuuchi, T. / Yamaguchi, C. / Tanaka- ...Authors: Nishikawa-Shimono, R. / Kuwabara, M. / Fujisaki, S. / Matsuda, D. / Endo, M. / Kamitani, M. / Futamura, A. / Nomura, Y. / Yamaguchi-Sasaki, T. / Yabuuchi, T. / Yamaguchi, C. / Tanaka-Yamamoto, N. / Satake, S. / Abe-Sato, K. / Funayama, K. / Sakata, M. / Takahashi, S. / Hirano, K. / Fukunaga, T. / Uozumi, Y. / Kato, S. / Tamura, Y. / Nakamori, T. / Mima, M. / Mishima-Tsumagari, C. / Nozawa, D. / Imai, Y. / Asami, T.
History
DepositionJul 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix metalloproteinase-9
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,71515
Polymers54,3512
Non-polymers1,36413
Water4,918273
1
A: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9068
Polymers27,1761
Non-polymers7307
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area11050 Å2
MethodPISA
2
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8097
Polymers27,1761
Non-polymers6336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.530, 73.990, 77.130
Angle α, β, γ (deg.)90.00, 103.36, 90.00
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 Matrix metalloproteinase-9 / MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B / GELB


Mass: 27175.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP9, CLG4B / Production host: Escherichia coli (E. coli) / References: UniProt: P14780, gelatinase B

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Non-polymers , 5 types, 286 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-VP6 / (3-azanyl-4-fluoranyl-5,7,8,9-tetrahydropyrido[4,3-c]azepin-6-yl)-[6-(2-oxidanylpropan-2-yl)-1H-indol-2-yl]methanone


Mass: 382.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23FN4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 25% w/v Polyethylene glycol 1500, 100mM SPG buffer pH5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.52→75.05 Å / Num. obs: 76843 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 11.17
Reflection shellResolution: 1.52→1.61 Å / Num. unique obs: 12130 / CC1/2: 0.541

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→49.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.676 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19788 3778 4.9 %RANDOM
Rwork0.17617 ---
obs0.17725 73064 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.724 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20.91 Å2
2--0.59 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.52→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 71 273 4030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133873
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173461
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.6655278
X-RAY DIFFRACTIONr_angle_other_deg1.4881.5997967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92821.644219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9515573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.061526
X-RAY DIFFRACTIONr_chiral_restr0.090.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02939
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_it2.0392.1591856
X-RAY DIFFRACTIONr_mcbond_other2.0292.1581854
X-RAY DIFFRACTIONr_mcangle_it2.943.232317
X-RAY DIFFRACTIONr_mcangle_other2.933.2292317
X-RAY DIFFRACTIONr_scbond_it3.1282.4892017
X-RAY DIFFRACTIONr_scbond_other3.1272.4892018
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7413.6012961
X-RAY DIFFRACTIONr_long_range_B_refined6.13941.71816187
X-RAY DIFFRACTIONr_long_range_B_other6.09941.56816000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 264 -
Rwork0.378 5369 -
obs--99.75 %

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