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- PDB-5ue3: proMMP-9desFnII -

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Basic information

Entry
Database: PDB / ID: 5ue3
TitleproMMP-9desFnII
ComponentsMatrix metalloproteinase-9
KeywordsHYDROLASE / prommp9 / zymogen
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / EPH-ephrin mediated repulsion of cells / collagen catabolic process / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / embryo implantation / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to cadmium ion / collagen binding / 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 / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of 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. / 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 / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.599 Å
AuthorsAlexander, R.S. / Spurlino, J. / Milligan, C.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Discovery of a highly selective chemical inhibitor of matrix metalloproteinase-9 (MMP-9) that allosterically inhibits zymogen activation.
Authors: Scannevin, R.H. / Alexander, R. / Haarlander, T.M. / Burke, S.L. / Singer, M. / Huo, C. / Zhang, Y.M. / Maguire, D. / Spurlino, J. / Deckman, I. / Carroll, K.I. / Lewandowski, F. / Devine, E. ...Authors: Scannevin, R.H. / Alexander, R. / Haarlander, T.M. / Burke, S.L. / Singer, M. / Huo, C. / Zhang, Y.M. / Maguire, D. / Spurlino, J. / Deckman, I. / Carroll, K.I. / Lewandowski, F. / Devine, E. / Dzordzorme, K. / Tounge, B. / Milligan, C. / Bayoumy, S. / Williams, R. / Schalk-Hihi, C. / Leonard, K. / Jackson, P. / Todd, M. / Kuo, L.C. / Rhodes, K.J.
History
DepositionDec 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)54,18618
Polymers53,0252
Non-polymers1,16116
Water10,575587
1
A: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9568
Polymers26,5131
Non-polymers4437
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,23010
Polymers26,5131
Non-polymers7179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Matrix metalloproteinase-9
hetero molecules

B: Matrix metalloproteinase-9
hetero molecules

A: Matrix metalloproteinase-9
hetero molecules

A: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,37236
Polymers106,0514
Non-polymers2,32132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
crystal symmetry operation3_556x+1/2,y+1/2,z+11
crystal symmetry operation4_656-x+3/2,y+1/2,-z+11
Buried area6700 Å2
ΔGint-242 kcal/mol
Surface area39680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.300, 73.200, 77.500
Angle α, β, γ (deg.)90.00, 106.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-307-

SO4

21B-665-

HOH

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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: 26512.721 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, 603 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG 8K 1% glycerol 0.2 M ammonium sulfate 100 mM NaCacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.599→49.19 Å / Num. obs: 62722 / % possible obs: 98.1 % / Redundancy: 3.19 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
d*TREKdata reduction
RefinementResolution: 1.599→32.84 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4
RfactorNum. reflection% reflection
Rfree0.1838 6345 10.12 %
Rwork0.1545 --
obs0.1575 62702 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.599→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 38 587 4207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113738
X-RAY DIFFRACTIONf_angle_d1.245094
X-RAY DIFFRACTIONf_dihedral_angle_d13.0952155
X-RAY DIFFRACTIONf_chiral_restr0.071519
X-RAY DIFFRACTIONf_plane_restr0.009667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5992-1.61740.21391840.16891853X-RAY DIFFRACTION94
1.6174-1.63640.19171990.16491820X-RAY DIFFRACTION97
1.6364-1.65630.19742230.16361879X-RAY DIFFRACTION97
1.6563-1.67730.2021970.15941828X-RAY DIFFRACTION97
1.6773-1.69940.20512120.15831886X-RAY DIFFRACTION98
1.6994-1.72260.18842270.14751858X-RAY DIFFRACTION98
1.7226-1.74730.19732100.15011854X-RAY DIFFRACTION97
1.7473-1.77330.19511800.1471879X-RAY DIFFRACTION97
1.7733-1.8010.20112260.14441851X-RAY DIFFRACTION98
1.801-1.83060.18622090.1471865X-RAY DIFFRACTION98
1.8306-1.86210.19812200.15951857X-RAY DIFFRACTION98
1.8621-1.8960.21712170.15651853X-RAY DIFFRACTION98
1.896-1.93250.20232160.14891908X-RAY DIFFRACTION98
1.9325-1.97190.17262270.14341840X-RAY DIFFRACTION98
1.9719-2.01480.15992050.13831910X-RAY DIFFRACTION98
2.0148-2.06160.16391900.1431863X-RAY DIFFRACTION98
2.0616-2.11320.18052240.15251886X-RAY DIFFRACTION99
2.1132-2.17030.17912100.14271900X-RAY DIFFRACTION99
2.1703-2.23410.16772040.14541911X-RAY DIFFRACTION99
2.2341-2.30620.18022040.14971906X-RAY DIFFRACTION99
2.3062-2.38860.20922170.16011897X-RAY DIFFRACTION99
2.3886-2.48420.16622300.15751876X-RAY DIFFRACTION99
2.4842-2.59730.18422060.16451947X-RAY DIFFRACTION99
2.5973-2.73410.19872010.15991915X-RAY DIFFRACTION99
2.7341-2.90530.20412100.15981912X-RAY DIFFRACTION99
2.9053-3.12950.18352370.15851896X-RAY DIFFRACTION99
3.1295-3.44410.17942310.15331905X-RAY DIFFRACTION99
3.4441-3.94180.15432170.15241877X-RAY DIFFRACTION98
3.9418-4.96350.16472250.13811886X-RAY DIFFRACTION98
4.9635-32.84690.21861870.19061839X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.87530.2570.40182.51430.7762.07490.1299-0.16430.2730.2133-0.15760.1917-0.1017-0.06970.01040.1133-0.02690.04320.14-0.00670.10998.413829.309219.5053
20.6820.0761-0.15771.113-0.08531.22280.0342-0.0119-0.00510.0442-0.0461-0.0491-0.00130.12720.01080.0730.0038-0.00320.0980.01390.087527.6620.31267.2373
32.8172-0.2922-0.62751.5553-0.01611.6268-0.22750.3403-0.2781-0.58530.2913-0.64290.08630.4719-0.0510.2524-0.03410.11550.2904-0.08950.280262.066153.371740.2322
41.8611-0.6845-0.66222.1365-0.1431.65130.01830.11640.1167-0.1740.02730.198-0.1056-0.0685-0.040.0967-0.0149-0.04860.124-0.0080.085137.985861.412248.1476
51.13420.26490.03951.53960.44841.5401-0.03380.0592-0.0827-0.06920.02070.05820.07160.00610.0080.08310.00090.00220.0720.00670.075743.843355.659852.0088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 443 )
3X-RAY DIFFRACTION3chain 'B' and (resid 41 through 104 )
4X-RAY DIFFRACTION4chain 'B' and (resid 105 through 133 )
5X-RAY DIFFRACTION5chain 'B' and (resid 134 through 444 )

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