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- PDB-2ow9: Crystal structure analysis of the MMP13 catalytic domain in compl... -

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Basic information

Entry
Database: PDB / ID: 2ow9
TitleCrystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor
ComponentsCollagenase 3
KeywordsHYDROLASE / Complex crystal structure / Martix Metalloproteinase / MMP13 / Specific MMP13 inhibitor / S1' MMP13 inhibitor
Function / homology
Function and homology information


growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Peptidoglycan binding-like / 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 ...Peptidoglycan binding-like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETOHYDROXAMIC ACID / Chem-SP6 / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsPavlovsky, A.G.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia side effects.
Authors: Johnson, A.R. / Pavlovsky, A.G. / Ortwine, D.F. / Prior, F. / Man, C.F. / Bornemeier, D.A. / Banotai, C.A. / Mueller, W.T. / McConnell, P. / Yan, C. / Baragi, V. / Lesch, C. / Roark, W.H. / ...Authors: Johnson, A.R. / Pavlovsky, A.G. / Ortwine, D.F. / Prior, F. / Man, C.F. / Bornemeier, D.A. / Banotai, C.A. / Mueller, W.T. / McConnell, P. / Yan, C. / Baragi, V. / Lesch, C. / Roark, W.H. / Wilson, M. / Datta, K. / Guzman, R. / Han, H.K. / Dyer, R.D.
History
DepositionFeb 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,71218
Polymers38,1392
Non-polymers1,57316
Water7,530418
1
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8849
Polymers19,0691
Non-polymers8158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8289
Polymers19,0691
Non-polymers7598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Collagenase 3
B: Collagenase 3
hetero molecules

A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,42436
Polymers76,2774
Non-polymers3,14632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14130 Å2
ΔGint-322 kcal/mol
Surface area28940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.764, 36.343, 71.684
Angle α, β, γ (deg.)90.000, 93.530, 90.000
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 Collagenase 3 / / Matrix metalloproteinase-13 / MMP-13


Mass: 19069.314 Da / Num. of mol.: 2 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: cartilage / Gene: MMP13 / Plasmid: pGEMEX1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 6 types, 434 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.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SP6 / BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE


Mass: 392.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16N2O4S
#6: Chemical ChemComp-HAE / ACETOHYDROXAMIC ACID / Acetohydroxamic acid


Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2 / Comment: inhibitor, medication*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein concentration: 7-20 mg/ml. Well solution: 18-22% PEG MME 5000, 0.2M Lithium sulfate, 0.1M Hepes buffer. 2-4 microliter drops with 1:1 ratio of protein complex solution and well ...Details: Protein concentration: 7-20 mg/ml. Well solution: 18-22% PEG MME 5000, 0.2M Lithium sulfate, 0.1M Hepes buffer. 2-4 microliter drops with 1:1 ratio of protein complex solution and well solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2000 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→70.71 Å / Num. obs: 37780 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.056 / Net I/σ(I): 17.7
Reflection shellResolution: 1.74→1.78 Å / Mean I/σ(I) obs: 1.9 / Num. unique all: 2606 / Rsym value: 0.226 / % possible all: 67.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CIZ

1ciz


Resolution: 1.74→70.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.487 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.112 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1847 5 %RANDOM
Rwork0.167 ---
obs0.168 35279 98.57 %-
all-37780 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.075 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.18 Å2
2---0.48 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.102 Å0.112 Å
Refinement stepCycle: LAST / Resolution: 1.74→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 82 418 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222870
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.9673894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.435331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12824135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38215437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.726156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022272
X-RAY DIFFRACTIONr_nbd_refined0.1810.21483
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2326
X-RAY DIFFRACTIONr_metal_ion_refined0.1090.231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.232
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3260.22
X-RAY DIFFRACTIONr_mcbond_it0.4531.51698
X-RAY DIFFRACTIONr_mcangle_it0.78822688
X-RAY DIFFRACTIONr_scbond_it1.13231394
X-RAY DIFFRACTIONr_scangle_it1.664.51206
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 111 -
Rwork0.241 2168 -
obs-2279 83.73 %
Refinement TLS params.Method: refined / Origin x: 73.6041 Å / Origin y: -5.0632 Å / Origin z: 21.1917 Å
111213212223313233
T0.0004 Å20.0092 Å20.0113 Å2--0.0266 Å2-0.012 Å2---0.0228 Å2
L0.2603 °20.0622 °20.1632 °2-0.1428 °2-0.0812 °2--0.2592 °2
S0.0101 Å °0.0163 Å °-0.0072 Å °-0.0541 Å °0.0012 Å °-0.017 Å °0.018 Å °0.0287 Å °-0.0113 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL

IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA83 - 2494 - 170
2BB83 - 2484 - 169

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