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- PDB-2wo8: MMP12 complex with a beta hydroxy carboxylic acid -

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Basic information

Entry
Database: PDB / ID: 2wo8
TitleMMP12 complex with a beta hydroxy carboxylic acid
ComponentsMACROPHAGE METALLOELASTASE
KeywordsHYDROLASE / POLYMORPHISM / GLYCOPROTEIN / METAL-BINDING / MATRIX METALLOPROTEASE MMP-12 COMPLEX STRUCTURE / METALLOPROTEASE / EXTRACELLULAR MATRIX / ZYMOGEN / PROTEASE / SECRETED
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / positive regulation of interferon-alpha production / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to virus / metalloendopeptidase activity / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm
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
Chem-023 / (3S)-5-biphenyl-4-yl-3-hydroxypentanoic acid / Macrophage metalloelastase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsHolmes, I.P. / Gaines, S. / Watson, S.P. / Lorthioir, O. / Walker, A. / Baddeley, S.J. / Herbert, S. / Egan, D. / Convery, M.A. / Singh, O.M.P. ...Holmes, I.P. / Gaines, S. / Watson, S.P. / Lorthioir, O. / Walker, A. / Baddeley, S.J. / Herbert, S. / Egan, D. / Convery, M.A. / Singh, O.M.P. / Gross, J.W. / Strelow, J.M. / Smith, R.H. / Amour, A.J. / Brown, D. / Martin, S.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: The Identification of Beta-Hydroxy Carboxylic Acids as Selective Mmp-12 Inhibitors.
Authors: Holmes, I.P. / Gaines, S. / Watson, S.P. / Lorthioir, O. / Walker, A. / Baddeley, S.J. / Herbert, S. / Egan, D. / Convery, M.A. / Singh, O.M.P. / Gross, J.W. / Strelow, J.M. / Smith, R.H. / ...Authors: Holmes, I.P. / Gaines, S. / Watson, S.P. / Lorthioir, O. / Walker, A. / Baddeley, S.J. / Herbert, S. / Egan, D. / Convery, M.A. / Singh, O.M.P. / Gross, J.W. / Strelow, J.M. / Smith, R.H. / Amour, A.J. / Brown, D. / Martin, S.L.
History
DepositionJul 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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_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_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: MACROPHAGE METALLOELASTASE
B: MACROPHAGE METALLOELASTASE
C: MACROPHAGE METALLOELASTASE
D: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,68129
Polymers72,9294
Non-polymers2,75225
Water9,674537
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A: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8667
Polymers18,2321
Non-polymers6336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9317
Polymers18,2321
Non-polymers6996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7706
Polymers18,2321
Non-polymers5375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1159
Polymers18,2321
Non-polymers8838
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.043, 65.264, 67.808
Angle α, β, γ (deg.)66.47, 83.86, 71.37
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
MACROPHAGE METALLOELASTASE / MATRIX METALLOPROTEINASE-12 / MMP12 / MACROPHAGE METALLOELASTASE / MACROPHAGE ELASTASE / ME


Mass: 18232.355 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 106-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: MACROPHAGE / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P39900, macrophage elastase

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Non-polymers , 7 types, 562 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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-077 / (3S)-5-biphenyl-4-yl-3-hydroxypentanoic acid


Mass: 270.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-023 / N^2^-[(2R)-2-{(1S)-1-[FORMYL(HYDROXY)AMINO]ETHYL}-5-PHENYLPENTANOYL]-N,3-DIMETHYL-L-VALINAMIDE


Mass: 391.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H33N3O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsINITIAL METHIONINE IS FROM THE EXPRESSION VECTOR

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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: 2.46 Å3/Da / Density % sol: 50.1 % / Description: NONE
Crystal growpH: 5.2
Details: 100MM MES PH 5.2-5.6, 16-20% PEG 5KMME, 200MM AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.96
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 45242 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 1.94 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.35 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0073refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.09 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS IS PRESENT BUT WAS NOT USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24589 2274 5 %RANDOM
Rwork0.18416 ---
obs0.18728 42858 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.526 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.79 Å2-1.38 Å2
2---2.65 Å21.45 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5095 0 147 537 5779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215449
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9417297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8215645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27223.205259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31915785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6491528
X-RAY DIFFRACTIONr_chiral_restr0.1070.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214228
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.28923223
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29145111
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.49252226
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.77772186
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 158 -
Rwork0.253 3014 -
obs--100 %

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