[English] 日本語
Yorodumi
- PDB-2ozr: MMP13 Catalytic Domain Complexed with 4-{[1-methyl-2,4-dioxo-6-(3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ozr
TitleMMP13 Catalytic Domain Complexed with 4-{[1-methyl-2,4-dioxo-6-(3-phenylprop-1-yn-1-yl)-1,4-dihydroquinazolin-3(2H)-yl]methyl}benzoic acid
ComponentsCollagenase 3
KeywordsHYDROLASE / Crystal Complex Structure / Matrix Metalloproteinase / MMP13 Catalytic Domain / MMP13 Specific 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
Chem-GG1 / ACETOHYDROXAMIC ACID / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJohnson, 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.H. ...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.H. / Baragi, V. / Lesch, C. / Roark, W.H. / Lie, J.J. / Fasquelle, V. / Wilson, M. / Robertson, D. / Datta, K. / Guzman, R. / Han, H.-K. / Dyer, R.D.
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 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 3, 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_ncs_dom_lim / struct_ref_seq_dif
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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Collagenase 3
B: Collagenase 3
C: Collagenase 3
D: Collagenase 3
E: Collagenase 3
F: Collagenase 3
G: Collagenase 3
H: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,25960
Polymers152,5558
Non-polymers5,70452
Water18,4471024
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)161.836, 71.974, 138.130
Angle α, β, γ (deg.)90.00, 124.59, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1TYRTYRASPASPAA83 - 2494 - 170
2TYRTYRASPASPBB83 - 2494 - 170
3TYRTYRASPASPCC83 - 2494 - 170
4ASNASNASPASPDD84 - 2495 - 170
5TYRTYRASPASPEE83 - 2494 - 170
6TYRTYRASPASPFF83 - 2494 - 170
7TYRTYRGLYGLYGG83 - 2484 - 169
8TYRTYRGLYGLYHH83 - 2484 - 169

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Collagenase 3 / Matrix metalloproteinase-13 / MMP-13


Mass: 19069.314 Da / Num. of mol.: 8 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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

-
Non-polymers , 5 types, 1076 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Details: Special chemical synthesis
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ca / Details: commersially synthesised
#4: Chemical
ChemComp-GG1 / 4-{[1-METHYL-2,4-DIOXO-6-(3-PHENYLPROP-1-YN-1-YL)-1,4-DIHYDROQUINAZOLIN-3(2H)-YL]METHYL}BENZOIC ACID


Mass: 424.448 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C26H20N2O4
#5: Chemical
ChemComp-HAE / ACETOHYDROXAMIC ACID


Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2 / Comment: inhibitor, medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1024 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Dissolved in DMSO inhibitor was mixed with protein (protein concentration: 1mg/ml) at 5:1 ratio, 0.1 M acetohydrohamic acid added. Ternary complex was concentrated (to 17 mg/ml protien ...Details: Dissolved in DMSO inhibitor was mixed with protein (protein concentration: 1mg/ml) at 5:1 ratio, 0.1 M acetohydrohamic acid added. Ternary complex was concentrated (to 17 mg/ml protien concentration). 1-2 uL hagind drops were mixed with same amount of reservoit solution (2.1 M ammonium sulfate in 0.1 M Hepes buffer) , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 160245 / Num. obs: 69624 / % possible obs: 90.7 % / Redundancy: 2.3 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.096 / Χ2: 1.433 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2 / Num. unique all: 4793 / Rsym value: 0.342 / Χ2: 0.991 / % possible all: 62.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2OW9

2ow9


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.898 / SU B: 18.324 / SU ML: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.841 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Used NCS Restraints
RfactorNum. reflection% reflectionSelection details
Rfree0.34 2869 5.1 %RANDOM
Rwork0.248 ---
obs0.253 53427 96.4 %-
all-56296 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.737 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10558 0 316 1024 11898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02111233
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.96615278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29151317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38123.939523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.114151609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2441524
X-RAY DIFFRACTIONr_chiral_restr0.080.21495
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028972
X-RAY DIFFRACTIONr_nbd_refined0.1990.25262
X-RAY DIFFRACTIONr_nbtor_refined0.3150.27487
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2785
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.2268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.264
X-RAY DIFFRACTIONr_mcbond_it0.5061.56734
X-RAY DIFFRACTIONr_mcangle_it0.885210626
X-RAY DIFFRACTIONr_scbond_it0.88935657
X-RAY DIFFRACTIONr_scangle_it1.3674.54652
Refine LS restraints NCS

Ens-ID: 1 / Number: 1279 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.960.5
2BMEDIUM POSITIONAL0.940.5
3CMEDIUM POSITIONAL0.840.5
4DMEDIUM POSITIONAL0.840.5
5EMEDIUM POSITIONAL1.050.5
6FMEDIUM POSITIONAL1.040.5
7GMEDIUM POSITIONAL0.960.5
8HMEDIUM POSITIONAL0.910.5
1AMEDIUM THERMAL0.482
2BMEDIUM THERMAL0.552
3CMEDIUM THERMAL0.632
4DMEDIUM THERMAL0.612
5EMEDIUM THERMAL0.732
6FMEDIUM THERMAL0.672
7GMEDIUM THERMAL0.472
8HMEDIUM THERMAL0.442
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 192 -
Rwork0.317 3659 -
obs-3851 89.81 %
Refinement TLS params.Method: refined / Origin x: 20.4251 Å / Origin y: 0.0314 Å / Origin z: 28.1447 Å
111213212223313233
T0.0062 Å20.0047 Å2-0.0259 Å2-0.0182 Å20.0051 Å2--0.0283 Å2
L0.0304 °2-0.0061 °2-0.0301 °2-0.0216 °2-0.0615 °2--0.2536 °2
S-0.0218 Å °-0.032 Å °0.0061 Å °0.0588 Å °-0.0134 Å °-0.0349 Å °0.0299 Å °0.1155 Å °0.0352 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 - 2494 - 170
3CC83 - 2494 - 170
4DD84 - 2495 - 170
5EE83 - 2494 - 170
6FF83 - 2494 - 170
7GG83 - 2484 - 169
8HH83 - 2484 - 169

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more