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- PDB-3tvc: Human MMP13 in complex with L-glutamate motif inhibitor -

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Basic information

Entry
Database: PDB / ID: 3tvc
TitleHuman MMP13 in complex with L-glutamate motif inhibitor
ComponentsCollagenase 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / pseudo dipeptides / potent inhibitors / metzincin / Zinc metalloprotease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / bone morphogenesis / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / bone mineralization / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / bone morphogenesis / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / bone mineralization / 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 / extracellular region / zinc ion binding
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / 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-E3P / DI(HYDROXYETHYL)ETHER / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsStura, E.A. / Dive, V. / Devel, L. / Czarny, B. / Beau, F. / Vera, L. / Cassar-Lajeunesse, E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Simple pseudo-dipeptides with a P2' glutamate: a novel inhibitor family of matrix metalloproteases and other metzincins.
Authors: Devel, L. / Beau, F. / Amoura, M. / Vera, L. / Cassar-Lajeunesse, E. / Garcia, S. / Czarny, B. / Stura, E.A. / Dive, V.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Sep 13, 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_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.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_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

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Assembly

Deposited unit
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,02410
Polymers19,0241
Non-polymers1,0009
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.303, 85.160, 40.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 19024.166 Da / Num. of mol.: 1 / Fragment: MMP-13 catalytic subunit (UNP residues 104-272)
Source method: isolated from a genetically manipulated source
Details: Expressed as Pro-MMP13 / Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 5 types, 114 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-E3P / N~2~-[3-(1,1':4',1''-terphenyl-4-yl)propanoyl]-L-alpha-glutamine


Mass: 430.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26N2O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PROTEIN-INHIBITOR SOLUTION: MMP13 AT 20 MG/ML CO-CRYSTALLIZED WITH E3P AT 1.1 MILLI-M. RESERVOIR SOLUTION: 17.5% PEG 20K, 0.1 M MES, 0.02 M NACL. CRYOPROTECTANT: 5% DIETHYLENE GLYCOL, 5% ...Details: PROTEIN-INHIBITOR SOLUTION: MMP13 AT 20 MG/ML CO-CRYSTALLIZED WITH E3P AT 1.1 MILLI-M. RESERVOIR SOLUTION: 17.5% PEG 20K, 0.1 M MES, 0.02 M NACL. CRYOPROTECTANT: 5% DIETHYLENE GLYCOL, 5% ETHYLENE GLYCOL, 5% MPD, 5% PROPYLENE GLYCOL, 5% DMSO, 5% GLYCEROL, 0.005 M 3-(-PYRIDINIO)-1-PROPANESULFONATE, 10% PEG 20K, 0.033 M SODIUM ACETATE, 0.033 M ADA, 0.033 M BICINE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2011 / Details: bent cylindrical mirror
RadiationMonochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.43→85.1 Å / Num. all: 8412 / Num. obs: 8151 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.21 % / Biso Wilson estimate: 35.49 Å2 / Rmerge(I) obs: 0.29 / Rsym value: 0.31 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.43-2.596.631.3992.8112311.2987.4
6.81-85.16.230.7924.274360.0798
4.84-6.816.910.13919.127170.12999.3
3.96-4.847.230.15619.148930.14599
3.43-3.967.40.23714.4810310.22199
3.07-3.437.450.4019.9511630.37498.9
2.8-3.077.520.6486.6712850.60498.8
2.59-2.87.580.9634.7213950.89898.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QJ2 catalytic domain only (Chain A)

3qj2
PDB Unreleased entry


Resolution: 2.43→40.916 Å / SU ML: 0.65 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 369 4.54 %RANDOM
Rwork0.1622 ---
obs0.1654 8127 97.02 %-
all-8377 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.386 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 24.782 Å2
Baniso -1Baniso -2Baniso -3
1--2.7543 Å20 Å20 Å2
2--1.2548 Å2-0 Å2
3---1.4995 Å2
Refinement stepCycle: LAST / Resolution: 2.43→40.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 58 105 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081480
X-RAY DIFFRACTIONf_angle_d1.1212005
X-RAY DIFFRACTIONf_dihedral_angle_d21.949525
X-RAY DIFFRACTIONf_chiral_restr0.083194
X-RAY DIFFRACTIONf_plane_restr0.006262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4304-2.7820.3271220.22172389X-RAY DIFFRACTION93
2.782-3.50470.23761220.15992627X-RAY DIFFRACTION99
3.5047-40.92150.19651250.14332742X-RAY DIFFRACTION99

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