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- PDB-1ztq: Crystal structure of the catalytic domain of MMP-13 complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1ztq
TitleCrystal structure of the catalytic domain of MMP-13 complexed with WAY-033
ComponentsCollagenase 3
KeywordsHYDROLASE / MMPs / METALLOPROTEASE / MMP-13 / COLLAGENASE / ZINC CHELATOR / hydroxamate / hydrophobic S1' / P1' group
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-033 / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWu, J. / Rush III, T.S. / Hotchandani, R. / Du, X. / Geck, M. / Collins, E. / Xu, Z.B. / Skotnicki, J. / Levin, J.I. / Lovering, F.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Identification of potent and selective MMP-13 inhibitors
Authors: Wu, J. / Rush III, T.S. / Hotchandani, R. / Du, X. / Geck, M. / Collins, E. / Xu, Z.B. / Skotnicki, J. / Levin, J.I. / Lovering, F.E.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _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_asym_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_asym_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600 HETEROGEN The Ca atoms 560, 561, 562 are associated with Chain A, 563, 564, 565 with chain B, 566, ... HETEROGEN The Ca atoms 560, 561, 562 are associated with Chain A, 563, 564, 565 with chain B, 566, 567, 568 with chain C and 569, 570 and 571 with chain D.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,40628
Polymers74,4314
Non-polymers2,97424
Water9,044502
1
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3517
Polymers18,6081
Non-polymers7446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3517
Polymers18,6081
Non-polymers7446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3517
Polymers18,6081
Non-polymers7446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3517
Polymers18,6081
Non-polymers7446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.937, 135.252, 69.385
Angle α, β, γ (deg.)90.00, 104.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18607.824 Da / Num. of mol.: 4 / Fragment: MMP-13 CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#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.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-033 / N-({4'-[(1-BENZOFURAN-2-YLCARBONYL)AMINO]-1,1'-BIPHENYL-4-YL}SULFONYL)-L-VALINE / WAY033


Mass: 492.544 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H24N2O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350, 0.15M Ammonium Sulfate, 0.1M tris pH 8.5, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2001
RadiationMonochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 43015 / Num. obs: 37032 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 6.9 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.46 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 37766.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1851 5 %RANDOM
Rwork0.236 ---
obs0.236 37032 86 %-
all-43015 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.3791 Å2 / ksol: 0.395928 e/Å3
Displacement parametersBiso mean: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.93 Å20 Å2-1.33 Å2
2--4.96 Å20 Å2
3----1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 160 502 5692
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.342.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2-2.130.34722450.27642350.023423562.8
2.13-2.290.3273060.2725538
2.29-2.520.3182860.2525852
2.52-2.880.33240.2426224
2.88-3.630.2693380.2156634
3.63-200.2573730.2246698
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4033cr.param033cr.top

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