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- PDB-4jpa: Mmp13 in complex with a piperazine hydantoin ligand -

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Basic information

Entry
Database: PDB / ID: 4jpa
TitleMmp13 in complex with a piperazine hydantoin ligand
ComponentsCollagenase 3
KeywordsHYDROLASE / matrix metalloprotease / calcium binding / zinc binding
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-AZ6 / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsGerhardt, S. / Hargreaves, D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Hydantoin based inhibitors of MMP13--discovery of AZD6605.
Authors: De Savi, C. / Waterson, D. / Pape, A. / Lamont, S. / Hadley, E. / Mills, M. / Page, K.M. / Bowyer, J. / Maciewicz, R.A.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 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_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_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_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)40,43014
Polymers38,9912
Non-polymers1,43912
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-60 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.771, 35.986, 101.492
Angle α, β, γ (deg.)90.00, 134.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-436-

HOH

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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: 19495.691 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 103-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Production host: Escherichia coli (E. coli)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 5 types, 385 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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-AZ6 / 3-[({2-[4-({[(4S)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl}sulfonyl)piperazin-1-yl]pyrimidin-5-yl}oxy)methyl]benzonitrile


Mass: 485.516 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23N7O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 27.5% PEG 4000 1.25M AmFormate, 100mM TrisHCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→35.9 Å / Num. all: 23660 / Num. obs: 23627 / % possible obs: 94.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
DENZOdata reduction
SCALEPACKdata scaling
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.549 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2.6 / ESU R: 0.219 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1140 5.1 %RANDOM
Rwork0.17735 ---
obs0.18002 21114 93.93 %-
all-22254 --
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 max: 79.11 Å2 / Biso mean: 16.432 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å2-1.77 Å2
2--0.08 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 78 373 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212810
X-RAY DIFFRACTIONr_bond_other_d0.0010.022297
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9663827
X-RAY DIFFRACTIONr_angle_other_deg0.71735376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38323.985133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.515402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.685156
X-RAY DIFFRACTIONr_chiral_restr0.0620.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02596
X-RAY DIFFRACTIONr_nbd_refined0.1960.2601
X-RAY DIFFRACTIONr_nbd_other0.1650.22243
X-RAY DIFFRACTIONr_nbtor_refined0.1960.21367
X-RAY DIFFRACTIONr_nbtor_other0.0820.21388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2245
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.232
X-RAY DIFFRACTIONr_mcbond_it0.3811.51645
X-RAY DIFFRACTIONr_mcbond_other0.0621.5673
X-RAY DIFFRACTIONr_mcangle_it0.71322647
X-RAY DIFFRACTIONr_scbond_it0.95231217
X-RAY DIFFRACTIONr_scangle_it1.4274.51180
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 64 -
Rwork0.217 1475 -
all-1539 -
obs--90.74 %
Refinement TLS params.Method: refined / Origin x: 26.086 Å / Origin y: 0.1641 Å / Origin z: 20.7925 Å
111213212223313233
T-0.018 Å2-0.0036 Å2-0.0018 Å2--0.0333 Å20.0018 Å2---0.0018 Å2
L0.2552 °2-0.0489 °2-0.0101 °2-0.091 °20.0154 °2--0.2516 °2
S0.014 Å °0.0088 Å °-0.0003 Å °-0.0157 Å °-0.0082 Å °0.014 Å °-0.0116 Å °0.0103 Å °-0.0058 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A104 - 272
2X-RAY DIFFRACTION1B104 - 269
3X-RAY DIFFRACTION1A301 - 305
4X-RAY DIFFRACTION1B301 - 305
5X-RAY DIFFRACTION1A306
6X-RAY DIFFRACTION1B306
7X-RAY DIFFRACTION1A401 - 589
8X-RAY DIFFRACTION1B401 - 584

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