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- PDB-3kry: Crystal structure of MMP-13 in complex with SC-78080 -

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Basic information

Entry
Database: PDB / ID: 3kry
TitleCrystal structure of MMP-13 in complex with SC-78080
ComponentsCollagenase 3
KeywordsHYDROLASE / collagenase / collagenase-3 / MMP-13 / Collagen degradation / Disease mutation / Disulfide bond / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Protease / Secreted
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-3KR / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKiefer, J.R. / Williams, J.M. / Becker, D.P.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Orally-active MMP-1 sparing alpha-tetrahydropyranyl and alpha-piperidinyl sulfone matrix metalloproteinase (MMP) inhibitors with efficacy in cancer, arthritis, and cardiovascular disease
Authors: Becker, D.P. / Barta, T.E. / Bedell, L.J. / Boehm, T.L. / Bond, B.R. / Carroll, J. / Carron, C.P. / Decrescenzo, G.A. / Easton, A.M. / Freskos, J.N. / Funckes-Shippy, C.L. / Heron, M. / ...Authors: Becker, D.P. / Barta, T.E. / Bedell, L.J. / Boehm, T.L. / Bond, B.R. / Carroll, J. / Carron, C.P. / Decrescenzo, G.A. / Easton, A.M. / Freskos, J.N. / Funckes-Shippy, C.L. / Heron, M. / Hockerman, S. / Howard, C.P. / Kiefer, J.R. / Li, M.H. / Mathis, K.J. / McDonald, J.J. / Mehta, P.P. / Munie, G.E. / Sunyer, T. / Swearingen, C.A. / Villamil, C.I. / Welsch, D. / Williams, J.M. / Yu, Y. / Yao, J.
History
DepositionNov 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 24, 2015Group: Data collection
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 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_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
C: Collagenase 3
D: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,95324
Polymers74,0434
Non-polymers2,91020
Water9,404522
1
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2386
Polymers18,5111
Non-polymers7275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2386
Polymers18,5111
Non-polymers7275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2386
Polymers18,5111
Non-polymers7275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2386
Polymers18,5111
Non-polymers7275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Collagenase 3
hetero molecules

A: Collagenase 3
B: Collagenase 3
D: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,95324
Polymers74,0434
Non-polymers2,91020
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_545x,y-1,z1
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-85 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.317, 70.016, 69.094
Angle α, β, γ (deg.)92.42, 94.23, 104.94
Int Tables number1
Space group name H-MP1
DetailsFour protein molecules were observed in the asymmetric unit of the crystal lattice, but their arrangement is not believed to be physiologically relevant.

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Components

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


Mass: 18510.707 Da / Num. of mol.: 4 / Fragment: catalytic domain, residues 104-267
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
#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.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-3KR / 1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-carboxamide


Mass: 516.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H23F3N2O7S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100mM Hepes buffer, pH 7.4 1.4M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 17, 2000 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 46273 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.6 Å2

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Processing

Software
NameVersionClassification
MAR345data collection
X-PLORmodel building
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.68 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.879 / SU B: 4.799 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25571 2425 5 %RANDOM
Rwork0.2063 ---
obs0.20879 46273 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0.09 Å20.29 Å2
2---0.62 Å20.21 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 156 522 5867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215535
X-RAY DIFFRACTIONr_bond_other_d0.0010.023567
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.9657546
X-RAY DIFFRACTIONr_angle_other_deg0.79838672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16923.961255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46815791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1011511
X-RAY DIFFRACTIONr_chiral_restr0.0670.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021173
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_it0.481.53266
X-RAY DIFFRACTIONr_mcbond_other0.0931.51323
X-RAY DIFFRACTIONr_mcangle_it0.8825256
X-RAY DIFFRACTIONr_scbond_it1.26432269
X-RAY DIFFRACTIONr_scangle_it2.0064.52290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 164 -
Rwork0.243 3061 -
obs--86.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.254-0.0391-0.09351.3709-0.58811.97440.00680.13390.0295-0.09520.0050.00960.0024-0.0307-0.01180.0088-0.0006-0.00380.0549-0.01360.0184-0.1822-0.35690.1363
20000000000000000.0688000.068800.0688000
30000000000000000.0688000.068800.0688000
40000000000000000.0688000.068800.0688000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1104 - 1267
2X-RAY DIFFRACTION2B1104 - 1267
3X-RAY DIFFRACTION3C1104 - 1267
4X-RAY DIFFRACTION4D1104 - 1267

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