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- PDB-3o2x: MMP-13 in complex with selective tetrazole core inhibitor -

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Basic information

Entry
Database: PDB / ID: 3o2x
TitleMMP-13 in complex with selective tetrazole core inhibitor
ComponentsCollagenase 3
KeywordsHYDROLASE
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-3O2 / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKiefer, J.R. / Barta, T.E. / Becker, D.P. / Mathis, K.J. / Williams, J.
CitationJournal: To be Published
Title: MMP-13 in complex with selective tetrazole core inhibitor
Authors: Barta, T.E. / Becker, D.P. / Bedell, L.J. / Hockerman, S.L. / Kiefer, J.R. / Li, M.H. / Villamill, C.I. / Rico, J.G. / Mcdonald, J.J.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 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)78,37435
Polymers73,6744
Non-polymers4,70031
Water12,286682
1
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,78510
Polymers18,4191
Non-polymers1,3669
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,78510
Polymers18,4191
Non-polymers1,3669
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3547
Polymers18,4191
Non-polymers9366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4508
Polymers18,4191
Non-polymers1,0327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Collagenase 3
D: Collagenase 3
hetero molecules

A: Collagenase 3
C: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,37435
Polymers73,6744
Non-polymers4,70031
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_466x-1/2,-y+3/2,-z+11
Buried area10570 Å2
ΔGint-205 kcal/mol
Surface area28440 Å2
MethodPISA
6
A: Collagenase 3
C: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,13917
Polymers36,8372
Non-polymers2,30215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-85 kcal/mol
Surface area16830 Å2
MethodPISA
7
B: Collagenase 3
D: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,23518
Polymers36,8372
Non-polymers2,39816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-96 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.864, 95.257, 120.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 18418.611 Da / Num. of mol.: 4 / Fragment: Catalytic domain
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 , 6 types, 713 molecules

#2: Chemical
ChemComp-3O2 / N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide


Mass: 628.621 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H31F3N6O7S
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: Lithium sulfate, HEPES buffer,pH 7.7, VAPOR DIFFUSION, HANGING 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: Jan 4, 2001
RadiationMonochromator: Crystal / Protocol: 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: 56980 / % possible obs: 84.3 % / Observed criterion σ(I): -3 / Rsym value: 0.084 / Net I/σ(I): 16.4
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.271 / % possible all: 79.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.72 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.915 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20956 2879 5.1 %RANDOM
Rwork0.17668 ---
obs0.17838 53767 84.09 %-
all-53767 --
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: 8.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 257 682 6139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0215660
X-RAY DIFFRACTIONr_bond_other_d0.0010.023611
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9837724
X-RAY DIFFRACTIONr_angle_other_deg0.78138779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7835660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12323.93257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77215793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8421512
X-RAY DIFFRACTIONr_chiral_restr0.0610.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021184
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_it0.3471.53288
X-RAY DIFFRACTIONr_mcbond_other0.0581.51332
X-RAY DIFFRACTIONr_mcangle_it0.64725292
X-RAY DIFFRACTIONr_scbond_it0.89432372
X-RAY DIFFRACTIONr_scangle_it1.4654.52432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 199 -
Rwork0.201 3649 -
obs--78.71 %
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)
11.26230.4347-0.05581.4560.2622.8833-0.0308-0.12150.03930.1768-0.00830.0213-0.0132-0.04290.03920.0480.0209-0.01340.0218-0.01720.046854.799486.499875.4179
21.09320.4484-0.07521.8190.35263.0611-0.0201-0.06980.03490.2532-0.00030.0982-0.008-0.1060.02040.06190.02170.0220.0297-0.0150.051517.27786.17576.901
31.7075-0.5870.25821.2989-0.31223.4170.00680.14650.0678-0.0829-0.0292-0.095-0.06670.13590.02240.0099-0.0059-0.00280.01920.01310.045264.277588.896245.7022
41.6128-0.3950.2051.1179-0.36633.41360.00130.10570.0732-0.0828-0.0104-0.0596-0.04350.04820.00910.0081-0.00190.00390.0150.01260.038227.490488.715247.3895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1104 - 2997
2X-RAY DIFFRACTION2B2104 - 2997
3X-RAY DIFFRACTION3C1104 - 2997
4X-RAY DIFFRACTION4D2104 - 2997

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