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- PDB-3zxh: MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor -

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Basic information

Entry
Database: PDB / ID: 3zxh
TitleMMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor
ComponentsCOLLAGENASE 3
KeywordsHYDROLASE / METALLO-ENZYME / CARBOXYLATE INHIBITOR / COLLAGEN DEGRADATION / EXTRACELLULAR MATRIX / METAL-BINDING / METALLOPROTEASE
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-E41 / Collagenase 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsClark, K.L. / Kulathila, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Potent and Selective 2-Naphthylsulfonamide Substituted Hydroxamic Acid Inhibitors of Matrix Metalloproteinase-13.
Authors: Tommasi, R.A. / Weiler, S. / Mcquire, L.W. / Rogel, O. / Chambers, M. / Clark, K.L. / Doughty, J. / Fang, J. / Ganu, V. / Grob, J. / Goldberg, R. / Goldstein, R. / Lavoie, S. / Kulathila, R. ...Authors: Tommasi, R.A. / Weiler, S. / Mcquire, L.W. / Rogel, O. / Chambers, M. / Clark, K.L. / Doughty, J. / Fang, J. / Ganu, V. / Grob, J. / Goldberg, R. / Goldstein, R. / Lavoie, S. / Kulathila, R. / Macchia, W. / Melton, R. / Springer, C. / Walker, M. / Zhang, J. / Zhu, L. / Shultz, M.
History
DepositionAug 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Atomic model
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,25820
Polymers38,4712
Non-polymers1,78818
Water7,440413
1
A: COLLAGENASE 3
B: COLLAGENASE 3
hetero molecules

A: COLLAGENASE 3
B: COLLAGENASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,51740
Polymers76,9424
Non-polymers3,57536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area15010 Å2
ΔGint-341.9 kcal/mol
Surface area28550 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-164.2 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.904, 36.141, 95.069
Angle α, β, γ (deg.)90.00, 131.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2090-

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: 19235.383 Da / Num. of mol.: 2 / Fragment: PROTEASE DOMAIN, RESIDUES 104-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 5 types, 431 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.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-E41 / N-hydroxy-N^2^-(3-methylbutyl)-N^2^-(naphthalen-2-ylsulfonyl)-D-valinamide


Mass: 392.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N2O4S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 1.83 Å3/Da / Density % sol: 32.43 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8.2
Details: 15% PEG 6K, 0.1M TRIS PH 8.2, 0.9 M HCOONA, 4 DEG. CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.0003
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 1.3→9 Å / Num. obs: 84772 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 9.84 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKLdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→9.004 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 14.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1585 1984 2.3 %
Rwork0.1454 --
obs0.1457 84772 99.4 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.926 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0059 Å20 Å21.3463 Å2
2--2.4339 Å20 Å2
3----2.428 Å2
Refinement stepCycle: LAST / Resolution: 1.3→9.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 95 413 3150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122856
X-RAY DIFFRACTIONf_angle_d1.3853886
X-RAY DIFFRACTIONf_dihedral_angle_d14.2041001
X-RAY DIFFRACTIONf_chiral_restr0.082389
X-RAY DIFFRACTIONf_plane_restr0.01500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.33250.24041410.20075707X-RAY DIFFRACTION97
1.3325-1.36840.19841390.18685859X-RAY DIFFRACTION99
1.3684-1.40850.19561580.17245863X-RAY DIFFRACTION99
1.4085-1.45380.15411340.15235932X-RAY DIFFRACTION100
1.4538-1.50550.16861440.14395898X-RAY DIFFRACTION100
1.5055-1.56550.15971420.14925885X-RAY DIFFRACTION100
1.5655-1.63640.14661340.12145940X-RAY DIFFRACTION100
1.6364-1.72210.13741440.12415935X-RAY DIFFRACTION100
1.7221-1.82910.13471400.12465910X-RAY DIFFRACTION100
1.8291-1.9690.15051410.13475938X-RAY DIFFRACTION100
1.969-2.16460.16321370.13255975X-RAY DIFFRACTION100
2.1646-2.47220.15151480.13865958X-RAY DIFFRACTION100
2.4722-3.09350.1511400.14696021X-RAY DIFFRACTION100
3.0935-9.00440.16161420.15675967X-RAY DIFFRACTION97
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)
10.31670.0238-0.42940.28330.06230.80780.0040.0170.0121-0.03870.0065-0.00520.004-0.0337-0.00870.06140.0011-0.00580.04420.00050.0594-4.962317.555751.963
20.26140.0058-0.01760.24570.01770.30350.0142-0.0004-0.0216-0.0447-0.0023-0.02670.03190.03120.01730.0440.008-0.00340.02560.00010.05625.46219.5561.8198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 104:401
2X-RAY DIFFRACTION2CHAIN B AND RESID 104:401

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