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- PDB-5uwm: Matrix metalloproteinase-13 complexed with selective inhibitor co... -

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Basic information

Entry
Database: PDB / ID: 5uwm
TitleMatrix metalloproteinase-13 complexed with selective inhibitor compound (R)-17a
Components(Collagenase 3) x 2
Keywordshydrolase/hydrolase inhibitor / Metalloproteinase / collagenase / MMP-13 / hydrolase / hydrolase-hydrolase inhibitor complex
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 / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / 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-8OA / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsTaylor, A.B. / Cao, X. / Hart, P.J.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors.
Authors: Choi, J.Y. / Fuerst, R. / Knapinska, A.M. / Taylor, A.B. / Smith, L. / Cao, X. / Hart, P.J. / Fields, G.B. / Roush, W.R.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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)41,28216
Polymers39,8184
Non-polymers1,46312
Water6,359353
1
A: Collagenase 3
C: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6418
Polymers19,9092
Non-polymers7326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-70 kcal/mol
Surface area8270 Å2
MethodPISA
2
B: Collagenase 3
D: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6418
Polymers19,9092
Non-polymers7326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-70 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.073, 140.073, 46.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 19366.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (UNP RESIDUES 104-274) / Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: PKA8H / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide Collagenase 3 /


Mass: 542.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Proteolytic fragment / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PKA8H / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P45452*PLUS

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Non-polymers , 4 types, 365 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-8OA / (R)-N-(3-methyl-1-(methylamino)-1-oxobutan-2-yl)-5-(4-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)phenyl)furan-2-carboxamide


Mass: 480.579 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H28N4O4S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate 0.1 M Tris:HCl pH 8.5, 30% polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.62→32.77 Å / Num. obs: 43442 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 16.1 Å2 / Rpim(I) all: 0.046 / Rsym value: 0.069 / Net I/σ(I): 13.2
Reflection shellResolution: 1.62→1.71 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6358 / Rpim(I) all: 0.43 / Rsym value: 0.646 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L19

4l19


Resolution: 1.62→32.77 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 18.4
RfactorNum. reflection% reflection
Rfree0.1779 2002 4.61 %
Rwork0.1288 --
obs0.1311 43436 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→32.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 78 354 2962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012752
X-RAY DIFFRACTIONf_angle_d0.9873755
X-RAY DIFFRACTIONf_dihedral_angle_d14.391976
X-RAY DIFFRACTIONf_chiral_restr0.053379
X-RAY DIFFRACTIONf_plane_restr0.007486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6203-1.66080.26781410.19982954X-RAY DIFFRACTION100
1.6608-1.70570.24991450.17122977X-RAY DIFFRACTION100
1.7057-1.75590.23381450.15712978X-RAY DIFFRACTION100
1.7559-1.81250.21461440.13482955X-RAY DIFFRACTION100
1.8125-1.87730.18691450.12492966X-RAY DIFFRACTION100
1.8773-1.95250.18491420.11792957X-RAY DIFFRACTION100
1.9525-2.04130.17011450.11162973X-RAY DIFFRACTION100
2.0413-2.14890.16361400.112939X-RAY DIFFRACTION100
2.1489-2.28350.16141450.11322978X-RAY DIFFRACTION100
2.2835-2.45980.1721460.12012952X-RAY DIFFRACTION100
2.4598-2.70720.19611390.13542974X-RAY DIFFRACTION100
2.7072-3.09870.21441450.14232953X-RAY DIFFRACTION100
3.0987-3.9030.16361400.12922965X-RAY DIFFRACTION100
3.903-32.77870.1381400.12132913X-RAY DIFFRACTION98

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