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- PDB-5bot: X-RAY Co-structure of MMP-13 with ethyl 5-carbamoyl-1H-indole-2-c... -

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Entry
Database: PDB / ID: 5bot
TitleX-RAY Co-structure of MMP-13 with ethyl 5-carbamoyl-1H-indole-2-carboxylate
ComponentsCollagenase 3
KeywordsHydrolase/Hydrolase inhibitor / Ridgefield / Protease / 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 / 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
ethyl 5-carbamoyl-1H-indole-2-carboxylate / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsFarrow, N.A. / Padyana, A.K.
CitationJournal: J. Med. Chem. / Year: 2011
Title: Fragment-based discovery of indole inhibitors of matrix metalloproteinase-13.
Authors: Taylor, S.J. / Abeywardane, A. / Liang, S. / Muegge, I. / Padyana, A.K. / Xiong, Z. / Hill-Drzewi, M. / Farmer, B. / Li, X. / Collins, B. / Li, J.X. / Heim-Riether, A. / Proudfoot, J. / ...Authors: Taylor, S.J. / Abeywardane, A. / Liang, S. / Muegge, I. / Padyana, A.K. / Xiong, Z. / Hill-Drzewi, M. / Farmer, B. / Li, X. / Collins, B. / Li, J.X. / Heim-Riether, A. / Proudfoot, J. / Zhang, Q. / Goldberg, D. / Zuvela-Jelaska, L. / Zaher, H. / Li, J. / Farrow, N.A.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Experimental preparation
Revision 1.2Jul 27, 2016Group: Data collection
Revision 1.3Jun 13, 2018Group: Data collection / Derived calculations / Category: diffrn_radiation / pdbx_struct_oper_list
Item: _diffrn_radiation.pdbx_diffrn_protocol / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 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
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_symmetry
Remark 650HELIX DETERMINATION METHOD: MOE
Remark 700SHEET DETERMINATION METHOD: MOE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,43714
Polymers38,4712
Non-polymers96712
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-136 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.641, 35.953, 95.824
Angle α, β, γ (deg.)90.00, 130.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-624-

HOH

21B-621-

HOH

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Components

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


Mass: 19235.383 Da / Num. of mol.: 2 / Fragment: UNP residues 104-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Fragment: 104-274 / Gene: MMP13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-4UM / ethyl 5-carbamoyl-1H-indole-2-carboxylate


Mass: 232.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details001 MOL_POTENCY [IC50 in nM] 65000 CDB_METHOD_ID 18655 BRD_ID 001 DICTIONARY 17 18 Other 001 C1 C1 ...001 MOL_POTENCY [IC50 in nM] 65000 CDB_METHOD_ID 18655 BRD_ID 001 DICTIONARY 17 18 Other 001 C1 C1 C 0 YNN 1 001 C2 C2 C 0 YNN 2 001 C3 C3 C 0 YNN 3 001 C4 C4 C 0 YNN 4 001 N5 N5 N 0 YNN 5 001 C6 C6 C 0 YNN 6 001 C7 C7 C 0 YNN 7 001 C8 C8 C 0 YNN 8 001 C9 C9 C 0 YNN 9 001 C10 C10 C 0 NNN 10 001 C11 C11 C 0 NNN 11 001 O12 O12 O 0 NNN 12 001 O13 O13 O 0 NNN 13 001 N14 N14 N 0 NNN 14 001 O15 O15 O 0 NNN 15 001 C16 C16 C 0 NNN 16 001 C17 C17 C 0 NNN 17 001 C1 C2 DOUB YN 1 001 C1 C3 SING YN 2 001 C1 C4 SING YN 3 001 C2 N5 SING YN 4 001 C2 C6 SING YN 5 001 C3 C7 DOUB YN 6 001 C4 C8 DOUB YN 7 001 N5 C7 SING YN 8 001 C6 C9 DOUB YN 9 001 C7 C10 SING NN 10 001 C8 C9 SING YN 11 001 C8 C11 SING NN 12 001 C10 O12 SING NN 13 001 C10 O13 DOUB NN 14 001 C11 N14 SING NN 15 001 C11 O15 DOUB NN 16 001 O12 C16 SING NN 17 001 C16 C17 SING NN 18 ZN2 DICTIONARY 1 0 Other ZN2 ZN ZN Zn 2 NNN 1

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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: 46.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14-28% PEG 4000 0.6M Ammonium Formate 0. M Tris pH 8

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Data collection

DiffractionMean temperature: 63 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.6 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 1.85→50.9766 Å / Num. obs: 28513 / % possible obs: 94.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 4.8
Reflection shellResolution: 1.85→1.9161 Å

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Processing

SoftwareName: PHENIX / Classification: refinement
RefinementResolution: 1.85→50.9766 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2286 --
obs0.1726 28513 94.41 %
Refinement stepCycle: LAST / Resolution: 1.85→50.9766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 44 471 3159
LS refinement shellResolution: 1.85→1.9161 Å

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