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- PDB-3o64: Crystal structure of catalytic domain of TACE with 2-(2-Aminothia... -

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Basic information

Entry
Database: PDB / ID: 3o64
TitleCrystal structure of catalytic domain of TACE with 2-(2-Aminothiazol-4-yl)pyrrolidine-Based Tartrate Diamides
ComponentsTACE
Keywordshydrolase/hydrolase inhibitor / Hydrolase / ADAM Proteins / Enzyme Inhibitors / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Metallo-peptidase family M12 / Domain of unknown function DUF3850 / Domain of unknown function (DUF3850) / ASCH / ASCH domain / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / PUA-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,N(D,L-[2-(HYDROXYAMINO-CARBONYL)METHYL]-4-METHYL PENTANOYL)L-3-(TERT-BUTYL)GLYCYL-L-ALANINE / Chem-786 / Chem-INN / ISOPROPYL ALCOHOL / DUF3850 domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsOrth, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: 2-(2-Aminothiazol-4-yl)pyrrolidine-based tartrate diamides as potent, selective and orally bioavailable TACE inhibitors.
Authors: Dai, C. / Li, D. / Popovici-Muller, J. / Zhao, L. / Girijavallabhan, V.M. / Rosner, K.E. / Lavey, B.J. / Rizvi, R. / Shankar, B.B. / Wong, M.K. / Guo, Z. / Orth, P. / Strickland, C.O. / Sun, ...Authors: Dai, C. / Li, D. / Popovici-Muller, J. / Zhao, L. / Girijavallabhan, V.M. / Rosner, K.E. / Lavey, B.J. / Rizvi, R. / Shankar, B.B. / Wong, M.K. / Guo, Z. / Orth, P. / Strickland, C.O. / Sun, J. / Niu, X. / Chen, S. / Kozlowski, J.A. / Lundell, D.J. / Piwinski, J.J. / Shih, N.Y. / Siddiqui, M.A.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TACE
B: TACE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,58812
Polymers61,1382
Non-polymers1,45010
Water5,188288
1
A: TACE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1505
Polymers30,5691
Non-polymers5814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TACE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4387
Polymers30,5691
Non-polymers8686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.446, 76.508, 103.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TACE / ADAM 17 / TNF-alpha-converting enzyme / TNF-alpha convertase / Snake venom-like protease / ...ADAM 17 / TNF-alpha-converting enzyme / TNF-alpha convertase / Snake venom-like protease / Disintegrin and metalloproteinase domain-containing protein 17


Mass: 30569.135 Da / Num. of mol.: 2 / Fragment: TACE / Mutation: S266A, V353G, N452Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM17, CSVP, TACE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P78536, EC: 3.4.24.86

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Non-polymers , 6 types, 298 molecules

#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-INN / N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(2-aminoethyl)-L-alaninamide


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 415.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H37N5O5
References: 3,N(D,L-[2-(HYDROXYAMINO-CARBONYL)METHYL]-4-METHYL PENTANOYL)L-3-(TERT-BUTYL)GLYCYL-L-ALANINE
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-786 / (2R,3R)-2,3-dihydroxy-4-{(2R)-2-[2-(methylamino)-5-(methylsulfonyl)-1,3-thiazol-4-yl]pyrrolidin-1-yl}-4-oxo-N-{(1R)-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}butanamide


Mass: 562.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30N6O6S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.6
Details: 15% PEG 6K, 10% 2-Propanol, 100mM Sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9766 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 13, 2002
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 1.88→20 Å / Num. all: 49102 / Num. obs: 48857 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.106 / Χ2: 1.05 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.88-1.950.6142.848241.037199.9
1.95-2.030.4673.648211.031199.7
2.03-2.120.3344.848331.035199.7
2.12-2.230.2436.148491.038199.8
2.23-2.370.1797.848601.036199.9
2.37-2.550.1478.948691.03199.9
2.55-2.810.11710.848961.036199.9
2.81-3.210.09613.249111.055199.8
3.21-4.040.08315.349521.071199.4
4.04-200.0816.250421.134197.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
BUSTER2.9.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKC

1bkc


Resolution: 1.88→19.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 943 1.94 %RANDOM
Rwork0.188 ---
obs0.188 48697 99.58 %-
all-49102 --
Displacement parametersBiso max: 123.4 Å2 / Biso mean: 37.624 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.849 Å20 Å20 Å2
2---1.039 Å20 Å2
3---1.888 Å2
Refine analyzeLuzzati coordinate error obs: 0.254 Å
Refinement stepCycle: LAST / Resolution: 1.88→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 90 288 4247
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 86 2.41 %
Rwork0.222 3485 -
all0.222 3571 -
obs--99.58 %

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