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- PDB-2ddf: Crystal structure of TACE in complex with TAPI-2 -

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Basic information

Entry
Database: PDB / ID: 2ddf
TitleCrystal structure of TACE in complex with TAPI-2
ComponentsADAM 17
KeywordsHYDROLASE / TACE ADAM17 ZN-Endopeptidase
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 / CITRIC ACID / IMIDAZOLE / Chem-INN / ISOPROPYL ALCOHOL / DUF3850 domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOrth, P.
CitationJournal: Protein Eng.Des.Sel. / Year: 2006
Title: Stabilization of the autoproteolysis of TNF-alpha converting enzyme (TACE) results in a novel crystal form suitable for structure-based drug design studies.
Authors: Ingram, R.N. / Orth, P. / Strickland, C.L. / Le, H.V. / Madison, V. / Beyer, B.M.
History
DepositionJan 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADAM 17
B: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,52313
Polymers58,0192
Non-polymers1,50411
Water5,999333
1
A: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5915
Polymers29,0091
Non-polymers5814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9328
Polymers29,0091
Non-polymers9227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.394, 75.639, 103.713
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, 2 molecules AB

#1: Protein ADAM 17 / A disintegrin and metalloproteinase domain 17 / TNF-alpha-converting enzyme / TNF-alpha convertase ...A disintegrin and metalloproteinase domain 17 / TNF-alpha-converting enzyme / TNF-alpha convertase / Snake venom-like protease / CD156b antigen


Mass: 29009.492 Da / Num. of mol.: 2 / Mutation: S266A, V353G, Q452N
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 , 7 types, 344 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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.: 2 / 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
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 6K, 10% 2-PROPANOL, 100 MM SODIUM CITRATE BUFFER , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 65325 / Num. obs: 63496 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKC

1bkc


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.077 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1259 2 %RANDOM
Rwork0.204 ---
all0.204 65325 --
obs0.204 63552 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.003 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---0.4 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 95 333 4320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224077
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9665522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00225.081185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98715635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0831511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023144
X-RAY DIFFRACTIONr_nbd_refined0.2010.21936
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2310
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.229
X-RAY DIFFRACTIONr_mcbond_it1.0721.52587
X-RAY DIFFRACTIONr_mcangle_it1.61623995
X-RAY DIFFRACTIONr_scbond_it2.41831711
X-RAY DIFFRACTIONr_scangle_it3.434.51527
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 108 -
Rwork0.266 4409 -
obs-4517 95.84 %

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