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- PDB-5n0z: hPAD4 crystal complex with AFM-41a -

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Basic information

Entry
Database: PDB / ID: 5n0z
TitlehPAD4 crystal complex with AFM-41a
ComponentsProtein-arginine deiminase type-4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification ...histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification / protein modification process / nucleosome assembly / chromatin organization / chromatin remodeling / innate immune response / calcium ion binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein-arginine deiminase, central domain / Protein-arginine deiminase, N-terminal domain / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain ...Protein-arginine deiminase, central domain / Protein-arginine deiminase, N-terminal domain / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-8FT / Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 Å
AuthorsBeaumont, E. / Kerry, P. / Thompson, P. / Muth, A. / Subramanian, V. / Nagar, M. / Srinath, H. / Clancy, K. / Parelkar, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthGM079357, GM110394, GM118112 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Development of a Selective Inhibitor of Protein Arginine Deiminase 2.
Authors: Muth, A. / Subramanian, V. / Beaumont, E. / Nagar, M. / Kerry, P. / McEwan, P. / Srinath, H. / Clancy, K. / Parelkar, S. / Thompson, P.R.
History
DepositionFeb 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-arginine deiminase type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7059
Polymers74,8181
Non-polymers8878
Water3,531196
1
A: Protein-arginine deiminase type-4
hetero molecules

A: Protein-arginine deiminase type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,41018
Polymers149,6352
Non-polymers1,77416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6350 Å2
ΔGint-152 kcal/mol
Surface area51550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.150, 60.940, 115.320
Angle α, β, γ (deg.)90.00, 124.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein-arginine deiminase type-4 / HL-60 PAD / Peptidylarginine deiminase IV / Protein-arginine deiminase type IV


Mass: 74817.742 Da / Num. of mol.: 1 / Mutation: G55S, V82A, G112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI4, PAD4, PADI5, PDI5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UM07, protein-arginine deiminase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-8FT / 2-ethyl-~{N}-[(1~{S})-4-(2-fluoranylethanimidoylamino)-1-(4-methoxy-1-methyl-benzimidazol-2-yl)butyl]-3-oxidanylidene-1~{H}-isoindole-4-carboxamide


Mass: 494.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H31FN6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M imidazole pH7.5, 0.2mM LiSO4, 8-11% PEG3350

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.52→55.79 Å / Num. obs: 28377 / % possible obs: 99.1 % / Redundancy: 3.4 % / CC1/2: 0.999 / Net I/σ(I): 17
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2073 / CC1/2: 0.644 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.52→55.79 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 13.041 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.261 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22936 1412 5 %RANDOM
Rwork0.18003 ---
obs0.18255 26964 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.638 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å2-0 Å2-3.14 Å2
2--9.81 Å2-0 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 2.52→55.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5024 0 50 196 5270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195199
X-RAY DIFFRACTIONr_bond_other_d0.0020.024791
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9787060
X-RAY DIFFRACTIONr_angle_other_deg1.033311175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3955636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8424.646226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70115887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3131525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215738
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021012
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.985.3562553
X-RAY DIFFRACTIONr_mcbond_other3.9815.3562552
X-RAY DIFFRACTIONr_mcangle_it6.2868.0123186
X-RAY DIFFRACTIONr_mcangle_other6.2858.0123187
X-RAY DIFFRACTIONr_scbond_it4.0055.7552646
X-RAY DIFFRACTIONr_scbond_other4.0045.7552647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4228.4523875
X-RAY DIFFRACTIONr_long_range_B_refined10.89899.24523081
X-RAY DIFFRACTIONr_long_range_B_other10.89899.24423082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 108 -
Rwork0.373 1962 -
obs--98.43 %

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