data_2YVO # _entry.id 2YVO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2YVO pdb_00002yvo 10.2210/pdb2yvo/pdb RCSB RCSB027192 ? ? WWPDB D_1000027192 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2YVM . unspecified PDB 2YVN . unspecified PDB 2YVP . unspecified TargetDB ttk003001256.2 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2YVO _pdbx_database_status.recvd_initial_deposition_date 2007-04-13 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Wakamatsu, T.' 1 'Nakagawa, N.' 2 'Kuramitsu, S.' 3 'Yokoyama, S.' 4 'Masui, R.' 5 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 6 # _citation.id primary _citation.title 'Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8' _citation.journal_abbrev J.Bacteriol. _citation.journal_volume 190 _citation.page_first 1108 _citation.page_last 1117 _citation.year 2008 _citation.journal_id_ASTM JOBAAY _citation.country US _citation.journal_id_ISSN 0021-9193 _citation.journal_id_CSD 0767 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18039767 _citation.pdbx_database_id_DOI 10.1128/JB.01522-07 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wakamatsu, T.' 1 ? primary 'Nakagawa, N.' 2 ? primary 'Kuramitsu, S.' 3 ? primary 'Masui, R.' 4 ? # _cell.entry_id 2YVO _cell.length_a 40.699 _cell.length_b 100.899 _cell.length_c 97.172 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 2YVO _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'MutT/nudix family protein' 20336.439 1 3.6.1.- ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 3 ? ? ? ? 3 non-polymer syn 'ADENOSINE MONOPHOSPHATE' 347.221 1 ? ? ? ? 4 water nat water 18.015 138 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name NDX2 # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;MSPWERILLEEILSEPVRLVKERVRTHTGRELTYVYRPGPVAASFVLPVTERGTALLVRQYRHPTGKFLLEVPAGKVDEG ETPEAAARRELREEVGAEAETLIPLPSFHPQPSFTAVVFHPFLALKARVVTPPTLEEGELLESLELPLTEVYALLAKGEI QDASTALTLFYAEPHLKRLGLL ; _entity_poly.pdbx_seq_one_letter_code_can ;MSPWERILLEEILSEPVRLVKERVRTHTGRELTYVYRPGPVAASFVLPVTERGTALLVRQYRHPTGKFLLEVPAGKVDEG ETPEAAARRELREEVGAEAETLIPLPSFHPQPSFTAVVFHPFLALKARVVTPPTLEEGELLESLELPLTEVYALLAKGEI QDASTALTLFYAEPHLKRLGLL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ttk003001256.2 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 SER n 1 3 PRO n 1 4 TRP n 1 5 GLU n 1 6 ARG n 1 7 ILE n 1 8 LEU n 1 9 LEU n 1 10 GLU n 1 11 GLU n 1 12 ILE n 1 13 LEU n 1 14 SER n 1 15 GLU n 1 16 PRO n 1 17 VAL n 1 18 ARG n 1 19 LEU n 1 20 VAL n 1 21 LYS n 1 22 GLU n 1 23 ARG n 1 24 VAL n 1 25 ARG n 1 26 THR n 1 27 HIS n 1 28 THR n 1 29 GLY n 1 30 ARG n 1 31 GLU n 1 32 LEU n 1 33 THR n 1 34 TYR n 1 35 VAL n 1 36 TYR n 1 37 ARG n 1 38 PRO n 1 39 GLY n 1 40 PRO n 1 41 VAL n 1 42 ALA n 1 43 ALA n 1 44 SER n 1 45 PHE n 1 46 VAL n 1 47 LEU n 1 48 PRO n 1 49 VAL n 1 50 THR n 1 51 GLU n 1 52 ARG n 1 53 GLY n 1 54 THR n 1 55 ALA n 1 56 LEU n 1 57 LEU n 1 58 VAL n 1 59 ARG n 1 60 GLN n 1 61 TYR n 1 62 ARG n 1 63 HIS n 1 64 PRO n 1 65 THR n 1 66 GLY n 1 67 LYS n 1 68 PHE n 1 69 LEU n 1 70 LEU n 1 71 GLU n 1 72 VAL n 1 73 PRO n 1 74 ALA n 1 75 GLY n 1 76 LYS n 1 77 VAL n 1 78 ASP n 1 79 GLU n 1 80 GLY n 1 81 GLU n 1 82 THR n 1 83 PRO n 1 84 GLU n 1 85 ALA n 1 86 ALA n 1 87 ALA n 1 88 ARG n 1 89 ARG n 1 90 GLU n 1 91 LEU n 1 92 ARG n 1 93 GLU n 1 94 GLU n 1 95 VAL n 1 96 GLY n 1 97 ALA n 1 98 GLU n 1 99 ALA n 1 100 GLU n 1 101 THR n 1 102 LEU n 1 103 ILE n 1 104 PRO n 1 105 LEU n 1 106 PRO n 1 107 SER n 1 108 PHE n 1 109 HIS n 1 110 PRO n 1 111 GLN n 1 112 PRO n 1 113 SER n 1 114 PHE n 1 115 THR n 1 116 ALA n 1 117 VAL n 1 118 VAL n 1 119 PHE n 1 120 HIS n 1 121 PRO n 1 122 PHE n 1 123 LEU n 1 124 ALA n 1 125 LEU n 1 126 LYS n 1 127 ALA n 1 128 ARG n 1 129 VAL n 1 130 VAL n 1 131 THR n 1 132 PRO n 1 133 PRO n 1 134 THR n 1 135 LEU n 1 136 GLU n 1 137 GLU n 1 138 GLY n 1 139 GLU n 1 140 LEU n 1 141 LEU n 1 142 GLU n 1 143 SER n 1 144 LEU n 1 145 GLU n 1 146 LEU n 1 147 PRO n 1 148 LEU n 1 149 THR n 1 150 GLU n 1 151 VAL n 1 152 TYR n 1 153 ALA n 1 154 LEU n 1 155 LEU n 1 156 ALA n 1 157 LYS n 1 158 GLY n 1 159 GLU n 1 160 ILE n 1 161 GLN n 1 162 ASP n 1 163 ALA n 1 164 SER n 1 165 THR n 1 166 ALA n 1 167 LEU n 1 168 THR n 1 169 LEU n 1 170 PHE n 1 171 TYR n 1 172 ALA n 1 173 GLU n 1 174 PRO n 1 175 HIS n 1 176 LEU n 1 177 LYS n 1 178 ARG n 1 179 LEU n 1 180 GLY n 1 181 LEU n 1 182 LEU n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus Thermus _entity_src_gen.pdbx_gene_src_gene ndx2 _entity_src_gen.gene_src_species 'Thermus thermophilus' _entity_src_gen.gene_src_strain HB8 _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Thermus thermophilus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 300852 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species 'Escherichia coli' _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type PLASMID _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET11a _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q5SJY9_THET8 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSPWERILLEEILSEPVRLVKERVRTHTGRELTYVYRPGPVAASFVLPVTERGTALLVRQYRHPTGKFLLEVPAGKVDEG ETPEAAARRELREEVGAEAETLIPLPSFHPQPSFTAVVFHPFLALKARVVTPPTLEEGELLESLELPLTEVYALLAKGEI QDASTALTLFYAEPHLKRLGLL ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession Q5SJY9 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2YVO _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 182 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q5SJY9 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 182 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 182 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 AMP non-polymer . 'ADENOSINE MONOPHOSPHATE' ? 'C10 H14 N5 O7 P' 347.221 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2YVO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.45 _exptl_crystal.density_percent_sol 49.81 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.9 _exptl_crystal_grow.pdbx_details ;0.033M MES, 0.053M MAGNESIUM ACETATE, 4.7%(W/V) PEG8000, 6.7%(W/V) GLYCEROL, 3.3mM AMP, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 95 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2004-11-30 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'TRANSPARENT DIAMOND DOUBLE CRYSTAL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL44B2' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL44B2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0000 # _reflns.entry_id 2YVO _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.67 _reflns.number_obs 23468 _reflns.number_all 23468 _reflns.percent_possible_obs 99.1 _reflns.pdbx_Rmerge_I_obs 0.031 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 48.2 _reflns.B_iso_Wilson_estimate 12.5 _reflns.pdbx_redundancy 4.9 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.67 _reflns_shell.d_res_low 1.73 _reflns_shell.percent_possible_all 97.6 _reflns_shell.Rmerge_I_obs 0.107 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 14.1 _reflns_shell.pdbx_redundancy 4.7 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 2264 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 2YVO _refine.ls_number_reflns_obs 23202 _refine.ls_number_reflns_all 23202 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 27.26 _refine.ls_d_res_high 1.67 _refine.ls_percent_reflns_obs 97.9 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.180 _refine.ls_R_factor_R_free 0.205 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 2292 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 14.3 _refine.aniso_B[1][1] 3.18 _refine.aniso_B[2][2] -1.47 _refine.aniso_B[3][3] -1.71 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 2YVM' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 2YVO _refine_analyze.Luzzati_coordinate_error_obs 0.16 _refine_analyze.Luzzati_sigma_a_obs -0.04 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.18 _refine_analyze.Luzzati_sigma_a_free 0.03 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1437 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 26 _refine_hist.number_atoms_solvent 138 _refine_hist.number_atoms_total 1601 _refine_hist.d_res_high 1.67 _refine_hist.d_res_low 27.26 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.6 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 24.6 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.01 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 0.90 ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 1.48 ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 1.58 ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 2.40 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.67 _refine_ls_shell.d_res_low 1.77 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.175 _refine_ls_shell.percent_reflns_obs 94.4 _refine_ls_shell.R_factor_R_free 0.211 _refine_ls_shell.R_factor_R_free_error 0.011 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 367 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 3313 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2YVO _struct.title 'Crystal structure of NDX2 in complex with MG2+ and AMP from thermus thermophilus HB8' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2YVO _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text ;NUDIX PROTEIN, ADP-RIBOSE, FAD, THERMUS THERMOPHILUS, HYDROLASE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 THR A 82 ? GLY A 96 ? THR A 82 GLY A 96 1 ? 15 HELX_P HELX_P2 2 LEU A 148 ? LYS A 157 ? LEU A 148 LYS A 157 1 ? 10 HELX_P HELX_P3 3 ASP A 162 ? LEU A 179 ? ASP A 162 LEU A 179 1 ? 18 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GLU 15 A . ? GLU 15 A PRO 16 A ? PRO 16 A 1 0.23 2 GLY 39 A . ? GLY 39 A PRO 40 A ? PRO 40 A 1 0.05 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 3 ? B ? 4 ? C ? 3 ? D ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? parallel B 3 4 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel D 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 GLU A 5 ? LEU A 13 ? GLU A 5 LEU A 13 A 2 LEU A 19 ? ARG A 25 ? LEU A 19 ARG A 25 A 3 GLU A 31 ? TYR A 36 ? GLU A 31 TYR A 36 B 1 ALA A 74 ? LYS A 76 ? ALA A 74 LYS A 76 B 2 ALA A 42 ? PRO A 48 ? ALA A 42 PRO A 48 B 3 VAL A 118 ? ALA A 124 ? VAL A 118 ALA A 124 B 4 LEU A 102 ? PRO A 104 ? LEU A 102 PRO A 104 C 1 PHE A 68 ? GLU A 71 ? PHE A 68 GLU A 71 C 2 THR A 54 ? TYR A 61 ? THR A 54 TYR A 61 C 3 LEU A 141 ? PRO A 147 ? LEU A 141 PRO A 147 D 1 ALA A 97 ? GLU A 98 ? ALA A 97 GLU A 98 D 2 ARG A 128 ? VAL A 129 ? ARG A 128 VAL A 129 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N ILE A 7 ? N ILE A 7 O ARG A 23 ? O ARG A 23 A 2 3 N GLU A 22 ? N GLU A 22 O TYR A 34 ? O TYR A 34 B 1 2 O GLY A 75 ? O GLY A 75 N SER A 44 ? N SER A 44 B 2 3 N LEU A 47 ? N LEU A 47 O ALA A 124 ? O ALA A 124 B 3 4 O LEU A 123 ? O LEU A 123 N ILE A 103 ? N ILE A 103 C 1 2 O LEU A 69 ? O LEU A 69 N GLN A 60 ? N GLN A 60 C 2 3 N ARG A 59 ? N ARG A 59 O GLU A 142 ? O GLU A 142 D 1 2 N GLU A 98 ? N GLU A 98 O ARG A 128 ? O ARG A 128 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A MG 1001 ? 5 'BINDING SITE FOR RESIDUE MG A 1001' AC2 Software A MG 1002 ? 6 'BINDING SITE FOR RESIDUE MG A 1002' AC3 Software A MG 1003 ? 5 'BINDING SITE FOR RESIDUE MG A 1003' AC4 Software A AMP 2001 ? 24 'BINDING SITE FOR RESIDUE AMP A 2001' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 5 GLU A 90 ? GLU A 90 . ? 1_555 ? 2 AC1 5 GLU A 94 ? GLU A 94 . ? 1_555 ? 3 AC1 5 GLU A 139 ? GLU A 139 . ? 1_555 ? 4 AC1 5 HOH F . ? HOH A 2003 . ? 1_555 ? 5 AC1 5 HOH F . ? HOH A 2004 . ? 1_555 ? 6 AC2 6 ALA A 74 ? ALA A 74 . ? 1_555 ? 7 AC2 6 GLU A 94 ? GLU A 94 . ? 1_555 ? 8 AC2 6 GLU A 139 ? GLU A 139 . ? 1_555 ? 9 AC2 6 HOH F . ? HOH A 2002 . ? 1_555 ? 10 AC2 6 HOH F . ? HOH A 2006 . ? 1_555 ? 11 AC2 6 HOH F . ? HOH A 2009 . ? 1_555 ? 12 AC3 5 GLU A 90 ? GLU A 90 . ? 1_555 ? 13 AC3 5 HOH F . ? HOH A 2004 . ? 1_555 ? 14 AC3 5 HOH F . ? HOH A 2007 . ? 1_555 ? 15 AC3 5 HOH F . ? HOH A 2011 . ? 1_555 ? 16 AC3 5 HOH F . ? HOH A 2027 . ? 1_555 ? 17 AC4 24 PRO A 16 ? PRO A 16 . ? 1_555 ? 18 AC4 24 THR A 33 ? THR A 33 . ? 3_656 ? 19 AC4 24 TYR A 34 ? TYR A 34 . ? 3_656 ? 20 AC4 24 ALA A 74 ? ALA A 74 . ? 1_555 ? 21 AC4 24 GLY A 75 ? GLY A 75 . ? 1_555 ? 22 AC4 24 LYS A 76 ? LYS A 76 . ? 1_555 ? 23 AC4 24 GLU A 90 ? GLU A 90 . ? 1_555 ? 24 AC4 24 GLU A 94 ? GLU A 94 . ? 1_555 ? 25 AC4 24 SER A 113 ? SER A 113 . ? 3_656 ? 26 AC4 24 PHE A 114 ? PHE A 114 . ? 3_656 ? 27 AC4 24 GLU A 136 ? GLU A 136 . ? 1_555 ? 28 AC4 24 GLU A 137 ? GLU A 137 . ? 1_555 ? 29 AC4 24 GLY A 138 ? GLY A 138 . ? 1_555 ? 30 AC4 24 GLU A 139 ? GLU A 139 . ? 1_555 ? 31 AC4 24 HOH F . ? HOH A 2004 . ? 1_555 ? 32 AC4 24 HOH F . ? HOH A 2006 . ? 1_555 ? 33 AC4 24 HOH F . ? HOH A 2009 . ? 1_555 ? 34 AC4 24 HOH F . ? HOH A 2011 . ? 1_555 ? 35 AC4 24 HOH F . ? HOH A 2015 . ? 1_555 ? 36 AC4 24 HOH F . ? HOH A 2027 . ? 1_555 ? 37 AC4 24 HOH F . ? HOH A 2034 . ? 1_555 ? 38 AC4 24 HOH F . ? HOH A 2058 . ? 1_555 ? 39 AC4 24 HOH F . ? HOH A 2061 . ? 1_555 ? 40 AC4 24 HOH F . ? HOH A 2137 . ? 1_555 ? # _database_PDB_matrix.entry_id 2YVO _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2YVO _atom_sites.fract_transf_matrix[1][1] 0.024571 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.009911 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.010291 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 1 1 MET MET A . n A 1 2 SER 2 2 2 SER SER A . n A 1 3 PRO 3 3 3 PRO PRO A . n A 1 4 TRP 4 4 4 TRP TRP A . n A 1 5 GLU 5 5 5 GLU GLU A . n A 1 6 ARG 6 6 6 ARG ARG A . n A 1 7 ILE 7 7 7 ILE ILE A . n A 1 8 LEU 8 8 8 LEU LEU A . n A 1 9 LEU 9 9 9 LEU LEU A . n A 1 10 GLU 10 10 10 GLU GLU A . n A 1 11 GLU 11 11 11 GLU GLU A . n A 1 12 ILE 12 12 12 ILE ILE A . n A 1 13 LEU 13 13 13 LEU LEU A . n A 1 14 SER 14 14 14 SER SER A . n A 1 15 GLU 15 15 15 GLU GLU A . n A 1 16 PRO 16 16 16 PRO PRO A . n A 1 17 VAL 17 17 17 VAL VAL A . n A 1 18 ARG 18 18 18 ARG ARG A . n A 1 19 LEU 19 19 19 LEU LEU A . n A 1 20 VAL 20 20 20 VAL VAL A . n A 1 21 LYS 21 21 21 LYS LYS A . n A 1 22 GLU 22 22 22 GLU GLU A . n A 1 23 ARG 23 23 23 ARG ARG A . n A 1 24 VAL 24 24 24 VAL VAL A . n A 1 25 ARG 25 25 25 ARG ARG A . n A 1 26 THR 26 26 26 THR THR A . n A 1 27 HIS 27 27 27 HIS HIS A . n A 1 28 THR 28 28 28 THR THR A . n A 1 29 GLY 29 29 29 GLY GLY A . n A 1 30 ARG 30 30 30 ARG ARG A . n A 1 31 GLU 31 31 31 GLU GLU A . n A 1 32 LEU 32 32 32 LEU LEU A . n A 1 33 THR 33 33 33 THR THR A . n A 1 34 TYR 34 34 34 TYR TYR A . n A 1 35 VAL 35 35 35 VAL VAL A . n A 1 36 TYR 36 36 36 TYR TYR A . n A 1 37 ARG 37 37 37 ARG ARG A . n A 1 38 PRO 38 38 38 PRO PRO A . n A 1 39 GLY 39 39 39 GLY GLY A . n A 1 40 PRO 40 40 40 PRO PRO A . n A 1 41 VAL 41 41 41 VAL VAL A . n A 1 42 ALA 42 42 42 ALA ALA A . n A 1 43 ALA 43 43 43 ALA ALA A . n A 1 44 SER 44 44 44 SER SER A . n A 1 45 PHE 45 45 45 PHE PHE A . n A 1 46 VAL 46 46 46 VAL VAL A . n A 1 47 LEU 47 47 47 LEU LEU A . n A 1 48 PRO 48 48 48 PRO PRO A . n A 1 49 VAL 49 49 49 VAL VAL A . n A 1 50 THR 50 50 50 THR THR A . n A 1 51 GLU 51 51 51 GLU GLU A . n A 1 52 ARG 52 52 52 ARG ARG A . n A 1 53 GLY 53 53 53 GLY GLY A . n A 1 54 THR 54 54 54 THR THR A . n A 1 55 ALA 55 55 55 ALA ALA A . n A 1 56 LEU 56 56 56 LEU LEU A . n A 1 57 LEU 57 57 57 LEU LEU A . n A 1 58 VAL 58 58 58 VAL VAL A . n A 1 59 ARG 59 59 59 ARG ARG A . n A 1 60 GLN 60 60 60 GLN GLN A . n A 1 61 TYR 61 61 61 TYR TYR A . n A 1 62 ARG 62 62 62 ARG ARG A . n A 1 63 HIS 63 63 63 HIS HIS A . n A 1 64 PRO 64 64 64 PRO PRO A . n A 1 65 THR 65 65 65 THR THR A . n A 1 66 GLY 66 66 66 GLY GLY A . n A 1 67 LYS 67 67 67 LYS LYS A . n A 1 68 PHE 68 68 68 PHE PHE A . n A 1 69 LEU 69 69 69 LEU LEU A . n A 1 70 LEU 70 70 70 LEU LEU A . n A 1 71 GLU 71 71 71 GLU GLU A . n A 1 72 VAL 72 72 72 VAL VAL A . n A 1 73 PRO 73 73 73 PRO PRO A . n A 1 74 ALA 74 74 74 ALA ALA A . n A 1 75 GLY 75 75 75 GLY GLY A . n A 1 76 LYS 76 76 76 LYS LYS A . n A 1 77 VAL 77 77 77 VAL VAL A . n A 1 78 ASP 78 78 78 ASP ASP A . n A 1 79 GLU 79 79 79 GLU GLU A . n A 1 80 GLY 80 80 80 GLY GLY A . n A 1 81 GLU 81 81 81 GLU GLU A . n A 1 82 THR 82 82 82 THR THR A . n A 1 83 PRO 83 83 83 PRO PRO A . n A 1 84 GLU 84 84 84 GLU GLU A . n A 1 85 ALA 85 85 85 ALA ALA A . n A 1 86 ALA 86 86 86 ALA ALA A . n A 1 87 ALA 87 87 87 ALA ALA A . n A 1 88 ARG 88 88 88 ARG ARG A . n A 1 89 ARG 89 89 89 ARG ARG A . n A 1 90 GLU 90 90 90 GLU GLU A . n A 1 91 LEU 91 91 91 LEU LEU A . n A 1 92 ARG 92 92 92 ARG ARG A . n A 1 93 GLU 93 93 93 GLU GLU A . n A 1 94 GLU 94 94 94 GLU GLU A . n A 1 95 VAL 95 95 95 VAL VAL A . n A 1 96 GLY 96 96 96 GLY GLY A . n A 1 97 ALA 97 97 97 ALA ALA A . n A 1 98 GLU 98 98 98 GLU GLU A . n A 1 99 ALA 99 99 99 ALA ALA A . n A 1 100 GLU 100 100 100 GLU GLU A . n A 1 101 THR 101 101 101 THR THR A . n A 1 102 LEU 102 102 102 LEU LEU A . n A 1 103 ILE 103 103 103 ILE ILE A . n A 1 104 PRO 104 104 104 PRO PRO A . n A 1 105 LEU 105 105 105 LEU LEU A . n A 1 106 PRO 106 106 106 PRO PRO A . n A 1 107 SER 107 107 107 SER SER A . n A 1 108 PHE 108 108 108 PHE PHE A . n A 1 109 HIS 109 109 109 HIS HIS A . n A 1 110 PRO 110 110 110 PRO PRO A . n A 1 111 GLN 111 111 111 GLN GLN A . n A 1 112 PRO 112 112 112 PRO PRO A . n A 1 113 SER 113 113 113 SER SER A . n A 1 114 PHE 114 114 114 PHE PHE A . n A 1 115 THR 115 115 115 THR THR A . n A 1 116 ALA 116 116 116 ALA ALA A . n A 1 117 VAL 117 117 117 VAL VAL A . n A 1 118 VAL 118 118 118 VAL VAL A . n A 1 119 PHE 119 119 119 PHE PHE A . n A 1 120 HIS 120 120 120 HIS HIS A . n A 1 121 PRO 121 121 121 PRO PRO A . n A 1 122 PHE 122 122 122 PHE PHE A . n A 1 123 LEU 123 123 123 LEU LEU A . n A 1 124 ALA 124 124 124 ALA ALA A . n A 1 125 LEU 125 125 125 LEU LEU A . n A 1 126 LYS 126 126 126 LYS LYS A . n A 1 127 ALA 127 127 127 ALA ALA A . n A 1 128 ARG 128 128 128 ARG ARG A . n A 1 129 VAL 129 129 129 VAL VAL A . n A 1 130 VAL 130 130 130 VAL VAL A . n A 1 131 THR 131 131 131 THR THR A . n A 1 132 PRO 132 132 132 PRO PRO A . n A 1 133 PRO 133 133 133 PRO PRO A . n A 1 134 THR 134 134 134 THR THR A . n A 1 135 LEU 135 135 135 LEU LEU A . n A 1 136 GLU 136 136 136 GLU GLU A . n A 1 137 GLU 137 137 137 GLU GLU A . n A 1 138 GLY 138 138 138 GLY GLY A . n A 1 139 GLU 139 139 139 GLU GLU A . n A 1 140 LEU 140 140 140 LEU LEU A . n A 1 141 LEU 141 141 141 LEU LEU A . n A 1 142 GLU 142 142 142 GLU GLU A . n A 1 143 SER 143 143 143 SER SER A . n A 1 144 LEU 144 144 144 LEU LEU A . n A 1 145 GLU 145 145 145 GLU GLU A . n A 1 146 LEU 146 146 146 LEU LEU A . n A 1 147 PRO 147 147 147 PRO PRO A . n A 1 148 LEU 148 148 148 LEU LEU A . n A 1 149 THR 149 149 149 THR THR A . n A 1 150 GLU 150 150 150 GLU GLU A . n A 1 151 VAL 151 151 151 VAL VAL A . n A 1 152 TYR 152 152 152 TYR TYR A . n A 1 153 ALA 153 153 153 ALA ALA A . n A 1 154 LEU 154 154 154 LEU LEU A . n A 1 155 LEU 155 155 155 LEU LEU A . n A 1 156 ALA 156 156 156 ALA ALA A . n A 1 157 LYS 157 157 157 LYS LYS A . n A 1 158 GLY 158 158 158 GLY GLY A . n A 1 159 GLU 159 159 159 GLU GLU A . n A 1 160 ILE 160 160 160 ILE ILE A . n A 1 161 GLN 161 161 161 GLN GLN A . n A 1 162 ASP 162 162 162 ASP ASP A . n A 1 163 ALA 163 163 163 ALA ALA A . n A 1 164 SER 164 164 164 SER SER A . n A 1 165 THR 165 165 165 THR THR A . n A 1 166 ALA 166 166 166 ALA ALA A . n A 1 167 LEU 167 167 167 LEU LEU A . n A 1 168 THR 168 168 168 THR THR A . n A 1 169 LEU 169 169 169 LEU LEU A . n A 1 170 PHE 170 170 170 PHE PHE A . n A 1 171 TYR 171 171 171 TYR TYR A . n A 1 172 ALA 172 172 172 ALA ALA A . n A 1 173 GLU 173 173 173 GLU GLU A . n A 1 174 PRO 174 174 174 PRO PRO A . n A 1 175 HIS 175 175 175 HIS HIS A . n A 1 176 LEU 176 176 176 LEU LEU A . n A 1 177 LYS 177 177 177 LYS LYS A . n A 1 178 ARG 178 178 178 ARG ARG A . n A 1 179 LEU 179 179 179 LEU LEU A . n A 1 180 GLY 180 180 180 GLY GLY A . n A 1 181 LEU 181 181 181 LEU LEU A . n A 1 182 LEU 182 182 182 LEU LEU A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'NPPSFA, National Project on Protein Structural and Functional Analyses' _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 MG 1 1001 1001 MG MG A . C 2 MG 1 1002 1002 MG MG A . D 2 MG 1 1003 1003 MG MG A . E 3 AMP 1 2001 2001 AMP AMP A . F 4 HOH 1 2002 1 HOH HOH A . F 4 HOH 2 2003 2 HOH HOH A . F 4 HOH 3 2004 3 HOH HOH A . F 4 HOH 4 2005 4 HOH HOH A . F 4 HOH 5 2006 5 HOH HOH A . F 4 HOH 6 2007 6 HOH HOH A . F 4 HOH 7 2008 7 HOH HOH A . F 4 HOH 8 2009 8 HOH HOH A . F 4 HOH 9 2010 9 HOH HOH A . F 4 HOH 10 2011 10 HOH HOH A . F 4 HOH 11 2012 11 HOH HOH A . F 4 HOH 12 2013 12 HOH HOH A . F 4 HOH 13 2014 13 HOH HOH A . F 4 HOH 14 2015 14 HOH HOH A . F 4 HOH 15 2016 15 HOH HOH A . F 4 HOH 16 2017 16 HOH HOH A . F 4 HOH 17 2018 17 HOH HOH A . F 4 HOH 18 2019 18 HOH HOH A . F 4 HOH 19 2020 19 HOH HOH A . F 4 HOH 20 2021 20 HOH HOH A . F 4 HOH 21 2022 21 HOH HOH A . F 4 HOH 22 2023 22 HOH HOH A . F 4 HOH 23 2024 23 HOH HOH A . F 4 HOH 24 2025 24 HOH HOH A . F 4 HOH 25 2026 25 HOH HOH A . F 4 HOH 26 2027 26 HOH HOH A . F 4 HOH 27 2028 27 HOH HOH A . F 4 HOH 28 2029 28 HOH HOH A . F 4 HOH 29 2030 29 HOH HOH A . F 4 HOH 30 2031 30 HOH HOH A . F 4 HOH 31 2032 31 HOH HOH A . F 4 HOH 32 2033 32 HOH HOH A . F 4 HOH 33 2034 33 HOH HOH A . F 4 HOH 34 2035 34 HOH HOH A . F 4 HOH 35 2036 35 HOH HOH A . F 4 HOH 36 2037 36 HOH HOH A . F 4 HOH 37 2038 37 HOH HOH A . F 4 HOH 38 2039 38 HOH HOH A . F 4 HOH 39 2040 39 HOH HOH A . F 4 HOH 40 2041 40 HOH HOH A . F 4 HOH 41 2042 41 HOH HOH A . F 4 HOH 42 2043 42 HOH HOH A . F 4 HOH 43 2044 43 HOH HOH A . F 4 HOH 44 2045 44 HOH HOH A . F 4 HOH 45 2046 45 HOH HOH A . F 4 HOH 46 2047 46 HOH HOH A . F 4 HOH 47 2048 47 HOH HOH A . F 4 HOH 48 2049 48 HOH HOH A . F 4 HOH 49 2050 49 HOH HOH A . F 4 HOH 50 2051 50 HOH HOH A . F 4 HOH 51 2052 51 HOH HOH A . F 4 HOH 52 2053 52 HOH HOH A . F 4 HOH 53 2054 53 HOH HOH A . F 4 HOH 54 2055 54 HOH HOH A . F 4 HOH 55 2056 55 HOH HOH A . F 4 HOH 56 2057 56 HOH HOH A . F 4 HOH 57 2058 57 HOH HOH A . F 4 HOH 58 2059 58 HOH HOH A . F 4 HOH 59 2060 59 HOH HOH A . F 4 HOH 60 2061 60 HOH HOH A . F 4 HOH 61 2062 61 HOH HOH A . F 4 HOH 62 2063 62 HOH HOH A . F 4 HOH 63 2064 63 HOH HOH A . F 4 HOH 64 2065 64 HOH HOH A . F 4 HOH 65 2066 65 HOH HOH A . F 4 HOH 66 2067 66 HOH HOH A . F 4 HOH 67 2068 67 HOH HOH A . F 4 HOH 68 2069 68 HOH HOH A . F 4 HOH 69 2070 69 HOH HOH A . F 4 HOH 70 2071 70 HOH HOH A . F 4 HOH 71 2072 71 HOH HOH A . F 4 HOH 72 2073 72 HOH HOH A . F 4 HOH 73 2074 73 HOH HOH A . F 4 HOH 74 2075 74 HOH HOH A . F 4 HOH 75 2076 75 HOH HOH A . F 4 HOH 76 2077 76 HOH HOH A . F 4 HOH 77 2078 77 HOH HOH A . F 4 HOH 78 2079 78 HOH HOH A . F 4 HOH 79 2080 79 HOH HOH A . F 4 HOH 80 2081 80 HOH HOH A . F 4 HOH 81 2082 81 HOH HOH A . F 4 HOH 82 2083 82 HOH HOH A . F 4 HOH 83 2084 83 HOH HOH A . F 4 HOH 84 2085 84 HOH HOH A . F 4 HOH 85 2086 85 HOH HOH A . F 4 HOH 86 2087 86 HOH HOH A . F 4 HOH 87 2088 87 HOH HOH A . F 4 HOH 88 2089 88 HOH HOH A . F 4 HOH 89 2090 89 HOH HOH A . F 4 HOH 90 2091 90 HOH HOH A . F 4 HOH 91 2092 91 HOH HOH A . F 4 HOH 92 2093 92 HOH HOH A . F 4 HOH 93 2094 93 HOH HOH A . F 4 HOH 94 2095 94 HOH HOH A . F 4 HOH 95 2096 95 HOH HOH A . F 4 HOH 96 2097 96 HOH HOH A . F 4 HOH 97 2098 97 HOH HOH A . F 4 HOH 98 2099 98 HOH HOH A . F 4 HOH 99 2100 99 HOH HOH A . F 4 HOH 100 2101 100 HOH HOH A . F 4 HOH 101 2102 101 HOH HOH A . F 4 HOH 102 2103 102 HOH HOH A . F 4 HOH 103 2104 103 HOH HOH A . F 4 HOH 104 2105 104 HOH HOH A . F 4 HOH 105 2106 105 HOH HOH A . F 4 HOH 106 2107 106 HOH HOH A . F 4 HOH 107 2108 107 HOH HOH A . F 4 HOH 108 2109 108 HOH HOH A . F 4 HOH 109 2110 109 HOH HOH A . F 4 HOH 110 2111 110 HOH HOH A . F 4 HOH 111 2112 111 HOH HOH A . F 4 HOH 112 2113 112 HOH HOH A . F 4 HOH 113 2114 113 HOH HOH A . F 4 HOH 114 2115 114 HOH HOH A . F 4 HOH 115 2116 115 HOH HOH A . F 4 HOH 116 2117 116 HOH HOH A . F 4 HOH 117 2118 117 HOH HOH A . F 4 HOH 118 2119 118 HOH HOH A . F 4 HOH 119 2120 119 HOH HOH A . F 4 HOH 120 2121 120 HOH HOH A . F 4 HOH 121 2122 121 HOH HOH A . F 4 HOH 122 2123 122 HOH HOH A . F 4 HOH 123 2124 123 HOH HOH A . F 4 HOH 124 2125 124 HOH HOH A . F 4 HOH 125 2126 125 HOH HOH A . F 4 HOH 126 2127 126 HOH HOH A . F 4 HOH 127 2128 127 HOH HOH A . F 4 HOH 128 2129 128 HOH HOH A . F 4 HOH 129 2130 129 HOH HOH A . F 4 HOH 130 2131 130 HOH HOH A . F 4 HOH 131 2132 131 HOH HOH A . F 4 HOH 132 2133 132 HOH HOH A . F 4 HOH 133 2134 133 HOH HOH A . F 4 HOH 134 2135 134 HOH HOH A . F 4 HOH 135 2136 135 HOH HOH A . F 4 HOH 136 2137 136 HOH HOH A . F 4 HOH 137 2138 137 HOH HOH A . F 4 HOH 138 2139 138 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 7030 ? 1 MORE -106 ? 1 'SSA (A^2)' 15480 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 3_656 -x+1,y,-z+3/2 -1.0000000000 0.0000000000 0.0000000000 40.6990000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 145.7580000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 2125 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id F _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2008-02-26 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-10-25 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Derived calculations' 2 2 'Structure model' 'Source and taxonomy' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' 6 3 'Structure model' 'Derived calculations' 7 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MLPHARE phasing . ? 1 CNS refinement 1.1 ? 2 HKL-2000 'data collection' . ? 3 HKL-2000 'data reduction' . ? 4 SCALEPACK 'data scaling' . ? 5 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLU A 100 ? ? -95.35 -103.57 2 1 GLN A 111 ? ? -154.90 77.70 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 AMP P P N N 14 AMP O1P O N N 15 AMP O2P O N N 16 AMP O3P O N N 17 AMP "O5'" O N N 18 AMP "C5'" C N N 19 AMP "C4'" C N R 20 AMP "O4'" O N N 21 AMP "C3'" C N S 22 AMP "O3'" O N N 23 AMP "C2'" C N R 24 AMP "O2'" O N N 25 AMP "C1'" C N R 26 AMP N9 N Y N 27 AMP C8 C Y N 28 AMP N7 N Y N 29 AMP C5 C Y N 30 AMP C6 C Y N 31 AMP N6 N N N 32 AMP N1 N Y N 33 AMP C2 C Y N 34 AMP N3 N Y N 35 AMP C4 C Y N 36 AMP HOP2 H N N 37 AMP HOP3 H N N 38 AMP "H5'1" H N N 39 AMP "H5'2" H N N 40 AMP "H4'" H N N 41 AMP "H3'" H N N 42 AMP "HO3'" H N N 43 AMP "H2'" H N N 44 AMP "HO2'" H N N 45 AMP "H1'" H N N 46 AMP H8 H N N 47 AMP HN61 H N N 48 AMP HN62 H N N 49 AMP H2 H N N 50 ARG N N N N 51 ARG CA C N S 52 ARG C C N N 53 ARG O O N N 54 ARG CB C N N 55 ARG CG C N N 56 ARG CD C N N 57 ARG NE N N N 58 ARG CZ C N N 59 ARG NH1 N N N 60 ARG NH2 N N N 61 ARG OXT O N N 62 ARG H H N N 63 ARG H2 H N N 64 ARG HA H N N 65 ARG HB2 H N N 66 ARG HB3 H N N 67 ARG HG2 H N N 68 ARG HG3 H N N 69 ARG HD2 H N N 70 ARG HD3 H N N 71 ARG HE H N N 72 ARG HH11 H N N 73 ARG HH12 H N N 74 ARG HH21 H N N 75 ARG HH22 H N N 76 ARG HXT H N N 77 ASP N N N N 78 ASP CA C N S 79 ASP C C N N 80 ASP O O N N 81 ASP CB C N N 82 ASP CG C N N 83 ASP OD1 O N N 84 ASP OD2 O N N 85 ASP OXT O N N 86 ASP H H N N 87 ASP H2 H N N 88 ASP HA H N N 89 ASP HB2 H N N 90 ASP HB3 H N N 91 ASP HD2 H N N 92 ASP HXT H N N 93 GLN N N N N 94 GLN CA C N S 95 GLN C C N N 96 GLN O O N N 97 GLN CB C N N 98 GLN CG C N N 99 GLN CD C N N 100 GLN OE1 O N N 101 GLN NE2 N N N 102 GLN OXT O N N 103 GLN H H N N 104 GLN H2 H N N 105 GLN HA H N N 106 GLN HB2 H N N 107 GLN HB3 H N N 108 GLN HG2 H N N 109 GLN HG3 H N N 110 GLN HE21 H N N 111 GLN HE22 H N N 112 GLN HXT H N N 113 GLU N N N N 114 GLU CA C N S 115 GLU C C N N 116 GLU O O N N 117 GLU CB C N N 118 GLU CG C N N 119 GLU CD C N N 120 GLU OE1 O N N 121 GLU OE2 O N N 122 GLU OXT O N N 123 GLU H H N N 124 GLU H2 H N N 125 GLU HA H N N 126 GLU HB2 H N N 127 GLU HB3 H N N 128 GLU HG2 H N N 129 GLU HG3 H N N 130 GLU HE2 H N N 131 GLU HXT H N N 132 GLY N N N N 133 GLY CA C N N 134 GLY C C N N 135 GLY O O N N 136 GLY OXT O N N 137 GLY H H N N 138 GLY H2 H N N 139 GLY HA2 H N N 140 GLY HA3 H N N 141 GLY HXT H N N 142 HIS N N N N 143 HIS CA C N S 144 HIS C C N N 145 HIS O O N N 146 HIS CB C N N 147 HIS CG C Y N 148 HIS ND1 N Y N 149 HIS CD2 C Y N 150 HIS CE1 C Y N 151 HIS NE2 N Y N 152 HIS OXT O N N 153 HIS H H N N 154 HIS H2 H N N 155 HIS HA H N N 156 HIS HB2 H N N 157 HIS HB3 H N N 158 HIS HD1 H N N 159 HIS HD2 H N N 160 HIS HE1 H N N 161 HIS HE2 H N N 162 HIS HXT H N N 163 HOH O O N N 164 HOH H1 H N N 165 HOH H2 H N N 166 ILE N N N N 167 ILE CA C N S 168 ILE C C N N 169 ILE O O N N 170 ILE CB C N S 171 ILE CG1 C N N 172 ILE CG2 C N N 173 ILE CD1 C N N 174 ILE OXT O N N 175 ILE H H N N 176 ILE H2 H N N 177 ILE HA H N N 178 ILE HB H N N 179 ILE HG12 H N N 180 ILE HG13 H N N 181 ILE HG21 H N N 182 ILE HG22 H N N 183 ILE HG23 H N N 184 ILE HD11 H N N 185 ILE HD12 H N N 186 ILE HD13 H N N 187 ILE HXT H N N 188 LEU N N N N 189 LEU CA C N S 190 LEU C C N N 191 LEU O O N N 192 LEU CB C N N 193 LEU CG C N N 194 LEU CD1 C N N 195 LEU CD2 C N N 196 LEU OXT O N N 197 LEU H H N N 198 LEU H2 H N N 199 LEU HA H N N 200 LEU HB2 H N N 201 LEU HB3 H N N 202 LEU HG H N N 203 LEU HD11 H N N 204 LEU HD12 H N N 205 LEU HD13 H N N 206 LEU HD21 H N N 207 LEU HD22 H N N 208 LEU HD23 H N N 209 LEU HXT H N N 210 LYS N N N N 211 LYS CA C N S 212 LYS C C N N 213 LYS O O N N 214 LYS CB C N N 215 LYS CG C N N 216 LYS CD C N N 217 LYS CE C N N 218 LYS NZ N N N 219 LYS OXT O N N 220 LYS H H N N 221 LYS H2 H N N 222 LYS HA H N N 223 LYS HB2 H N N 224 LYS HB3 H N N 225 LYS HG2 H N N 226 LYS HG3 H N N 227 LYS HD2 H N N 228 LYS HD3 H N N 229 LYS HE2 H N N 230 LYS HE3 H N N 231 LYS HZ1 H N N 232 LYS HZ2 H N N 233 LYS HZ3 H N N 234 LYS HXT H N N 235 MET N N N N 236 MET CA C N S 237 MET C C N N 238 MET O O N N 239 MET CB C N N 240 MET CG C N N 241 MET SD S N N 242 MET CE C N N 243 MET OXT O N N 244 MET H H N N 245 MET H2 H N N 246 MET HA H N N 247 MET HB2 H N N 248 MET HB3 H N N 249 MET HG2 H N N 250 MET HG3 H N N 251 MET HE1 H N N 252 MET HE2 H N N 253 MET HE3 H N N 254 MET HXT H N N 255 MG MG MG N N 256 PHE N N N N 257 PHE CA C N S 258 PHE C C N N 259 PHE O O N N 260 PHE CB C N N 261 PHE CG C Y N 262 PHE CD1 C Y N 263 PHE CD2 C Y N 264 PHE CE1 C Y N 265 PHE CE2 C Y N 266 PHE CZ C Y N 267 PHE OXT O N N 268 PHE H H N N 269 PHE H2 H N N 270 PHE HA H N N 271 PHE HB2 H N N 272 PHE HB3 H N N 273 PHE HD1 H N N 274 PHE HD2 H N N 275 PHE HE1 H N N 276 PHE HE2 H N N 277 PHE HZ H N N 278 PHE HXT H N N 279 PRO N N N N 280 PRO CA C N S 281 PRO C C N N 282 PRO O O N N 283 PRO CB C N N 284 PRO CG C N N 285 PRO CD C N N 286 PRO OXT O N N 287 PRO H H N N 288 PRO HA H N N 289 PRO HB2 H N N 290 PRO HB3 H N N 291 PRO HG2 H N N 292 PRO HG3 H N N 293 PRO HD2 H N N 294 PRO HD3 H N N 295 PRO HXT H N N 296 SER N N N N 297 SER CA C N S 298 SER C C N N 299 SER O O N N 300 SER CB C N N 301 SER OG O N N 302 SER OXT O N N 303 SER H H N N 304 SER H2 H N N 305 SER HA H N N 306 SER HB2 H N N 307 SER HB3 H N N 308 SER HG H N N 309 SER HXT H N N 310 THR N N N N 311 THR CA C N S 312 THR C C N N 313 THR O O N N 314 THR CB C N R 315 THR OG1 O N N 316 THR CG2 C N N 317 THR OXT O N N 318 THR H H N N 319 THR H2 H N N 320 THR HA H N N 321 THR HB H N N 322 THR HG1 H N N 323 THR HG21 H N N 324 THR HG22 H N N 325 THR HG23 H N N 326 THR HXT H N N 327 TRP N N N N 328 TRP CA C N S 329 TRP C C N N 330 TRP O O N N 331 TRP CB C N N 332 TRP CG C Y N 333 TRP CD1 C Y N 334 TRP CD2 C Y N 335 TRP NE1 N Y N 336 TRP CE2 C Y N 337 TRP CE3 C Y N 338 TRP CZ2 C Y N 339 TRP CZ3 C Y N 340 TRP CH2 C Y N 341 TRP OXT O N N 342 TRP H H N N 343 TRP H2 H N N 344 TRP HA H N N 345 TRP HB2 H N N 346 TRP HB3 H N N 347 TRP HD1 H N N 348 TRP HE1 H N N 349 TRP HE3 H N N 350 TRP HZ2 H N N 351 TRP HZ3 H N N 352 TRP HH2 H N N 353 TRP HXT H N N 354 TYR N N N N 355 TYR CA C N S 356 TYR C C N N 357 TYR O O N N 358 TYR CB C N N 359 TYR CG C Y N 360 TYR CD1 C Y N 361 TYR CD2 C Y N 362 TYR CE1 C Y N 363 TYR CE2 C Y N 364 TYR CZ C Y N 365 TYR OH O N N 366 TYR OXT O N N 367 TYR H H N N 368 TYR H2 H N N 369 TYR HA H N N 370 TYR HB2 H N N 371 TYR HB3 H N N 372 TYR HD1 H N N 373 TYR HD2 H N N 374 TYR HE1 H N N 375 TYR HE2 H N N 376 TYR HH H N N 377 TYR HXT H N N 378 VAL N N N N 379 VAL CA C N S 380 VAL C C N N 381 VAL O O N N 382 VAL CB C N N 383 VAL CG1 C N N 384 VAL CG2 C N N 385 VAL OXT O N N 386 VAL H H N N 387 VAL H2 H N N 388 VAL HA H N N 389 VAL HB H N N 390 VAL HG11 H N N 391 VAL HG12 H N N 392 VAL HG13 H N N 393 VAL HG21 H N N 394 VAL HG22 H N N 395 VAL HG23 H N N 396 VAL HXT H N N 397 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 AMP P O1P doub N N 13 AMP P O2P sing N N 14 AMP P O3P sing N N 15 AMP P "O5'" sing N N 16 AMP O2P HOP2 sing N N 17 AMP O3P HOP3 sing N N 18 AMP "O5'" "C5'" sing N N 19 AMP "C5'" "C4'" sing N N 20 AMP "C5'" "H5'1" sing N N 21 AMP "C5'" "H5'2" sing N N 22 AMP "C4'" "O4'" sing N N 23 AMP "C4'" "C3'" sing N N 24 AMP "C4'" "H4'" sing N N 25 AMP "O4'" "C1'" sing N N 26 AMP "C3'" "O3'" sing N N 27 AMP "C3'" "C2'" sing N N 28 AMP "C3'" "H3'" sing N N 29 AMP "O3'" "HO3'" sing N N 30 AMP "C2'" "O2'" sing N N 31 AMP "C2'" "C1'" sing N N 32 AMP "C2'" "H2'" sing N N 33 AMP "O2'" "HO2'" sing N N 34 AMP "C1'" N9 sing N N 35 AMP "C1'" "H1'" sing N N 36 AMP N9 C8 sing Y N 37 AMP N9 C4 sing Y N 38 AMP C8 N7 doub Y N 39 AMP C8 H8 sing N N 40 AMP N7 C5 sing Y N 41 AMP C5 C6 sing Y N 42 AMP C5 C4 doub Y N 43 AMP C6 N6 sing N N 44 AMP C6 N1 doub Y N 45 AMP N6 HN61 sing N N 46 AMP N6 HN62 sing N N 47 AMP N1 C2 sing Y N 48 AMP C2 N3 doub Y N 49 AMP C2 H2 sing N N 50 AMP N3 C4 sing Y N 51 ARG N CA sing N N 52 ARG N H sing N N 53 ARG N H2 sing N N 54 ARG CA C sing N N 55 ARG CA CB sing N N 56 ARG CA HA sing N N 57 ARG C O doub N N 58 ARG C OXT sing N N 59 ARG CB CG sing N N 60 ARG CB HB2 sing N N 61 ARG CB HB3 sing N N 62 ARG CG CD sing N N 63 ARG CG HG2 sing N N 64 ARG CG HG3 sing N N 65 ARG CD NE sing N N 66 ARG CD HD2 sing N N 67 ARG CD HD3 sing N N 68 ARG NE CZ sing N N 69 ARG NE HE sing N N 70 ARG CZ NH1 sing N N 71 ARG CZ NH2 doub N N 72 ARG NH1 HH11 sing N N 73 ARG NH1 HH12 sing N N 74 ARG NH2 HH21 sing N N 75 ARG NH2 HH22 sing N N 76 ARG OXT HXT sing N N 77 ASP N CA sing N N 78 ASP N H sing N N 79 ASP N H2 sing N N 80 ASP CA C sing N N 81 ASP CA CB sing N N 82 ASP CA HA sing N N 83 ASP C O doub N N 84 ASP C OXT sing N N 85 ASP CB CG sing N N 86 ASP CB HB2 sing N N 87 ASP CB HB3 sing N N 88 ASP CG OD1 doub N N 89 ASP CG OD2 sing N N 90 ASP OD2 HD2 sing N N 91 ASP OXT HXT sing N N 92 GLN N CA sing N N 93 GLN N H sing N N 94 GLN N H2 sing N N 95 GLN CA C sing N N 96 GLN CA CB sing N N 97 GLN CA HA sing N N 98 GLN C O doub N N 99 GLN C OXT sing N N 100 GLN CB CG sing N N 101 GLN CB HB2 sing N N 102 GLN CB HB3 sing N N 103 GLN CG CD sing N N 104 GLN CG HG2 sing N N 105 GLN CG HG3 sing N N 106 GLN CD OE1 doub N N 107 GLN CD NE2 sing N N 108 GLN NE2 HE21 sing N N 109 GLN NE2 HE22 sing N N 110 GLN OXT HXT sing N N 111 GLU N CA sing N N 112 GLU N H sing N N 113 GLU N H2 sing N N 114 GLU CA C sing N N 115 GLU CA CB sing N N 116 GLU CA HA sing N N 117 GLU C O doub N N 118 GLU C OXT sing N N 119 GLU CB CG sing N N 120 GLU CB HB2 sing N N 121 GLU CB HB3 sing N N 122 GLU CG CD sing N N 123 GLU CG HG2 sing N N 124 GLU CG HG3 sing N N 125 GLU CD OE1 doub N N 126 GLU CD OE2 sing N N 127 GLU OE2 HE2 sing N N 128 GLU OXT HXT sing N N 129 GLY N CA sing N N 130 GLY N H sing N N 131 GLY N H2 sing N N 132 GLY CA C sing N N 133 GLY CA HA2 sing N N 134 GLY CA HA3 sing N N 135 GLY C O doub N N 136 GLY C OXT sing N N 137 GLY OXT HXT sing N N 138 HIS N CA sing N N 139 HIS N H sing N N 140 HIS N H2 sing N N 141 HIS CA C sing N N 142 HIS CA CB sing N N 143 HIS CA HA sing N N 144 HIS C O doub N N 145 HIS C OXT sing N N 146 HIS CB CG sing N N 147 HIS CB HB2 sing N N 148 HIS CB HB3 sing N N 149 HIS CG ND1 sing Y N 150 HIS CG CD2 doub Y N 151 HIS ND1 CE1 doub Y N 152 HIS ND1 HD1 sing N N 153 HIS CD2 NE2 sing Y N 154 HIS CD2 HD2 sing N N 155 HIS CE1 NE2 sing Y N 156 HIS CE1 HE1 sing N N 157 HIS NE2 HE2 sing N N 158 HIS OXT HXT sing N N 159 HOH O H1 sing N N 160 HOH O H2 sing N N 161 ILE N CA sing N N 162 ILE N H sing N N 163 ILE N H2 sing N N 164 ILE CA C sing N N 165 ILE CA CB sing N N 166 ILE CA HA sing N N 167 ILE C O doub N N 168 ILE C OXT sing N N 169 ILE CB CG1 sing N N 170 ILE CB CG2 sing N N 171 ILE CB HB sing N N 172 ILE CG1 CD1 sing N N 173 ILE CG1 HG12 sing N N 174 ILE CG1 HG13 sing N N 175 ILE CG2 HG21 sing N N 176 ILE CG2 HG22 sing N N 177 ILE CG2 HG23 sing N N 178 ILE CD1 HD11 sing N N 179 ILE CD1 HD12 sing N N 180 ILE CD1 HD13 sing N N 181 ILE OXT HXT sing N N 182 LEU N CA sing N N 183 LEU N H sing N N 184 LEU N H2 sing N N 185 LEU CA C sing N N 186 LEU CA CB sing N N 187 LEU CA HA sing N N 188 LEU C O doub N N 189 LEU C OXT sing N N 190 LEU CB CG sing N N 191 LEU CB HB2 sing N N 192 LEU CB HB3 sing N N 193 LEU CG CD1 sing N N 194 LEU CG CD2 sing N N 195 LEU CG HG sing N N 196 LEU CD1 HD11 sing N N 197 LEU CD1 HD12 sing N N 198 LEU CD1 HD13 sing N N 199 LEU CD2 HD21 sing N N 200 LEU CD2 HD22 sing N N 201 LEU CD2 HD23 sing N N 202 LEU OXT HXT sing N N 203 LYS N CA sing N N 204 LYS N H sing N N 205 LYS N H2 sing N N 206 LYS CA C sing N N 207 LYS CA CB sing N N 208 LYS CA HA sing N N 209 LYS C O doub N N 210 LYS C OXT sing N N 211 LYS CB CG sing N N 212 LYS CB HB2 sing N N 213 LYS CB HB3 sing N N 214 LYS CG CD sing N N 215 LYS CG HG2 sing N N 216 LYS CG HG3 sing N N 217 LYS CD CE sing N N 218 LYS CD HD2 sing N N 219 LYS CD HD3 sing N N 220 LYS CE NZ sing N N 221 LYS CE HE2 sing N N 222 LYS CE HE3 sing N N 223 LYS NZ HZ1 sing N N 224 LYS NZ HZ2 sing N N 225 LYS NZ HZ3 sing N N 226 LYS OXT HXT sing N N 227 MET N CA sing N N 228 MET N H sing N N 229 MET N H2 sing N N 230 MET CA C sing N N 231 MET CA CB sing N N 232 MET CA HA sing N N 233 MET C O doub N N 234 MET C OXT sing N N 235 MET CB CG sing N N 236 MET CB HB2 sing N N 237 MET CB HB3 sing N N 238 MET CG SD sing N N 239 MET CG HG2 sing N N 240 MET CG HG3 sing N N 241 MET SD CE sing N N 242 MET CE HE1 sing N N 243 MET CE HE2 sing N N 244 MET CE HE3 sing N N 245 MET OXT HXT sing N N 246 PHE N CA sing N N 247 PHE N H sing N N 248 PHE N H2 sing N N 249 PHE CA C sing N N 250 PHE CA CB sing N N 251 PHE CA HA sing N N 252 PHE C O doub N N 253 PHE C OXT sing N N 254 PHE CB CG sing N N 255 PHE CB HB2 sing N N 256 PHE CB HB3 sing N N 257 PHE CG CD1 doub Y N 258 PHE CG CD2 sing Y N 259 PHE CD1 CE1 sing Y N 260 PHE CD1 HD1 sing N N 261 PHE CD2 CE2 doub Y N 262 PHE CD2 HD2 sing N N 263 PHE CE1 CZ doub Y N 264 PHE CE1 HE1 sing N N 265 PHE CE2 CZ sing Y N 266 PHE CE2 HE2 sing N N 267 PHE CZ HZ sing N N 268 PHE OXT HXT sing N N 269 PRO N CA sing N N 270 PRO N CD sing N N 271 PRO N H sing N N 272 PRO CA C sing N N 273 PRO CA CB sing N N 274 PRO CA HA sing N N 275 PRO C O doub N N 276 PRO C OXT sing N N 277 PRO CB CG sing N N 278 PRO CB HB2 sing N N 279 PRO CB HB3 sing N N 280 PRO CG CD sing N N 281 PRO CG HG2 sing N N 282 PRO CG HG3 sing N N 283 PRO CD HD2 sing N N 284 PRO CD HD3 sing N N 285 PRO OXT HXT sing N N 286 SER N CA sing N N 287 SER N H sing N N 288 SER N H2 sing N N 289 SER CA C sing N N 290 SER CA CB sing N N 291 SER CA HA sing N N 292 SER C O doub N N 293 SER C OXT sing N N 294 SER CB OG sing N N 295 SER CB HB2 sing N N 296 SER CB HB3 sing N N 297 SER OG HG sing N N 298 SER OXT HXT sing N N 299 THR N CA sing N N 300 THR N H sing N N 301 THR N H2 sing N N 302 THR CA C sing N N 303 THR CA CB sing N N 304 THR CA HA sing N N 305 THR C O doub N N 306 THR C OXT sing N N 307 THR CB OG1 sing N N 308 THR CB CG2 sing N N 309 THR CB HB sing N N 310 THR OG1 HG1 sing N N 311 THR CG2 HG21 sing N N 312 THR CG2 HG22 sing N N 313 THR CG2 HG23 sing N N 314 THR OXT HXT sing N N 315 TRP N CA sing N N 316 TRP N H sing N N 317 TRP N H2 sing N N 318 TRP CA C sing N N 319 TRP CA CB sing N N 320 TRP CA HA sing N N 321 TRP C O doub N N 322 TRP C OXT sing N N 323 TRP CB CG sing N N 324 TRP CB HB2 sing N N 325 TRP CB HB3 sing N N 326 TRP CG CD1 doub Y N 327 TRP CG CD2 sing Y N 328 TRP CD1 NE1 sing Y N 329 TRP CD1 HD1 sing N N 330 TRP CD2 CE2 doub Y N 331 TRP CD2 CE3 sing Y N 332 TRP NE1 CE2 sing Y N 333 TRP NE1 HE1 sing N N 334 TRP CE2 CZ2 sing Y N 335 TRP CE3 CZ3 doub Y N 336 TRP CE3 HE3 sing N N 337 TRP CZ2 CH2 doub Y N 338 TRP CZ2 HZ2 sing N N 339 TRP CZ3 CH2 sing Y N 340 TRP CZ3 HZ3 sing N N 341 TRP CH2 HH2 sing N N 342 TRP OXT HXT sing N N 343 TYR N CA sing N N 344 TYR N H sing N N 345 TYR N H2 sing N N 346 TYR CA C sing N N 347 TYR CA CB sing N N 348 TYR CA HA sing N N 349 TYR C O doub N N 350 TYR C OXT sing N N 351 TYR CB CG sing N N 352 TYR CB HB2 sing N N 353 TYR CB HB3 sing N N 354 TYR CG CD1 doub Y N 355 TYR CG CD2 sing Y N 356 TYR CD1 CE1 sing Y N 357 TYR CD1 HD1 sing N N 358 TYR CD2 CE2 doub Y N 359 TYR CD2 HD2 sing N N 360 TYR CE1 CZ doub Y N 361 TYR CE1 HE1 sing N N 362 TYR CE2 CZ sing Y N 363 TYR CE2 HE2 sing N N 364 TYR CZ OH sing N N 365 TYR OH HH sing N N 366 TYR OXT HXT sing N N 367 VAL N CA sing N N 368 VAL N H sing N N 369 VAL N H2 sing N N 370 VAL CA C sing N N 371 VAL CA CB sing N N 372 VAL CA HA sing N N 373 VAL C O doub N N 374 VAL C OXT sing N N 375 VAL CB CG1 sing N N 376 VAL CB CG2 sing N N 377 VAL CB HB sing N N 378 VAL CG1 HG11 sing N N 379 VAL CG1 HG12 sing N N 380 VAL CG1 HG13 sing N N 381 VAL CG2 HG21 sing N N 382 VAL CG2 HG22 sing N N 383 VAL CG2 HG23 sing N N 384 VAL OXT HXT sing N N 385 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 'ADENOSINE MONOPHOSPHATE' AMP 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2YVM _pdbx_initial_refinement_model.details 'PDB ENTRY 2YVM' #