data_4JVF # _entry.id 4JVF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 4JVF pdb_00004jvf 10.2210/pdb4jvf/pdb RCSB RCSB078553 ? ? WWPDB D_1000078553 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4JV6 . unspecified PDB 4JV8 . unspecified PDB 4JVB . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4JVF _pdbx_database_status.recvd_initial_deposition_date 2013-03-25 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gunther, Z.' 1 'Papke, B.' 2 'Ismail, S.' 3 'Vartak, N.' 4 'Chandra, A.' 5 'Hoffmann, M.' 6 'Hahn, S.' 7 'Triola, G.' 8 'Wittinghofer, A.' 9 'Bastiaens, P.' 10 'Waldmann, H.' 11 # _citation.id primary _citation.title 'Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling' _citation.journal_abbrev Nature _citation.journal_volume 497 _citation.page_first 638 _citation.page_last 642 _citation.year 2013 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23698361 _citation.pdbx_database_id_DOI 10.1038/nature12205 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zimmermann, G.' 1 ? primary 'Papke, B.' 2 ? primary 'Ismail, S.' 3 ? primary 'Vartak, N.' 4 ? primary 'Chandra, A.' 5 ? primary 'Hoffmann, M.' 6 ? primary 'Hahn, S.A.' 7 ? primary 'Triola, G.' 8 ? primary 'Wittinghofer, A.' 9 ? primary 'Bastiaens, P.I.' 10 ? primary 'Waldmann, H.' 11 ? # _cell.entry_id 4JVF _cell.length_a 55.910 _cell.length_b 55.910 _cell.length_c 116.670 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 4JVF _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _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 ;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ; 17585.121 1 ? ? ? ? 2 non-polymer syn '(2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate' 638.800 1 ? ? ? ? 3 water nat water 18.015 47 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'GMP-PDE delta, Protein p17' # _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 ;GSMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQ KVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV ; _entity_poly.pdbx_seq_one_letter_code_can ;GSMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQ KVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV ; _entity_poly.pdbx_strand_id B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 SER n 1 3 MET n 1 4 SER n 1 5 ALA n 1 6 LYS n 1 7 ASP n 1 8 GLU n 1 9 ARG n 1 10 ALA n 1 11 ARG n 1 12 GLU n 1 13 ILE n 1 14 LEU n 1 15 ARG n 1 16 GLY n 1 17 PHE n 1 18 LYS n 1 19 LEU n 1 20 ASN n 1 21 TRP n 1 22 MET n 1 23 ASN n 1 24 LEU n 1 25 ARG n 1 26 ASP n 1 27 ALA n 1 28 GLU n 1 29 THR n 1 30 GLY n 1 31 LYS n 1 32 ILE n 1 33 LEU n 1 34 TRP n 1 35 GLN n 1 36 GLY n 1 37 THR n 1 38 GLU n 1 39 ASP n 1 40 LEU n 1 41 SER n 1 42 VAL n 1 43 PRO n 1 44 GLY n 1 45 VAL n 1 46 GLU n 1 47 HIS n 1 48 GLU n 1 49 ALA n 1 50 ARG n 1 51 VAL n 1 52 PRO n 1 53 LYS n 1 54 LYS n 1 55 ILE n 1 56 LEU n 1 57 LYS n 1 58 CYS n 1 59 LYS n 1 60 ALA n 1 61 VAL n 1 62 SER n 1 63 ARG n 1 64 GLU n 1 65 LEU n 1 66 ASN n 1 67 PHE n 1 68 SER n 1 69 SER n 1 70 THR n 1 71 GLU n 1 72 GLN n 1 73 MET n 1 74 GLU n 1 75 LYS n 1 76 PHE n 1 77 ARG n 1 78 LEU n 1 79 GLU n 1 80 GLN n 1 81 LYS n 1 82 VAL n 1 83 TYR n 1 84 PHE n 1 85 LYS n 1 86 GLY n 1 87 GLN n 1 88 CYS n 1 89 LEU n 1 90 GLU n 1 91 GLU n 1 92 TRP n 1 93 PHE n 1 94 PHE n 1 95 GLU n 1 96 PHE n 1 97 GLY n 1 98 PHE n 1 99 VAL n 1 100 ILE n 1 101 PRO n 1 102 ASN n 1 103 SER n 1 104 THR n 1 105 ASN n 1 106 THR n 1 107 TRP n 1 108 GLN n 1 109 SER n 1 110 LEU n 1 111 ILE n 1 112 GLU n 1 113 ALA n 1 114 ALA n 1 115 PRO n 1 116 GLU n 1 117 SER n 1 118 GLN n 1 119 MET n 1 120 MET n 1 121 PRO n 1 122 ALA n 1 123 SER n 1 124 VAL n 1 125 LEU n 1 126 THR n 1 127 GLY n 1 128 ASN n 1 129 VAL n 1 130 ILE n 1 131 ILE n 1 132 GLU n 1 133 THR n 1 134 LYS n 1 135 PHE n 1 136 PHE n 1 137 ASP n 1 138 ASP n 1 139 ASP n 1 140 LEU n 1 141 LEU n 1 142 VAL n 1 143 SER n 1 144 THR n 1 145 SER n 1 146 ARG n 1 147 VAL n 1 148 ARG n 1 149 LEU n 1 150 PHE n 1 151 TYR n 1 152 VAL 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 human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'PDE6D, PDED' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _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 ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PDE6D_HUMAN _struct_ref.pdbx_db_accession O43924 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKV YFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4JVF _struct_ref_seq.pdbx_strand_id B _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 152 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O43924 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 150 _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 150 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4JVF GLY B 1 ? UNP O43924 ? ? 'expression tag' -1 1 1 4JVF SER B 2 ? UNP O43924 ? ? 'expression tag' 0 2 # 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 17X non-polymer . '(2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate' ? 'C40 H42 N6 O2' 638.800 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 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 4JVF _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.99 _exptl_crystal.density_percent_sol 58.91 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.4 _exptl_crystal_grow.pdbx_details '18% PEG 4000, 25mM Sodium Acetate, 200mM Ammonium Sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2012-03-01 _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 'SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X10SA' _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X10SA _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1 # _reflns.entry_id 4JVF _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F -3 _reflns.d_resolution_low 27.9 _reflns.d_resolution_high 2.4 _reflns.number_obs 8659 _reflns.number_all 8659 _reflns.percent_possible_obs 99 _reflns.pdbx_Rmerge_I_obs 0.122 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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 2.4 _reflns_shell.d_res_low 2.5 _reflns_shell.percent_possible_all 98.8 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _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 4JVF _refine.ls_number_reflns_obs 8225 _refine.ls_number_reflns_all 8225 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F -3 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 27.9 _refine.ls_d_res_high 2.40 _refine.ls_percent_reflns_obs 99.04 _refine.ls_R_factor_obs 0.20949 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20697 _refine.ls_R_factor_R_free 0.25659 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 433 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.936 _refine.correlation_coeff_Fo_to_Fc_free 0.906 _refine.B_iso_mean 31.222 _refine.aniso_B[1][1] 1.46 _refine.aniso_B[2][2] 1.46 _refine.aniso_B[3][3] -2.20 _refine.aniso_B[1][2] 0.73 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT' _refine.pdbx_starting_model 3T5G _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.317 _refine.pdbx_overall_ESU_R_Free 0.245 _refine.overall_SU_ML 0.174 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 7.480 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1158 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 48 _refine_hist.number_atoms_solvent 47 _refine_hist.number_atoms_total 1253 _refine_hist.d_res_high 2.40 _refine_hist.d_res_low 27.9 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.022 0.022 ? 1237 ? 'X-RAY DIFFRACTION' r_bond_other_d ? ? ? ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.980 2.001 ? 1668 ? 'X-RAY DIFFRACTION' r_angle_other_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 7.743 5.000 ? 139 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 41.363 23.793 ? 58 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 18.107 15.000 ? 220 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 17.629 15.000 ? 9 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.123 0.200 ? 177 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.009 0.021 ? 924 ? 'X-RAY DIFFRACTION' r_gen_planes_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_scbond_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_scangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_rigid_bond_restr ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_free ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded ? ? ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.400 _refine_ls_shell.d_res_low 2.462 _refine_ls_shell.number_reflns_R_work 520 _refine_ls_shell.R_factor_R_work 0.250 _refine_ls_shell.percent_reflns_obs 98.56 _refine_ls_shell.R_factor_R_free 0.409 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 27 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 4JVF _struct.title 'The Crystal structure of PDE6D in complex with the inhibitor (s)-5' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4JVF _struct_keywords.pdbx_keywords 'Protein binding/inhibitor' _struct_keywords.text 'Immunoglobulin-like beta-sandwich, GDI-like solubilizing factor, Prenyl binding, Protein binding-inhibitor complex' # 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 3 ? # _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 LYS A 6 ? GLY A 16 ? LYS B 4 GLY B 14 1 ? 11 HELX_P HELX_P2 2 LYS A 54 ? LYS A 57 ? LYS B 52 LYS B 55 5 ? 4 HELX_P HELX_P3 3 PRO A 121 ? THR A 126 ? PRO B 119 THR B 124 1 ? 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 5 ? # 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 A 3 4 ? anti-parallel B 1 2 ? parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? 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 ILE A 32 ? GLY A 36 ? ILE B 30 GLY B 34 A 2 PHE A 17 ? ASP A 26 ? PHE B 15 ASP B 24 A 3 ALA A 60 ? SER A 69 ? ALA B 58 SER B 67 A 4 SER A 103 ? GLU A 112 ? SER B 101 GLU B 110 B 1 GLU A 46 ? PRO A 52 ? GLU B 44 PRO B 50 B 2 LEU A 140 ? VAL A 152 ? LEU B 138 VAL B 150 B 3 VAL A 129 ? ASP A 137 ? VAL B 127 ASP B 135 B 4 MET A 73 ? PHE A 84 ? MET B 71 PHE B 82 B 5 GLN A 87 ? VAL A 99 ? GLN B 85 VAL B 97 # 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 O TRP A 34 ? O TRP B 32 N LEU A 24 ? N LEU B 22 A 2 3 N ARG A 25 ? N ARG B 23 O SER A 62 ? O SER B 60 A 3 4 N ARG A 63 ? N ARG B 61 O SER A 109 ? O SER B 107 B 1 2 N HIS A 47 ? N HIS B 45 O ARG A 148 ? O ARG B 146 B 2 3 O VAL A 142 ? O VAL B 140 N PHE A 135 ? N PHE B 133 B 3 4 O ILE A 130 ? O ILE B 128 N TYR A 83 ? N TYR B 81 B 4 5 N VAL A 82 ? N VAL B 80 O LEU A 89 ? O LEU B 87 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id 17X _struct_site.pdbx_auth_seq_id 201 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 14 _struct_site.details 'BINDING SITE FOR RESIDUE 17X B 201' # 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 14 LEU A 40 ? LEU B 38 . ? 1_555 ? 2 AC1 14 ALA A 49 ? ALA B 47 . ? 1_555 ? 3 AC1 14 ILE A 55 ? ILE B 53 . ? 1_555 ? 4 AC1 14 LEU A 56 ? LEU B 54 . ? 1_555 ? 5 AC1 14 CYS A 58 ? CYS B 56 . ? 1_555 ? 6 AC1 14 LYS A 59 ? LYS B 57 . ? 1_555 ? 7 AC1 14 ARG A 63 ? ARG B 61 . ? 1_555 ? 8 AC1 14 GLN A 80 ? GLN B 78 . ? 1_555 ? 9 AC1 14 VAL A 82 ? VAL B 80 . ? 1_555 ? 10 AC1 14 TRP A 92 ? TRP B 90 . ? 1_555 ? 11 AC1 14 ILE A 111 ? ILE B 109 . ? 1_555 ? 12 AC1 14 ILE A 131 ? ILE B 129 . ? 1_555 ? 13 AC1 14 LEU A 149 ? LEU B 147 . ? 1_555 ? 14 AC1 14 TYR A 151 ? TYR B 149 . ? 1_555 ? # _database_PDB_matrix.entry_id 4JVF _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 4JVF _atom_sites.fract_transf_matrix[1][1] 0.017886 _atom_sites.fract_transf_matrix[1][2] 0.010326 _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] 0.020653 _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] 0.008571 _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 N O 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 GLY 1 -1 ? ? ? B . n A 1 2 SER 2 0 ? ? ? B . n A 1 3 MET 3 1 ? ? ? B . n A 1 4 SER 4 2 ? ? ? B . n A 1 5 ALA 5 3 ? ? ? B . n A 1 6 LYS 6 4 4 LYS LYS B . n A 1 7 ASP 7 5 5 ASP ASP B . n A 1 8 GLU 8 6 6 GLU GLU B . n A 1 9 ARG 9 7 7 ARG ARG B . n A 1 10 ALA 10 8 8 ALA ALA B . n A 1 11 ARG 11 9 9 ARG ARG B . n A 1 12 GLU 12 10 10 GLU GLU B . n A 1 13 ILE 13 11 11 ILE ILE B . n A 1 14 LEU 14 12 12 LEU LEU B . n A 1 15 ARG 15 13 13 ARG ARG B . n A 1 16 GLY 16 14 14 GLY GLY B . n A 1 17 PHE 17 15 15 PHE PHE B . n A 1 18 LYS 18 16 16 LYS LYS B . n A 1 19 LEU 19 17 17 LEU LEU B . n A 1 20 ASN 20 18 18 ASN ASN B . n A 1 21 TRP 21 19 19 TRP TRP B . n A 1 22 MET 22 20 20 MET MET B . n A 1 23 ASN 23 21 21 ASN ASN B . n A 1 24 LEU 24 22 22 LEU LEU B . n A 1 25 ARG 25 23 23 ARG ARG B . n A 1 26 ASP 26 24 24 ASP ASP B . n A 1 27 ALA 27 25 25 ALA ALA B . n A 1 28 GLU 28 26 26 GLU ALA B . n A 1 29 THR 29 27 27 THR THR B . n A 1 30 GLY 30 28 28 GLY GLY B . n A 1 31 LYS 31 29 29 LYS LYS B . n A 1 32 ILE 32 30 30 ILE ILE B . n A 1 33 LEU 33 31 31 LEU LEU B . n A 1 34 TRP 34 32 32 TRP TRP B . n A 1 35 GLN 35 33 33 GLN GLN B . n A 1 36 GLY 36 34 34 GLY GLY B . n A 1 37 THR 37 35 35 THR THR B . n A 1 38 GLU 38 36 36 GLU GLU B . n A 1 39 ASP 39 37 37 ASP ASP B . n A 1 40 LEU 40 38 38 LEU LEU B . n A 1 41 SER 41 39 39 SER SER B . n A 1 42 VAL 42 40 40 VAL VAL B . n A 1 43 PRO 43 41 41 PRO PRO B . n A 1 44 GLY 44 42 42 GLY GLY B . n A 1 45 VAL 45 43 43 VAL VAL B . n A 1 46 GLU 46 44 44 GLU GLU B . n A 1 47 HIS 47 45 45 HIS HIS B . n A 1 48 GLU 48 46 46 GLU GLU B . n A 1 49 ALA 49 47 47 ALA ALA B . n A 1 50 ARG 50 48 48 ARG ARG B . n A 1 51 VAL 51 49 49 VAL VAL B . n A 1 52 PRO 52 50 50 PRO PRO B . n A 1 53 LYS 53 51 51 LYS LYS B . n A 1 54 LYS 54 52 52 LYS LYS B . n A 1 55 ILE 55 53 53 ILE ILE B . n A 1 56 LEU 56 54 54 LEU LEU B . n A 1 57 LYS 57 55 55 LYS LYS B . n A 1 58 CYS 58 56 56 CYS CYS B . n A 1 59 LYS 59 57 57 LYS LYS B . n A 1 60 ALA 60 58 58 ALA ALA B . n A 1 61 VAL 61 59 59 VAL VAL B . n A 1 62 SER 62 60 60 SER SER B . n A 1 63 ARG 63 61 61 ARG ARG B . n A 1 64 GLU 64 62 62 GLU GLU B . n A 1 65 LEU 65 63 63 LEU LEU B . n A 1 66 ASN 66 64 64 ASN ASN B . n A 1 67 PHE 67 65 65 PHE PHE B . n A 1 68 SER 68 66 66 SER SER B . n A 1 69 SER 69 67 67 SER SER B . n A 1 70 THR 70 68 68 THR THR B . n A 1 71 GLU 71 69 69 GLU GLU B . n A 1 72 GLN 72 70 70 GLN GLN B . n A 1 73 MET 73 71 71 MET MET B . n A 1 74 GLU 74 72 72 GLU GLU B . n A 1 75 LYS 75 73 73 LYS LYS B . n A 1 76 PHE 76 74 74 PHE PHE B . n A 1 77 ARG 77 75 75 ARG ARG B . n A 1 78 LEU 78 76 76 LEU LEU B . n A 1 79 GLU 79 77 77 GLU GLU B . n A 1 80 GLN 80 78 78 GLN GLN B . n A 1 81 LYS 81 79 79 LYS LYS B . n A 1 82 VAL 82 80 80 VAL VAL B . n A 1 83 TYR 83 81 81 TYR TYR B . n A 1 84 PHE 84 82 82 PHE PHE B . n A 1 85 LYS 85 83 83 LYS LYS B . n A 1 86 GLY 86 84 84 GLY GLY B . n A 1 87 GLN 87 85 85 GLN GLN B . n A 1 88 CYS 88 86 86 CYS CYS B . n A 1 89 LEU 89 87 87 LEU LEU B . n A 1 90 GLU 90 88 88 GLU GLU B . n A 1 91 GLU 91 89 89 GLU GLU B . n A 1 92 TRP 92 90 90 TRP TRP B . n A 1 93 PHE 93 91 91 PHE PHE B . n A 1 94 PHE 94 92 92 PHE PHE B . n A 1 95 GLU 95 93 93 GLU GLU B . n A 1 96 PHE 96 94 94 PHE PHE B . n A 1 97 GLY 97 95 95 GLY GLY B . n A 1 98 PHE 98 96 96 PHE PHE B . n A 1 99 VAL 99 97 97 VAL VAL B . n A 1 100 ILE 100 98 98 ILE ILE B . n A 1 101 PRO 101 99 99 PRO PRO B . n A 1 102 ASN 102 100 100 ASN ASN B . n A 1 103 SER 103 101 101 SER SER B . n A 1 104 THR 104 102 102 THR THR B . n A 1 105 ASN 105 103 103 ASN ASN B . n A 1 106 THR 106 104 104 THR THR B . n A 1 107 TRP 107 105 105 TRP TRP B . n A 1 108 GLN 108 106 106 GLN GLN B . n A 1 109 SER 109 107 107 SER SER B . n A 1 110 LEU 110 108 108 LEU LEU B . n A 1 111 ILE 111 109 109 ILE ILE B . n A 1 112 GLU 112 110 110 GLU GLU B . n A 1 113 ALA 113 111 111 ALA ALA B . n A 1 114 ALA 114 112 ? ? ? B . n A 1 115 PRO 115 113 ? ? ? B . n A 1 116 GLU 116 114 ? ? ? B . n A 1 117 SER 117 115 ? ? ? B . n A 1 118 GLN 118 116 ? ? ? B . n A 1 119 MET 119 117 ? ? ? B . n A 1 120 MET 120 118 118 MET MET B . n A 1 121 PRO 121 119 119 PRO PRO B . n A 1 122 ALA 122 120 120 ALA ALA B . n A 1 123 SER 123 121 121 SER SER B . n A 1 124 VAL 124 122 122 VAL VAL B . n A 1 125 LEU 125 123 123 LEU LEU B . n A 1 126 THR 126 124 124 THR THR B . n A 1 127 GLY 127 125 125 GLY GLY B . n A 1 128 ASN 128 126 126 ASN ASN B . n A 1 129 VAL 129 127 127 VAL VAL B . n A 1 130 ILE 130 128 128 ILE ILE B . n A 1 131 ILE 131 129 129 ILE ILE B . n A 1 132 GLU 132 130 130 GLU GLU B . n A 1 133 THR 133 131 131 THR THR B . n A 1 134 LYS 134 132 132 LYS LYS B . n A 1 135 PHE 135 133 133 PHE PHE B . n A 1 136 PHE 136 134 134 PHE PHE B . n A 1 137 ASP 137 135 135 ASP ASP B . n A 1 138 ASP 138 136 136 ASP ASP B . n A 1 139 ASP 139 137 137 ASP ASP B . n A 1 140 LEU 140 138 138 LEU LEU B . n A 1 141 LEU 141 139 139 LEU LEU B . n A 1 142 VAL 142 140 140 VAL VAL B . n A 1 143 SER 143 141 141 SER SER B . n A 1 144 THR 144 142 142 THR THR B . n A 1 145 SER 145 143 143 SER SER B . n A 1 146 ARG 146 144 144 ARG ARG B . n A 1 147 VAL 147 145 145 VAL VAL B . n A 1 148 ARG 148 146 146 ARG ARG B . n A 1 149 LEU 149 147 147 LEU LEU B . n A 1 150 PHE 150 148 148 PHE PHE B . n A 1 151 TYR 151 149 149 TYR TYR B . n A 1 152 VAL 152 150 150 VAL VAL B . n # 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 17X 1 201 1 17X DRG B . C 3 HOH 1 301 4 HOH HOH B . C 3 HOH 2 302 6 HOH HOH B . C 3 HOH 3 303 7 HOH HOH B . C 3 HOH 4 304 8 HOH HOH B . C 3 HOH 5 305 9 HOH HOH B . C 3 HOH 6 306 11 HOH HOH B . C 3 HOH 7 307 12 HOH HOH B . C 3 HOH 8 308 13 HOH HOH B . C 3 HOH 9 309 14 HOH HOH B . C 3 HOH 10 310 15 HOH HOH B . C 3 HOH 11 311 16 HOH HOH B . C 3 HOH 12 312 17 HOH HOH B . C 3 HOH 13 313 18 HOH HOH B . C 3 HOH 14 314 19 HOH HOH B . C 3 HOH 15 315 20 HOH HOH B . C 3 HOH 16 316 22 HOH HOH B . C 3 HOH 17 317 23 HOH HOH B . C 3 HOH 18 318 24 HOH HOH B . C 3 HOH 19 319 25 HOH HOH B . C 3 HOH 20 320 26 HOH HOH B . C 3 HOH 21 321 27 HOH HOH B . C 3 HOH 22 322 28 HOH HOH B . C 3 HOH 23 323 29 HOH HOH B . C 3 HOH 24 324 30 HOH HOH B . C 3 HOH 25 325 31 HOH HOH B . C 3 HOH 26 326 32 HOH HOH B . C 3 HOH 27 327 34 HOH HOH B . C 3 HOH 28 328 36 HOH HOH B . C 3 HOH 29 329 38 HOH HOH B . C 3 HOH 30 330 39 HOH HOH B . C 3 HOH 31 331 40 HOH HOH B . C 3 HOH 32 332 41 HOH HOH B . C 3 HOH 33 333 43 HOH HOH B . C 3 HOH 34 334 46 HOH HOH B . C 3 HOH 35 335 47 HOH HOH B . C 3 HOH 36 336 49 HOH HOH B . C 3 HOH 37 337 50 HOH HOH B . C 3 HOH 38 338 52 HOH HOH B . C 3 HOH 39 339 53 HOH HOH B . C 3 HOH 40 340 54 HOH HOH B . C 3 HOH 41 341 55 HOH HOH B . C 3 HOH 42 342 57 HOH HOH B . C 3 HOH 43 343 58 HOH HOH B . C 3 HOH 44 344 61 HOH HOH B . C 3 HOH 45 345 62 HOH HOH B . C 3 HOH 46 346 63 HOH HOH B . C 3 HOH 47 347 64 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # 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 2013-05-22 2 'Structure model' 1 1 2013-06-05 3 'Structure model' 1 2 2017-11-15 4 'Structure model' 1 3 2023-09-20 # _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' 'Database references' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 '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' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_initial_refinement_model 6 4 'Structure model' struct_ref_seq_dif 7 4 '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' '_software.name' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_struct_ref_seq_dif.details' 5 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ProDC 'data collection' . ? 1 MOLREP phasing . ? 2 REFMAC refinement 5.6.0093 ? 3 XDS 'data reduction' . ? 4 XSCALE 'data scaling' . ? 5 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 NE _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 ARG _pdbx_validate_close_contact.auth_seq_id_1 144 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 325 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.18 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 CG _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 ARG _pdbx_validate_rmsd_angle.auth_seq_id_1 13 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CD _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 ARG _pdbx_validate_rmsd_angle.auth_seq_id_2 13 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 NE _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 ARG _pdbx_validate_rmsd_angle.auth_seq_id_3 13 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 97.73 _pdbx_validate_rmsd_angle.angle_target_value 111.80 _pdbx_validate_rmsd_angle.angle_deviation -14.07 _pdbx_validate_rmsd_angle.angle_standard_deviation 2.10 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ASP _pdbx_validate_torsion.auth_asym_id B _pdbx_validate_torsion.auth_seq_id 136 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi 52.39 _pdbx_validate_torsion.psi -114.44 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 PHE _pdbx_validate_peptide_omega.auth_asym_id_1 B _pdbx_validate_peptide_omega.auth_seq_id_1 134 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 ? _pdbx_validate_peptide_omega.auth_comp_id_2 ASP _pdbx_validate_peptide_omega.auth_asym_id_2 B _pdbx_validate_peptide_omega.auth_seq_id_2 135 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega 147.48 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 B GLU 26 ? CG ? A GLU 28 CG 2 1 Y 1 B GLU 26 ? CD ? A GLU 28 CD 3 1 Y 1 B GLU 26 ? OE1 ? A GLU 28 OE1 4 1 Y 1 B GLU 26 ? OE2 ? A GLU 28 OE2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 B GLY -1 ? A GLY 1 2 1 Y 1 B SER 0 ? A SER 2 3 1 Y 1 B MET 1 ? A MET 3 4 1 Y 1 B SER 2 ? A SER 4 5 1 Y 1 B ALA 3 ? A ALA 5 6 1 Y 1 B ALA 112 ? A ALA 114 7 1 Y 1 B PRO 113 ? A PRO 115 8 1 Y 1 B GLU 114 ? A GLU 116 9 1 Y 1 B SER 115 ? A SER 117 10 1 Y 1 B GLN 116 ? A GLN 118 11 1 Y 1 B MET 117 ? A MET 119 # 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 17X CAI C Y N 1 17X CAJ C Y N 2 17X CAK C Y N 3 17X CAL C Y N 4 17X CAM C Y N 5 17X CAH C Y N 6 17X CAG C N N 7 17X NAD N Y N 8 17X CAC C Y N 9 17X CAF C Y N 10 17X CAE C Y N 11 17X CAX C Y N 12 17X CAW C Y N 13 17X CAV C Y N 14 17X NAY N Y N 15 17X CAB C Y N 16 17X NAA N N N 17 17X CAR C N N 18 17X CAQ C N N 19 17X CAN C N N 20 17X CAO C N N 21 17X CAP C N N 22 17X CAS C N N 23 17X OAT O N N 24 17X OAU O N N 25 17X CBP C N N 26 17X CBO C N S 27 17X CBQ C N N 28 17X CBR C N N 29 17X CBS C N N 30 17X NBV N N N 31 17X CBT C N N 32 17X CBU C N N 33 17X NBH N Y N 34 17X CBD C Y N 35 17X CBE C Y N 36 17X CAZ C Y N 37 17X CBA C Y N 38 17X CBB C Y N 39 17X CBC C Y N 40 17X NBF N Y N 41 17X CBG C Y N 42 17X CBI C Y N 43 17X CBJ C Y N 44 17X CBK C Y N 45 17X CBL C Y N 46 17X CBM C Y N 47 17X CBN C Y N 48 17X H1 H N N 49 17X H2 H N N 50 17X H3 H N N 51 17X H4 H N N 52 17X H5 H N N 53 17X H6 H N N 54 17X H7 H N N 55 17X H8 H N N 56 17X H9 H N N 57 17X H10 H N N 58 17X H11 H N N 59 17X H12 H N N 60 17X H13 H N N 61 17X H14 H N N 62 17X H15 H N N 63 17X H16 H N N 64 17X H17 H N N 65 17X H18 H N N 66 17X H19 H N N 67 17X H20 H N N 68 17X H21 H N N 69 17X H22 H N N 70 17X H23 H N N 71 17X H24 H N N 72 17X H25 H N N 73 17X H26 H N N 74 17X H27 H N N 75 17X H28 H N N 76 17X H29 H N N 77 17X H31 H N N 78 17X H32 H N N 79 17X H33 H N N 80 17X H34 H N N 81 17X H35 H N N 82 17X H36 H N N 83 17X H37 H N N 84 17X H38 H N N 85 17X H39 H N N 86 17X H40 H N N 87 17X H41 H N N 88 17X H42 H N N 89 17X H43 H N N 90 ALA N N N N 91 ALA CA C N S 92 ALA C C N N 93 ALA O O N N 94 ALA CB C N N 95 ALA OXT O N N 96 ALA H H N N 97 ALA H2 H N N 98 ALA HA H N N 99 ALA HB1 H N N 100 ALA HB2 H N N 101 ALA HB3 H N N 102 ALA HXT H N N 103 ARG N N N N 104 ARG CA C N S 105 ARG C C N N 106 ARG O O N N 107 ARG CB C N N 108 ARG CG C N N 109 ARG CD C N N 110 ARG NE N N N 111 ARG CZ C N N 112 ARG NH1 N N N 113 ARG NH2 N N N 114 ARG OXT O N N 115 ARG H H N N 116 ARG H2 H N N 117 ARG HA H N N 118 ARG HB2 H N N 119 ARG HB3 H N N 120 ARG HG2 H N N 121 ARG HG3 H N N 122 ARG HD2 H N N 123 ARG HD3 H N N 124 ARG HE H N N 125 ARG HH11 H N N 126 ARG HH12 H N N 127 ARG HH21 H N N 128 ARG HH22 H N N 129 ARG HXT H N N 130 ASN N N N N 131 ASN CA C N S 132 ASN C C N N 133 ASN O O N N 134 ASN CB C N N 135 ASN CG C N N 136 ASN OD1 O N N 137 ASN ND2 N N N 138 ASN OXT O N N 139 ASN H H N N 140 ASN H2 H N N 141 ASN HA H N N 142 ASN HB2 H N N 143 ASN HB3 H N N 144 ASN HD21 H N N 145 ASN HD22 H N N 146 ASN HXT H N N 147 ASP N N N N 148 ASP CA C N S 149 ASP C C N N 150 ASP O O N N 151 ASP CB C N N 152 ASP CG C N N 153 ASP OD1 O N N 154 ASP OD2 O N N 155 ASP OXT O N N 156 ASP H H N N 157 ASP H2 H N N 158 ASP HA H N N 159 ASP HB2 H N N 160 ASP HB3 H N N 161 ASP HD2 H N N 162 ASP HXT H N N 163 CYS N N N N 164 CYS CA C N R 165 CYS C C N N 166 CYS O O N N 167 CYS CB C N N 168 CYS SG S N N 169 CYS OXT O N N 170 CYS H H N N 171 CYS H2 H N N 172 CYS HA H N N 173 CYS HB2 H N N 174 CYS HB3 H N N 175 CYS HG H N N 176 CYS HXT H N N 177 GLN N N N N 178 GLN CA C N S 179 GLN C C N N 180 GLN O O N N 181 GLN CB C N N 182 GLN CG C N N 183 GLN CD C N N 184 GLN OE1 O N N 185 GLN NE2 N N N 186 GLN OXT O N N 187 GLN H H N N 188 GLN H2 H N N 189 GLN HA H N N 190 GLN HB2 H N N 191 GLN HB3 H N N 192 GLN HG2 H N N 193 GLN HG3 H N N 194 GLN HE21 H N N 195 GLN HE22 H N N 196 GLN HXT H N N 197 GLU N N N N 198 GLU CA C N S 199 GLU C C N N 200 GLU O O N N 201 GLU CB C N N 202 GLU CG C N N 203 GLU CD C N N 204 GLU OE1 O N N 205 GLU OE2 O N N 206 GLU OXT O N N 207 GLU H H N N 208 GLU H2 H N N 209 GLU HA H N N 210 GLU HB2 H N N 211 GLU HB3 H N N 212 GLU HG2 H N N 213 GLU HG3 H N N 214 GLU HE2 H N N 215 GLU HXT H N N 216 GLY N N N N 217 GLY CA C N N 218 GLY C C N N 219 GLY O O N N 220 GLY OXT O N N 221 GLY H H N N 222 GLY H2 H N N 223 GLY HA2 H N N 224 GLY HA3 H N N 225 GLY HXT H N N 226 HIS N N N N 227 HIS CA C N S 228 HIS C C N N 229 HIS O O N N 230 HIS CB C N N 231 HIS CG C Y N 232 HIS ND1 N Y N 233 HIS CD2 C Y N 234 HIS CE1 C Y N 235 HIS NE2 N Y N 236 HIS OXT O N N 237 HIS H H N N 238 HIS H2 H N N 239 HIS HA H N N 240 HIS HB2 H N N 241 HIS HB3 H N N 242 HIS HD1 H N N 243 HIS HD2 H N N 244 HIS HE1 H N N 245 HIS HE2 H N N 246 HIS HXT H N N 247 HOH O O N N 248 HOH H1 H N N 249 HOH H2 H N N 250 ILE N N N N 251 ILE CA C N S 252 ILE C C N N 253 ILE O O N N 254 ILE CB C N S 255 ILE CG1 C N N 256 ILE CG2 C N N 257 ILE CD1 C N N 258 ILE OXT O N N 259 ILE H H N N 260 ILE H2 H N N 261 ILE HA H N N 262 ILE HB H N N 263 ILE HG12 H N N 264 ILE HG13 H N N 265 ILE HG21 H N N 266 ILE HG22 H N N 267 ILE HG23 H N N 268 ILE HD11 H N N 269 ILE HD12 H N N 270 ILE HD13 H N N 271 ILE HXT H N N 272 LEU N N N N 273 LEU CA C N S 274 LEU C C N N 275 LEU O O N N 276 LEU CB C N N 277 LEU CG C N N 278 LEU CD1 C N N 279 LEU CD2 C N N 280 LEU OXT O N N 281 LEU H H N N 282 LEU H2 H N N 283 LEU HA H N N 284 LEU HB2 H N N 285 LEU HB3 H N N 286 LEU HG H N N 287 LEU HD11 H N N 288 LEU HD12 H N N 289 LEU HD13 H N N 290 LEU HD21 H N N 291 LEU HD22 H N N 292 LEU HD23 H N N 293 LEU HXT H N N 294 LYS N N N N 295 LYS CA C N S 296 LYS C C N N 297 LYS O O N N 298 LYS CB C N N 299 LYS CG C N N 300 LYS CD C N N 301 LYS CE C N N 302 LYS NZ N N N 303 LYS OXT O N N 304 LYS H H N N 305 LYS H2 H N N 306 LYS HA H N N 307 LYS HB2 H N N 308 LYS HB3 H N N 309 LYS HG2 H N N 310 LYS HG3 H N N 311 LYS HD2 H N N 312 LYS HD3 H N N 313 LYS HE2 H N N 314 LYS HE3 H N N 315 LYS HZ1 H N N 316 LYS HZ2 H N N 317 LYS HZ3 H N N 318 LYS HXT H N N 319 MET N N N N 320 MET CA C N S 321 MET C C N N 322 MET O O N N 323 MET CB C N N 324 MET CG C N N 325 MET SD S N N 326 MET CE C N N 327 MET OXT O N N 328 MET H H N N 329 MET H2 H N N 330 MET HA H N N 331 MET HB2 H N N 332 MET HB3 H N N 333 MET HG2 H N N 334 MET HG3 H N N 335 MET HE1 H N N 336 MET HE2 H N N 337 MET HE3 H N N 338 MET HXT H N N 339 PHE N N N N 340 PHE CA C N S 341 PHE C C N N 342 PHE O O N N 343 PHE CB C N N 344 PHE CG C Y N 345 PHE CD1 C Y N 346 PHE CD2 C Y N 347 PHE CE1 C Y N 348 PHE CE2 C Y N 349 PHE CZ C Y N 350 PHE OXT O N N 351 PHE H H N N 352 PHE H2 H N N 353 PHE HA H N N 354 PHE HB2 H N N 355 PHE HB3 H N N 356 PHE HD1 H N N 357 PHE HD2 H N N 358 PHE HE1 H N N 359 PHE HE2 H N N 360 PHE HZ H N N 361 PHE HXT H N N 362 PRO N N N N 363 PRO CA C N S 364 PRO C C N N 365 PRO O O N N 366 PRO CB C N N 367 PRO CG C N N 368 PRO CD C N N 369 PRO OXT O N N 370 PRO H H N N 371 PRO HA H N N 372 PRO HB2 H N N 373 PRO HB3 H N N 374 PRO HG2 H N N 375 PRO HG3 H N N 376 PRO HD2 H N N 377 PRO HD3 H N N 378 PRO HXT H N N 379 SER N N N N 380 SER CA C N S 381 SER C C N N 382 SER O O N N 383 SER CB C N N 384 SER OG O N N 385 SER OXT O N N 386 SER H H N N 387 SER H2 H N N 388 SER HA H N N 389 SER HB2 H N N 390 SER HB3 H N N 391 SER HG H N N 392 SER HXT H N N 393 THR N N N N 394 THR CA C N S 395 THR C C N N 396 THR O O N N 397 THR CB C N R 398 THR OG1 O N N 399 THR CG2 C N N 400 THR OXT O N N 401 THR H H N N 402 THR H2 H N N 403 THR HA H N N 404 THR HB H N N 405 THR HG1 H N N 406 THR HG21 H N N 407 THR HG22 H N N 408 THR HG23 H N N 409 THR HXT H N N 410 TRP N N N N 411 TRP CA C N S 412 TRP C C N N 413 TRP O O N N 414 TRP CB C N N 415 TRP CG C Y N 416 TRP CD1 C Y N 417 TRP CD2 C Y N 418 TRP NE1 N Y N 419 TRP CE2 C Y N 420 TRP CE3 C Y N 421 TRP CZ2 C Y N 422 TRP CZ3 C Y N 423 TRP CH2 C Y N 424 TRP OXT O N N 425 TRP H H N N 426 TRP H2 H N N 427 TRP HA H N N 428 TRP HB2 H N N 429 TRP HB3 H N N 430 TRP HD1 H N N 431 TRP HE1 H N N 432 TRP HE3 H N N 433 TRP HZ2 H N N 434 TRP HZ3 H N N 435 TRP HH2 H N N 436 TRP HXT H N N 437 TYR N N N N 438 TYR CA C N S 439 TYR C C N N 440 TYR O O N N 441 TYR CB C N N 442 TYR CG C Y N 443 TYR CD1 C Y N 444 TYR CD2 C Y N 445 TYR CE1 C Y N 446 TYR CE2 C Y N 447 TYR CZ C Y N 448 TYR OH O N N 449 TYR OXT O N N 450 TYR H H N N 451 TYR H2 H N N 452 TYR HA H N N 453 TYR HB2 H N N 454 TYR HB3 H N N 455 TYR HD1 H N N 456 TYR HD2 H N N 457 TYR HE1 H N N 458 TYR HE2 H N N 459 TYR HH H N N 460 TYR HXT H N N 461 VAL N N N N 462 VAL CA C N S 463 VAL C C N N 464 VAL O O N N 465 VAL CB C N N 466 VAL CG1 C N N 467 VAL CG2 C N N 468 VAL OXT O N N 469 VAL H H N N 470 VAL H2 H N N 471 VAL HA H N N 472 VAL HB H N N 473 VAL HG11 H N N 474 VAL HG12 H N N 475 VAL HG13 H N N 476 VAL HG21 H N N 477 VAL HG22 H N N 478 VAL HG23 H N N 479 VAL HXT H N N 480 # 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 17X CAW CAX doub Y N 1 17X CAW CAV sing Y N 2 17X CAX CAE sing Y N 3 17X NAY CAV sing Y N 4 17X NAY CAB doub Y N 5 17X CAV CAC doub Y N 6 17X CAN CAO sing N N 7 17X CAN NAA sing N N 8 17X CAE CAF doub Y N 9 17X CAO CAP sing N N 10 17X CAB NAA sing N N 11 17X CAB NAD sing Y N 12 17X NAA CAR sing N N 13 17X CBT CBU sing N N 14 17X CBT NBV sing N N 15 17X CAC CAF sing Y N 16 17X CAC NAD sing Y N 17 17X CBU CBQ sing N N 18 17X CAP CAS sing N N 19 17X CAP CAQ sing N N 20 17X NAD CAG sing N N 21 17X OAU CBP sing N N 22 17X OAU CAS sing N N 23 17X CAR CAQ sing N N 24 17X CBP CBO sing N N 25 17X NBV CBS sing N N 26 17X CAS OAT doub N N 27 17X CBQ CBO sing N N 28 17X CBQ CBR sing N N 29 17X CBS CBR sing N N 30 17X CBO NBH sing N N 31 17X CAG CAH sing N N 32 17X CAI CAH doub Y N 33 17X CAI CAJ sing Y N 34 17X CBE CAZ doub Y N 35 17X CBE CBD sing Y N 36 17X CAZ CBA sing Y N 37 17X CAH CAM sing Y N 38 17X CAJ CAK doub Y N 39 17X NBH CBD sing Y N 40 17X NBH CBG sing Y N 41 17X CBD CBC doub Y N 42 17X CBA CBB doub Y N 43 17X CAM CAL doub Y N 44 17X CAK CAL sing Y N 45 17X CBC CBB sing Y N 46 17X CBC NBF sing Y N 47 17X CBG CBI sing N N 48 17X CBG NBF doub Y N 49 17X CBN CBI doub Y N 50 17X CBN CBM sing Y N 51 17X CBI CBJ sing Y N 52 17X CBM CBL doub Y N 53 17X CBJ CBK doub Y N 54 17X CBL CBK sing Y N 55 17X CAI H1 sing N N 56 17X CAJ H2 sing N N 57 17X CAK H3 sing N N 58 17X CAL H4 sing N N 59 17X CAM H5 sing N N 60 17X CAG H6 sing N N 61 17X CAG H7 sing N N 62 17X CAF H8 sing N N 63 17X CAE H9 sing N N 64 17X CAX H10 sing N N 65 17X CAW H11 sing N N 66 17X CAR H12 sing N N 67 17X CAR H13 sing N N 68 17X CAQ H14 sing N N 69 17X CAQ H15 sing N N 70 17X CAN H16 sing N N 71 17X CAN H17 sing N N 72 17X CAO H18 sing N N 73 17X CAO H19 sing N N 74 17X CAP H20 sing N N 75 17X CBP H21 sing N N 76 17X CBP H22 sing N N 77 17X CBO H23 sing N N 78 17X CBQ H24 sing N N 79 17X CBR H25 sing N N 80 17X CBR H26 sing N N 81 17X CBS H27 sing N N 82 17X CBS H28 sing N N 83 17X NBV H29 sing N N 84 17X CBT H31 sing N N 85 17X CBT H32 sing N N 86 17X CBU H33 sing N N 87 17X CBU H34 sing N N 88 17X CBE H35 sing N N 89 17X CAZ H36 sing N N 90 17X CBA H37 sing N N 91 17X CBB H38 sing N N 92 17X CBJ H39 sing N N 93 17X CBK H40 sing N N 94 17X CBL H41 sing N N 95 17X CBM H42 sing N N 96 17X CBN H43 sing N N 97 ALA N CA sing N N 98 ALA N H sing N N 99 ALA N H2 sing N N 100 ALA CA C sing N N 101 ALA CA CB sing N N 102 ALA CA HA sing N N 103 ALA C O doub N N 104 ALA C OXT sing N N 105 ALA CB HB1 sing N N 106 ALA CB HB2 sing N N 107 ALA CB HB3 sing N N 108 ALA OXT HXT sing N N 109 ARG N CA sing N N 110 ARG N H sing N N 111 ARG N H2 sing N N 112 ARG CA C sing N N 113 ARG CA CB sing N N 114 ARG CA HA sing N N 115 ARG C O doub N N 116 ARG C OXT sing N N 117 ARG CB CG sing N N 118 ARG CB HB2 sing N N 119 ARG CB HB3 sing N N 120 ARG CG CD sing N N 121 ARG CG HG2 sing N N 122 ARG CG HG3 sing N N 123 ARG CD NE sing N N 124 ARG CD HD2 sing N N 125 ARG CD HD3 sing N N 126 ARG NE CZ sing N N 127 ARG NE HE sing N N 128 ARG CZ NH1 sing N N 129 ARG CZ NH2 doub N N 130 ARG NH1 HH11 sing N N 131 ARG NH1 HH12 sing N N 132 ARG NH2 HH21 sing N N 133 ARG NH2 HH22 sing N N 134 ARG OXT HXT sing N N 135 ASN N CA sing N N 136 ASN N H sing N N 137 ASN N H2 sing N N 138 ASN CA C sing N N 139 ASN CA CB sing N N 140 ASN CA HA sing N N 141 ASN C O doub N N 142 ASN C OXT sing N N 143 ASN CB CG sing N N 144 ASN CB HB2 sing N N 145 ASN CB HB3 sing N N 146 ASN CG OD1 doub N N 147 ASN CG ND2 sing N N 148 ASN ND2 HD21 sing N N 149 ASN ND2 HD22 sing N N 150 ASN OXT HXT sing N N 151 ASP N CA sing N N 152 ASP N H sing N N 153 ASP N H2 sing N N 154 ASP CA C sing N N 155 ASP CA CB sing N N 156 ASP CA HA sing N N 157 ASP C O doub N N 158 ASP C OXT sing N N 159 ASP CB CG sing N N 160 ASP CB HB2 sing N N 161 ASP CB HB3 sing N N 162 ASP CG OD1 doub N N 163 ASP CG OD2 sing N N 164 ASP OD2 HD2 sing N N 165 ASP OXT HXT sing N N 166 CYS N CA sing N N 167 CYS N H sing N N 168 CYS N H2 sing N N 169 CYS CA C sing N N 170 CYS CA CB sing N N 171 CYS CA HA sing N N 172 CYS C O doub N N 173 CYS C OXT sing N N 174 CYS CB SG sing N N 175 CYS CB HB2 sing N N 176 CYS CB HB3 sing N N 177 CYS SG HG sing N N 178 CYS OXT HXT sing N N 179 GLN N CA sing N N 180 GLN N H sing N N 181 GLN N H2 sing N N 182 GLN CA C sing N N 183 GLN CA CB sing N N 184 GLN CA HA sing N N 185 GLN C O doub N N 186 GLN C OXT sing N N 187 GLN CB CG sing N N 188 GLN CB HB2 sing N N 189 GLN CB HB3 sing N N 190 GLN CG CD sing N N 191 GLN CG HG2 sing N N 192 GLN CG HG3 sing N N 193 GLN CD OE1 doub N N 194 GLN CD NE2 sing N N 195 GLN NE2 HE21 sing N N 196 GLN NE2 HE22 sing N N 197 GLN OXT HXT sing N N 198 GLU N CA sing N N 199 GLU N H sing N N 200 GLU N H2 sing N N 201 GLU CA C sing N N 202 GLU CA CB sing N N 203 GLU CA HA sing N N 204 GLU C O doub N N 205 GLU C OXT sing N N 206 GLU CB CG sing N N 207 GLU CB HB2 sing N N 208 GLU CB HB3 sing N N 209 GLU CG CD sing N N 210 GLU CG HG2 sing N N 211 GLU CG HG3 sing N N 212 GLU CD OE1 doub N N 213 GLU CD OE2 sing N N 214 GLU OE2 HE2 sing N N 215 GLU OXT HXT sing N N 216 GLY N CA sing N N 217 GLY N H sing N N 218 GLY N H2 sing N N 219 GLY CA C sing N N 220 GLY CA HA2 sing N N 221 GLY CA HA3 sing N N 222 GLY C O doub N N 223 GLY C OXT sing N N 224 GLY OXT HXT sing N N 225 HIS N CA sing N N 226 HIS N H sing N N 227 HIS N H2 sing N N 228 HIS CA C sing N N 229 HIS CA CB sing N N 230 HIS CA HA sing N N 231 HIS C O doub N N 232 HIS C OXT sing N N 233 HIS CB CG sing N N 234 HIS CB HB2 sing N N 235 HIS CB HB3 sing N N 236 HIS CG ND1 sing Y N 237 HIS CG CD2 doub Y N 238 HIS ND1 CE1 doub Y N 239 HIS ND1 HD1 sing N N 240 HIS CD2 NE2 sing Y N 241 HIS CD2 HD2 sing N N 242 HIS CE1 NE2 sing Y N 243 HIS CE1 HE1 sing N N 244 HIS NE2 HE2 sing N N 245 HIS OXT HXT sing N N 246 HOH O H1 sing N N 247 HOH O H2 sing N N 248 ILE N CA sing N N 249 ILE N H sing N N 250 ILE N H2 sing N N 251 ILE CA C sing N N 252 ILE CA CB sing N N 253 ILE CA HA sing N N 254 ILE C O doub N N 255 ILE C OXT sing N N 256 ILE CB CG1 sing N N 257 ILE CB CG2 sing N N 258 ILE CB HB sing N N 259 ILE CG1 CD1 sing N N 260 ILE CG1 HG12 sing N N 261 ILE CG1 HG13 sing N N 262 ILE CG2 HG21 sing N N 263 ILE CG2 HG22 sing N N 264 ILE CG2 HG23 sing N N 265 ILE CD1 HD11 sing N N 266 ILE CD1 HD12 sing N N 267 ILE CD1 HD13 sing N N 268 ILE OXT HXT sing N N 269 LEU N CA sing N N 270 LEU N H sing N N 271 LEU N H2 sing N N 272 LEU CA C sing N N 273 LEU CA CB sing N N 274 LEU CA HA sing N N 275 LEU C O doub N N 276 LEU C OXT sing N N 277 LEU CB CG sing N N 278 LEU CB HB2 sing N N 279 LEU CB HB3 sing N N 280 LEU CG CD1 sing N N 281 LEU CG CD2 sing N N 282 LEU CG HG sing N N 283 LEU CD1 HD11 sing N N 284 LEU CD1 HD12 sing N N 285 LEU CD1 HD13 sing N N 286 LEU CD2 HD21 sing N N 287 LEU CD2 HD22 sing N N 288 LEU CD2 HD23 sing N N 289 LEU OXT HXT sing N N 290 LYS N CA sing N N 291 LYS N H sing N N 292 LYS N H2 sing N N 293 LYS CA C sing N N 294 LYS CA CB sing N N 295 LYS CA HA sing N N 296 LYS C O doub N N 297 LYS C OXT sing N N 298 LYS CB CG sing N N 299 LYS CB HB2 sing N N 300 LYS CB HB3 sing N N 301 LYS CG CD sing N N 302 LYS CG HG2 sing N N 303 LYS CG HG3 sing N N 304 LYS CD CE sing N N 305 LYS CD HD2 sing N N 306 LYS CD HD3 sing N N 307 LYS CE NZ sing N N 308 LYS CE HE2 sing N N 309 LYS CE HE3 sing N N 310 LYS NZ HZ1 sing N N 311 LYS NZ HZ2 sing N N 312 LYS NZ HZ3 sing N N 313 LYS OXT HXT sing N N 314 MET N CA sing N N 315 MET N H sing N N 316 MET N H2 sing N N 317 MET CA C sing N N 318 MET CA CB sing N N 319 MET CA HA sing N N 320 MET C O doub N N 321 MET C OXT sing N N 322 MET CB CG sing N N 323 MET CB HB2 sing N N 324 MET CB HB3 sing N N 325 MET CG SD sing N N 326 MET CG HG2 sing N N 327 MET CG HG3 sing N N 328 MET SD CE sing N N 329 MET CE HE1 sing N N 330 MET CE HE2 sing N N 331 MET CE HE3 sing N N 332 MET OXT HXT sing N N 333 PHE N CA sing N N 334 PHE N H sing N N 335 PHE N H2 sing N N 336 PHE CA C sing N N 337 PHE CA CB sing N N 338 PHE CA HA sing N N 339 PHE C O doub N N 340 PHE C OXT sing N N 341 PHE CB CG sing N N 342 PHE CB HB2 sing N N 343 PHE CB HB3 sing N N 344 PHE CG CD1 doub Y N 345 PHE CG CD2 sing Y N 346 PHE CD1 CE1 sing Y N 347 PHE CD1 HD1 sing N N 348 PHE CD2 CE2 doub Y N 349 PHE CD2 HD2 sing N N 350 PHE CE1 CZ doub Y N 351 PHE CE1 HE1 sing N N 352 PHE CE2 CZ sing Y N 353 PHE CE2 HE2 sing N N 354 PHE CZ HZ sing N N 355 PHE OXT HXT sing N N 356 PRO N CA sing N N 357 PRO N CD sing N N 358 PRO N H sing N N 359 PRO CA C sing N N 360 PRO CA CB sing N N 361 PRO CA HA sing N N 362 PRO C O doub N N 363 PRO C OXT sing N N 364 PRO CB CG sing N N 365 PRO CB HB2 sing N N 366 PRO CB HB3 sing N N 367 PRO CG CD sing N N 368 PRO CG HG2 sing N N 369 PRO CG HG3 sing N N 370 PRO CD HD2 sing N N 371 PRO CD HD3 sing N N 372 PRO OXT HXT sing N N 373 SER N CA sing N N 374 SER N H sing N N 375 SER N H2 sing N N 376 SER CA C sing N N 377 SER CA CB sing N N 378 SER CA HA sing N N 379 SER C O doub N N 380 SER C OXT sing N N 381 SER CB OG sing N N 382 SER CB HB2 sing N N 383 SER CB HB3 sing N N 384 SER OG HG sing N N 385 SER OXT HXT sing N N 386 THR N CA sing N N 387 THR N H sing N N 388 THR N H2 sing N N 389 THR CA C sing N N 390 THR CA CB sing N N 391 THR CA HA sing N N 392 THR C O doub N N 393 THR C OXT sing N N 394 THR CB OG1 sing N N 395 THR CB CG2 sing N N 396 THR CB HB sing N N 397 THR OG1 HG1 sing N N 398 THR CG2 HG21 sing N N 399 THR CG2 HG22 sing N N 400 THR CG2 HG23 sing N N 401 THR OXT HXT sing N N 402 TRP N CA sing N N 403 TRP N H sing N N 404 TRP N H2 sing N N 405 TRP CA C sing N N 406 TRP CA CB sing N N 407 TRP CA HA sing N N 408 TRP C O doub N N 409 TRP C OXT sing N N 410 TRP CB CG sing N N 411 TRP CB HB2 sing N N 412 TRP CB HB3 sing N N 413 TRP CG CD1 doub Y N 414 TRP CG CD2 sing Y N 415 TRP CD1 NE1 sing Y N 416 TRP CD1 HD1 sing N N 417 TRP CD2 CE2 doub Y N 418 TRP CD2 CE3 sing Y N 419 TRP NE1 CE2 sing Y N 420 TRP NE1 HE1 sing N N 421 TRP CE2 CZ2 sing Y N 422 TRP CE3 CZ3 doub Y N 423 TRP CE3 HE3 sing N N 424 TRP CZ2 CH2 doub Y N 425 TRP CZ2 HZ2 sing N N 426 TRP CZ3 CH2 sing Y N 427 TRP CZ3 HZ3 sing N N 428 TRP CH2 HH2 sing N N 429 TRP OXT HXT sing N N 430 TYR N CA sing N N 431 TYR N H sing N N 432 TYR N H2 sing N N 433 TYR CA C sing N N 434 TYR CA CB sing N N 435 TYR CA HA sing N N 436 TYR C O doub N N 437 TYR C OXT sing N N 438 TYR CB CG sing N N 439 TYR CB HB2 sing N N 440 TYR CB HB3 sing N N 441 TYR CG CD1 doub Y N 442 TYR CG CD2 sing Y N 443 TYR CD1 CE1 sing Y N 444 TYR CD1 HD1 sing N N 445 TYR CD2 CE2 doub Y N 446 TYR CD2 HD2 sing N N 447 TYR CE1 CZ doub Y N 448 TYR CE1 HE1 sing N N 449 TYR CE2 CZ sing Y N 450 TYR CE2 HE2 sing N N 451 TYR CZ OH sing N N 452 TYR OH HH sing N N 453 TYR OXT HXT sing N N 454 VAL N CA sing N N 455 VAL N H sing N N 456 VAL N H2 sing N N 457 VAL CA C sing N N 458 VAL CA CB sing N N 459 VAL CA HA sing N N 460 VAL C O doub N N 461 VAL C OXT sing N N 462 VAL CB CG1 sing N N 463 VAL CB CG2 sing N N 464 VAL CB HB sing N N 465 VAL CG1 HG11 sing N N 466 VAL CG1 HG12 sing N N 467 VAL CG1 HG13 sing N N 468 VAL CG2 HG21 sing N N 469 VAL CG2 HG22 sing N N 470 VAL CG2 HG23 sing N N 471 VAL OXT HXT sing N N 472 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '(2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate' 17X 3 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 3T5G _pdbx_initial_refinement_model.details ? #