data_5SVR # _model_server_result.job_id 6is3fEqW5TRMeyNs8wox_g _model_server_result.datetime_utc '2024-11-23 08:54:18' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5svr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 5SVR # _exptl.entry_id 5SVR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 565.569 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '5-{[(3-phenoxyphenyl)methyl][(1S)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}benzene-1,2,4-tricarboxylic acid' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 5SVR _cell.length_a 123.17 _cell.length_b 123.17 _cell.length_c 237.46 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVR _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _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[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 B C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 289 A ASN 290 1_555 C C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? # _chem_comp.formula 'C33 H27 N O8' _chem_comp.formula_weight 565.569 _chem_comp.id 71C _chem_comp.mon_nstd_flag . _chem_comp.name '5-{[(3-phenoxyphenyl)methyl][(1S)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}benzene-1,2,4-tricarboxylic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'antagonist A-317491' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C30 C29 71C doub 1 n y C30 C31 71C sing 2 n y C29 C28 71C sing 3 n y C31 C26 71C doub 4 n y C28 C27 71C doub 5 n y C27 C26 71C sing 6 n y C26 O25 71C sing 7 n n O25 C24 71C sing 8 n n C24 C23 71C doub 9 n y C24 C32 71C sing 10 n y C23 C22 71C sing 11 n y C32 C20 71C doub 12 n y C22 C21 71C doub 13 n y C20 C21 71C sing 14 n y C20 C19 71C sing 15 n n C19 N18 71C sing 16 n n C36 C35 71C sing 17 n n C36 C37 71C sing 18 n n C35 C34 71C sing 19 n n N18 C33 71C sing 20 n n N18 C16 71C sing 21 n n C34 C33 71C sing 22 n n C37 C38 71C sing 23 n y C37 C42 71C doub 24 n y C38 C39 71C doub 25 n y O17 C16 71C doub 26 n n C39 C40 71C sing 27 n y C42 C33 71C sing 28 n n C42 C41 71C sing 29 n y C40 C41 71C doub 30 n y C16 C10 71C sing 31 n n O09 C07 71C doub 32 n n C07 O08 71C sing 33 n n C07 C06 71C sing 34 n n C10 C06 71C doub 35 n y C10 C11 71C sing 36 n y C06 C05 71C sing 37 n y C11 C12 71C doub 38 n y C05 C04 71C doub 39 n y C12 C04 71C sing 40 n y C12 C13 71C sing 41 n n C04 C02 71C sing 42 n n C13 O14 71C doub 43 n n C13 O15 71C sing 44 n n C02 O03 71C doub 45 n n C02 O01 71C sing 46 n n C11 H1 71C sing 47 n n C19 H2 71C sing 48 n n C19 H3 71C sing 49 n n C28 H4 71C sing 50 n n C31 H5 71C sing 51 n n C32 H6 71C sing 52 n n C34 H7 71C sing 53 n n C35 H8 71C sing 54 n n C36 H9 71C sing 55 n n O01 H10 71C sing 56 n n C05 H11 71C sing 57 n n O08 H12 71C sing 58 n n O15 H13 71C sing 59 n n C21 H14 71C sing 60 n n C22 H15 71C sing 61 n n C23 H16 71C sing 62 n n C27 H17 71C sing 63 n n C29 H18 71C sing 64 n n C30 H19 71C sing 65 n n C38 H20 71C sing 66 n n C39 H21 71C sing 67 n n C40 H22 71C sing 68 n n C41 H23 71C sing 69 n n C33 H24 71C sing 70 n n C34 H25 71C sing 71 n n C35 H26 71C sing 72 n n C36 H27 71C sing 73 n n # _atom_sites.entry_id 5SVR _atom_sites.fract_transf_matrix[1][1] 0.008119 _atom_sites.fract_transf_matrix[1][2] 0.004687 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009375 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004211 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code B 2 NAG A 1 401 500 NAG NAG . C 2 NAG A 1 402 502 NAG NAG . D 3 MG A 1 403 1 MG MG . E 4 NA A 1 404 1 NA NA . F 5 71C A 1 405 1 71C 317 . G 6 HOH A 1 501 3 HOH HOH . G 6 HOH A 2 502 1 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C10 71C . . . F 5 16.952 -13.93 -36.263 1 159.03 ? C10 71C 405 A 1 HETATM 2 C C11 71C . . . F 5 16.25 -13.139 -35.377 1 163.68 ? C11 71C 405 A 1 HETATM 3 C C19 71C . . . F 5 17.495 -12.459 -39.913 1 116.18 ? C19 71C 405 A 1 HETATM 4 C C20 71C . . . F 5 18.282 -13.463 -40.822 1 115.17 ? C20 71C 405 A 1 HETATM 5 C C26 71C . . . F 5 19.591 -14.014 -45.324 1 127.16 ? C26 71C 405 A 1 HETATM 6 C C28 71C . . . F 5 18.469 -15.777 -46.529 1 132.71 ? C28 71C 405 A 1 HETATM 7 C C31 71C . . . F 5 19.973 -13.447 -46.535 1 119.79 ? C31 71C 405 A 1 HETATM 8 C C32 71C . . . F 5 18.79 -13.009 -42.044 1 108.44 ? C32 71C 405 A 1 HETATM 9 C C33 71C . . . F 5 18.788 -12.207 -37.833 1 103.8 ? C33 71C 405 A 1 HETATM 10 C C34 71C . . . F 5 20.191 -12.737 -38.452 1 116.97 ? C34 71C 405 A 1 HETATM 11 C C35 71C . . . F 5 21.196 -11.631 -38.583 1 102.58 ? C35 71C 405 A 1 HETATM 12 C C36 71C . . . F 5 21.005 -10.304 -38.618 1 92.11 ? C36 71C 405 A 1 HETATM 13 O O01 71C . . . F 5 16.435 -14.329 -31.32 1 204.65 ? O01 71C 405 A 1 HETATM 14 C C02 71C . . . F 5 17.338 -14.585 -32.158 1 206.56 ? C02 71C 405 A 1 HETATM 15 O O03 71C . . . F 5 18.385 -15.089 -31.677 1 206.35 ? O03 71C 405 A 1 HETATM 16 C C04 71C . . . F 5 17.197 -14.35 -33.524 1 193.49 ? C04 71C 405 A 1 HETATM 17 C C05 71C . . . F 5 17.903 -15.145 -34.42 1 177.4 ? C05 71C 405 A 1 HETATM 18 C C06 71C . . . F 5 17.793 -14.943 -35.788 1 162.36 ? C06 71C 405 A 1 HETATM 19 C C07 71C . . . F 5 18.498 -15.741 -36.679 1 157.72 ? C07 71C 405 A 1 HETATM 20 O O08 71C . . . F 5 19.711 -16.08 -36.608 1 157.64 ? O08 71C 405 A 1 HETATM 21 O O09 71C . . . F 5 18.053 -16.27 -37.731 1 158.93 ? O09 71C 405 A 1 HETATM 22 C C12 71C . . . F 5 16.366 -13.339 -34.009 1 183.59 ? C12 71C 405 A 1 HETATM 23 C C13 71C . . . F 5 15.553 -12.422 -33.098 1 185.68 ? C13 71C 405 A 1 HETATM 24 O O14 71C . . . F 5 14.297 -12.446 -32.987 1 170.56 ? O14 71C 405 A 1 HETATM 25 O O15 71C . . . F 5 16.034 -11.52 -32.359 1 222.37 ? O15 71C 405 A 1 HETATM 26 C C16 71C . . . F 5 16.76 -13.629 -37.791 1 132.19 ? C16 71C 405 A 1 HETATM 27 O O17 71C . . . F 5 15.832 -14.08 -38.377 1 141.59 ? O17 71C 405 A 1 HETATM 28 N N18 71C . . . F 5 17.73 -12.746 -38.499 1 100.51 ? N18 71C 405 A 1 HETATM 29 C C21 71C . . . F 5 18.48 -14.778 -40.417 1 125.77 ? C21 71C 405 A 1 HETATM 30 C C22 71C . . . F 5 19.193 -15.655 -41.248 1 129.41 ? C22 71C 405 A 1 HETATM 31 C C23 71C . . . F 5 19.709 -15.2 -42.473 1 132.46 ? C23 71C 405 A 1 HETATM 32 C C24 71C . . . F 5 19.496 -13.884 -42.882 1 125.27 ? C24 71C 405 A 1 HETATM 33 O O25 71C . . . F 5 20.011 -13.358 -44.117 1 141.01 ? O25 71C 405 A 1 HETATM 34 C C27 71C . . . F 5 18.839 -15.182 -45.328 1 132.63 ? C27 71C 405 A 1 HETATM 35 C C29 71C . . . F 5 18.851 -15.203 -47.736 1 133.05 ? C29 71C 405 A 1 HETATM 36 C C30 71C . . . F 5 19.597 -14.038 -47.738 1 125.95 ? C30 71C 405 A 1 HETATM 37 C C37 71C . . . F 5 19.901 -9.63 -38.401 1 99.89 ? C37 71C 405 A 1 HETATM 38 C C38 71C . . . F 5 19.312 -8.251 -38.399 1 93.46 ? C38 71C 405 A 1 HETATM 39 C C39 71C . . . F 5 18.127 -7.944 -38.119 1 93.72 ? C39 71C 405 A 1 HETATM 40 C C40 71C . . . F 5 17.313 -8.661 -37.83 1 94.9 ? C40 71C 405 A 1 HETATM 41 C C41 71C . . . F 5 17.432 -9.857 -37.733 1 96.28 ? C41 71C 405 A 1 HETATM 42 C C42 71C . . . F 5 18.636 -10.601 -37.963 1 101.89 ? C42 71C 405 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 42 #