data_3GUP # _model_server_result.job_id HYY7dZD0DzZ3gToHHwPtww _model_server_result.datetime_utc '2024-11-25 21:38:50' _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 3gup # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":169}' # _entry.id 3GUP # _exptl.entry_id 3GUP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 79.1 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description pyridine _entity.pdbx_number_of_molecules 3 _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 90 _cell.entry_id 3GUP _cell.length_a 48.957 _cell.length_b 48.957 _cell.length_c 129.315 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GUP _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,M 1 1 B,I,J,K,L,N 2 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 H N N ? 2 I N 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 21 A CYS 21 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 B SG CYS 21 B CYS 21 1_555 B SG CYS 142 B CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A C ARG 96 A ARG 96 1_555 A N CME 97 A CME 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C CME 97 A CME 97 1_555 A N ALA 98 A ALA 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.365 ? covale ? covale3 B C ARG 96 B ARG 96 1_555 B N CME 97 B CME 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale4 B C CME 97 B CME 97 1_555 B N ALA 98 B ALA 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? # _chem_comp.formula 'C5 H5 N' _chem_comp.formula_weight 79.1 _chem_comp.id 0PY _chem_comp.mon_nstd_flag . _chem_comp.name pyridine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Azabenzene;Azine # 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 C4 C5 0PY doub 1 n y N1 C5 0PY sing 2 n y C5 H5 0PY sing 3 n n C1 N1 0PY doub 4 n y C3 C4 0PY sing 5 n y C4 H4 0PY sing 6 n n C2 C3 0PY doub 7 n y C3 H3 0PY sing 8 n n C2 C1 0PY sing 9 n y C2 H2 0PY sing 10 n n C1 H1 0PY sing 11 n n # _atom_sites.entry_id 3GUP _atom_sites.fract_transf_matrix[1][1] 0.020426 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020426 _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] 0.007733 _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 C 2 0PY A 1 501 501 0PY 0PY . D 3 CO3 A 1 165 165 CO3 CO3 . E 4 MG A 1 166 166 MG MG . F 5 CL A 1 167 167 CL CL . G 5 CL A 1 168 168 CL CL . H 2 0PY A 1 169 169 0PY 0PY . I 2 0PY B 1 501 501 0PY 0PY . J 3 CO3 B 1 165 165 CO3 CO3 . K 5 CL B 1 166 166 CL CL . L 5 CL B 1 167 167 CL CL . M 6 HOH A 1 170 170 HOH HOH . M 6 HOH A 2 172 172 HOH HOH . M 6 HOH A 3 173 177 HOH HOH . M 6 HOH A 4 174 178 HOH HOH . M 6 HOH A 5 175 175 HOH HOH . M 6 HOH A 6 176 176 HOH HOH . M 6 HOH A 7 177 177 HOH HOH . M 6 HOH A 8 178 178 HOH HOH . M 6 HOH A 9 179 179 HOH HOH . M 6 HOH A 10 180 180 HOH HOH . M 6 HOH A 11 181 180 HOH HOH . M 6 HOH A 12 182 182 HOH HOH . M 6 HOH A 13 183 183 HOH HOH . M 6 HOH A 14 184 184 HOH HOH . M 6 HOH A 15 185 185 HOH HOH . M 6 HOH A 16 186 182 HOH HOH . M 6 HOH A 17 187 183 HOH HOH . M 6 HOH A 18 188 188 HOH HOH . M 6 HOH A 19 189 184 HOH HOH . M 6 HOH A 20 190 190 HOH HOH . M 6 HOH A 21 191 191 HOH HOH . M 6 HOH A 22 192 192 HOH HOH . M 6 HOH A 23 193 193 HOH HOH . M 6 HOH A 24 194 191 HOH HOH . M 6 HOH A 25 195 192 HOH HOH . M 6 HOH A 26 196 196 HOH HOH . M 6 HOH A 27 197 197 HOH HOH . M 6 HOH A 28 198 197 HOH HOH . M 6 HOH A 29 199 199 HOH HOH . M 6 HOH A 30 200 200 HOH HOH . M 6 HOH A 31 201 204 HOH HOH . M 6 HOH A 32 202 202 HOH HOH . M 6 HOH A 33 203 203 HOH HOH . M 6 HOH A 34 204 204 HOH HOH . M 6 HOH A 35 205 205 HOH HOH . M 6 HOH A 36 207 207 HOH HOH . M 6 HOH A 37 208 208 HOH HOH . M 6 HOH A 38 210 210 HOH HOH . M 6 HOH A 39 211 211 HOH HOH . M 6 HOH A 40 212 212 HOH HOH . M 6 HOH A 41 213 213 HOH HOH . M 6 HOH A 42 214 214 HOH HOH . M 6 HOH A 43 222 222 HOH HOH . M 6 HOH A 44 223 223 HOH HOH . M 6 HOH A 45 225 225 HOH HOH . M 6 HOH A 46 226 226 HOH HOH . M 6 HOH A 47 227 227 HOH HOH . M 6 HOH A 48 228 228 HOH HOH . M 6 HOH A 49 230 230 HOH HOH . M 6 HOH A 50 232 232 HOH HOH . M 6 HOH A 51 233 233 HOH HOH . M 6 HOH A 52 234 234 HOH HOH . M 6 HOH A 53 238 238 HOH HOH . M 6 HOH A 54 244 244 HOH HOH . M 6 HOH A 55 245 245 HOH HOH . M 6 HOH A 56 246 246 HOH HOH . M 6 HOH A 57 247 247 HOH HOH . M 6 HOH A 58 248 248 HOH HOH . M 6 HOH A 59 601 601 HOH HOH . M 6 HOH A 60 602 602 HOH HOH . M 6 HOH A 61 605 605 HOH HOH . M 6 HOH A 62 606 606 HOH HOH . M 6 HOH A 63 607 607 HOH HOH . M 6 HOH A 64 609 609 HOH HOH . M 6 HOH A 65 611 611 HOH HOH . M 6 HOH A 66 613 613 HOH HOH . M 6 HOH A 67 615 615 HOH HOH . M 6 HOH A 68 617 617 HOH HOH . M 6 HOH A 69 620 620 HOH HOH . M 6 HOH A 70 623 623 HOH HOH . M 6 HOH A 71 624 624 HOH HOH . M 6 HOH A 72 627 627 HOH HOH . M 6 HOH A 73 629 629 HOH HOH . M 6 HOH A 74 631 631 HOH HOH . M 6 HOH A 75 632 632 HOH HOH . M 6 HOH A 76 634 634 HOH HOH . M 6 HOH A 77 636 636 HOH HOH . M 6 HOH A 78 639 639 HOH HOH . M 6 HOH A 79 643 643 HOH HOH . M 6 HOH A 80 644 644 HOH HOH . M 6 HOH A 81 646 646 HOH HOH . M 6 HOH A 82 647 647 HOH HOH . M 6 HOH A 83 648 648 HOH HOH . M 6 HOH A 84 649 649 HOH HOH . M 6 HOH A 85 651 651 HOH HOH . M 6 HOH A 86 654 654 HOH HOH . M 6 HOH A 87 656 656 HOH HOH . M 6 HOH A 88 660 660 HOH HOH . M 6 HOH A 89 662 662 HOH HOH . M 6 HOH A 90 663 663 HOH HOH . M 6 HOH A 91 665 665 HOH HOH . M 6 HOH A 92 667 667 HOH HOH . M 6 HOH A 93 668 668 HOH HOH . M 6 HOH A 94 670 670 HOH HOH . M 6 HOH A 95 671 671 HOH HOH . M 6 HOH A 96 673 673 HOH HOH . M 6 HOH A 97 674 674 HOH HOH . M 6 HOH A 98 676 676 HOH HOH . M 6 HOH A 99 678 678 HOH HOH . M 6 HOH A 100 679 679 HOH HOH . M 6 HOH A 101 681 681 HOH HOH . M 6 HOH A 102 685 685 HOH HOH . M 6 HOH A 103 687 687 HOH HOH . M 6 HOH A 104 688 688 HOH HOH . M 6 HOH A 105 689 689 HOH HOH . M 6 HOH A 106 691 691 HOH HOH . M 6 HOH A 107 692 692 HOH HOH . M 6 HOH A 108 696 696 HOH HOH . M 6 HOH A 109 698 698 HOH HOH . M 6 HOH A 110 699 699 HOH HOH . M 6 HOH A 111 700 700 HOH HOH . M 6 HOH A 112 701 701 HOH HOH . M 6 HOH A 113 702 702 HOH HOH . M 6 HOH A 114 703 703 HOH HOH . M 6 HOH A 115 706 706 HOH HOH . M 6 HOH A 116 708 708 HOH HOH . M 6 HOH A 117 710 710 HOH HOH . M 6 HOH A 118 714 714 HOH HOH . M 6 HOH A 119 715 715 HOH HOH . M 6 HOH A 120 716 716 HOH HOH . M 6 HOH A 121 718 718 HOH HOH . M 6 HOH A 122 721 721 HOH HOH . M 6 HOH A 123 722 722 HOH HOH . M 6 HOH A 124 725 725 HOH HOH . M 6 HOH A 125 730 730 HOH HOH . M 6 HOH A 126 733 733 HOH HOH . M 6 HOH A 127 734 734 HOH HOH . M 6 HOH A 128 735 735 HOH HOH . N 6 HOH B 1 168 168 HOH HOH . N 6 HOH B 2 169 169 HOH HOH . N 6 HOH B 3 170 170 HOH HOH . N 6 HOH B 4 171 171 HOH HOH . N 6 HOH B 5 172 172 HOH HOH . N 6 HOH B 6 173 173 HOH HOH . N 6 HOH B 7 174 174 HOH HOH . N 6 HOH B 8 175 175 HOH HOH . N 6 HOH B 9 176 176 HOH HOH . N 6 HOH B 10 177 171 HOH HOH . N 6 HOH B 11 178 173 HOH HOH . N 6 HOH B 12 179 179 HOH HOH . N 6 HOH B 13 180 174 HOH HOH . N 6 HOH B 14 181 181 HOH HOH . N 6 HOH B 15 182 181 HOH HOH . N 6 HOH B 16 183 186 HOH HOH . N 6 HOH B 17 184 187 HOH HOH . N 6 HOH B 18 185 185 HOH HOH . N 6 HOH B 19 186 186 HOH HOH . N 6 HOH B 20 187 187 HOH HOH . N 6 HOH B 21 188 188 HOH HOH . N 6 HOH B 22 189 189 HOH HOH . N 6 HOH B 23 190 190 HOH HOH . N 6 HOH B 24 191 189 HOH HOH . N 6 HOH B 25 192 194 HOH HOH . N 6 HOH B 26 193 193 HOH HOH . N 6 HOH B 27 194 194 HOH HOH . N 6 HOH B 28 195 195 HOH HOH . N 6 HOH B 29 196 196 HOH HOH . N 6 HOH B 30 197 195 HOH HOH . N 6 HOH B 31 198 198 HOH HOH . N 6 HOH B 32 199 199 HOH HOH . N 6 HOH B 33 200 200 HOH HOH . N 6 HOH B 34 201 201 HOH HOH . N 6 HOH B 35 202 202 HOH HOH . N 6 HOH B 36 203 203 HOH HOH . N 6 HOH B 37 204 198 HOH HOH . N 6 HOH B 38 205 205 HOH HOH . N 6 HOH B 39 206 206 HOH HOH . N 6 HOH B 40 207 201 HOH HOH . N 6 HOH B 41 209 209 HOH HOH . N 6 HOH B 42 215 215 HOH HOH . N 6 HOH B 43 216 216 HOH HOH . N 6 HOH B 44 218 218 HOH HOH . N 6 HOH B 45 219 219 HOH HOH . N 6 HOH B 46 220 220 HOH HOH . N 6 HOH B 47 221 221 HOH HOH . N 6 HOH B 48 224 224 HOH HOH . N 6 HOH B 49 229 229 HOH HOH . N 6 HOH B 50 231 231 HOH HOH . N 6 HOH B 51 235 235 HOH HOH . N 6 HOH B 52 236 236 HOH HOH . N 6 HOH B 53 237 237 HOH HOH . N 6 HOH B 54 239 239 HOH HOH . N 6 HOH B 55 240 240 HOH HOH . N 6 HOH B 56 241 241 HOH HOH . N 6 HOH B 57 242 242 HOH HOH . N 6 HOH B 58 243 243 HOH HOH . N 6 HOH B 59 249 249 HOH HOH . N 6 HOH B 60 250 250 HOH HOH . N 6 HOH B 61 603 603 HOH HOH . N 6 HOH B 62 604 604 HOH HOH . N 6 HOH B 63 608 608 HOH HOH . N 6 HOH B 64 610 610 HOH HOH . N 6 HOH B 65 612 612 HOH HOH . N 6 HOH B 66 614 614 HOH HOH . N 6 HOH B 67 616 616 HOH HOH . N 6 HOH B 68 618 618 HOH HOH . N 6 HOH B 69 619 619 HOH HOH . N 6 HOH B 70 621 621 HOH HOH . N 6 HOH B 71 622 622 HOH HOH . N 6 HOH B 72 625 625 HOH HOH . N 6 HOH B 73 626 626 HOH HOH . N 6 HOH B 74 628 628 HOH HOH . N 6 HOH B 75 630 630 HOH HOH . N 6 HOH B 76 633 633 HOH HOH . N 6 HOH B 77 635 635 HOH HOH . N 6 HOH B 78 637 637 HOH HOH . N 6 HOH B 79 638 638 HOH HOH . N 6 HOH B 80 640 640 HOH HOH . N 6 HOH B 81 641 641 HOH HOH . N 6 HOH B 82 642 642 HOH HOH . N 6 HOH B 83 645 645 HOH HOH . N 6 HOH B 84 650 650 HOH HOH . N 6 HOH B 85 652 652 HOH HOH . N 6 HOH B 86 653 653 HOH HOH . N 6 HOH B 87 655 655 HOH HOH . N 6 HOH B 88 657 657 HOH HOH . N 6 HOH B 89 658 658 HOH HOH . N 6 HOH B 90 659 659 HOH HOH . N 6 HOH B 91 661 661 HOH HOH . N 6 HOH B 92 664 664 HOH HOH . N 6 HOH B 93 666 666 HOH HOH . N 6 HOH B 94 669 669 HOH HOH . N 6 HOH B 95 672 672 HOH HOH . N 6 HOH B 96 675 675 HOH HOH . N 6 HOH B 97 677 677 HOH HOH . N 6 HOH B 98 680 680 HOH HOH . N 6 HOH B 99 682 682 HOH HOH . N 6 HOH B 100 683 683 HOH HOH . N 6 HOH B 101 684 684 HOH HOH . N 6 HOH B 102 686 686 HOH HOH . N 6 HOH B 103 690 690 HOH HOH . N 6 HOH B 104 693 693 HOH HOH . N 6 HOH B 105 694 694 HOH HOH . N 6 HOH B 106 695 695 HOH HOH . N 6 HOH B 107 697 697 HOH HOH . N 6 HOH B 108 704 704 HOH HOH . N 6 HOH B 109 705 705 HOH HOH . N 6 HOH B 110 707 707 HOH HOH . N 6 HOH B 111 709 709 HOH HOH . N 6 HOH B 112 711 711 HOH HOH . N 6 HOH B 113 712 712 HOH HOH . N 6 HOH B 114 713 713 HOH HOH . N 6 HOH B 115 717 717 HOH HOH . N 6 HOH B 116 719 719 HOH HOH . N 6 HOH B 117 720 720 HOH HOH . N 6 HOH B 118 723 723 HOH HOH . N 6 HOH B 119 724 724 HOH HOH . N 6 HOH B 120 726 726 HOH HOH . N 6 HOH B 121 727 727 HOH HOH . N 6 HOH B 122 728 728 HOH HOH . N 6 HOH B 123 729 729 HOH HOH . N 6 HOH B 124 731 731 HOH HOH . N 6 HOH B 125 732 732 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 C5 0PY . . . H 2 -10.946 -12.815 58.511 1 38.68 ? C5 0PY 169 A 1 HETATM 2 N N1 0PY . . . H 2 -11.803 -12.768 57.461 1 39.93 ? N1 0PY 169 A 1 HETATM 3 C C4 0PY . . . H 2 -9.933 -13.773 58.508 1 41.76 ? C4 0PY 169 A 1 HETATM 4 C C3 0PY . . . H 2 -9.827 -14.616 57.391 1 39.78 ? C3 0PY 169 A 1 HETATM 5 C C2 0PY . . . H 2 -10.715 -14.537 56.299 1 39.06 ? C2 0PY 169 A 1 HETATM 6 C C1 0PY . . . H 2 -11.72 -13.58 56.374 1 40.01 ? C1 0PY 169 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 6 #