data_5DVP # _model_server_result.job_id j9YxbEJnPYfMwfOm_JyTBw _model_server_result.datetime_utc '2024-10-19 19:19:38' _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 5dvp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5DVP # _exptl.entry_id 5DVP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 422.52 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.91 _cell.angle_gamma 90 _cell.entry_id 5DVP _cell.length_a 60.866 _cell.length_b 93.062 _cell.length_c 75.213 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DVP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,H 1 1 B,F,G,I 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 F 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 covale ? covale1 A SG CYS 297 A CYS 354 1_555 C CAJ DRW . A DRW 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? covale ? covale2 B SG CYS 297 B CYS 354 1_555 F CAJ DRW . B DRW 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? # _chem_comp.formula 'C15 H26 N4 O6 S2' _chem_comp.formula_weight 422.52 _chem_comp.id DRW _chem_comp.mon_nstd_flag . _chem_comp.name '(2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Doripenem(open form, pyrroline tautomer form 2, SP3 connection to Thio as S isomer)' # 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 CAA CAT DRW sing 83 n n CAA HAA DRW sing 84 n n CAA HAAA DRW sing 85 n n CAA HAAB DRW sing 86 n n CAB CAU DRW sing 87 n n CAB HAB DRW sing 88 n n CAB HABA DRW sing 89 n n CAB HABB DRW sing 90 n n NAC SBA DRW sing 91 n n NAC HNAC DRW sing 92 n n NAC HNAA DRW sing 93 n n OAD CAJ DRW doub 94 n n OAE HOAE DRW sing 95 n n OAG SBA DRW doub 96 n n OAH CAR DRW doub 97 n n OAI HOAI DRW sing 98 n n CAJ HAJ DRW sing 99 n n CAK CAW DRW sing 100 n n CAK HAK DRW sing 101 n n CAK HAKA DRW sing 102 n n CAL CAV DRW sing 103 n n CAL HAL DRW sing 104 n n CAL HALA DRW sing 105 n n CAM CAW DRW sing 106 n n CAM HAM DRW sing 107 n n CAM HAMA DRW sing 108 n n NAO CAK DRW sing 109 n n NAO HNAO DRW sing 110 n n NAP CAL DRW sing 111 n n NAP HNAP DRW sing 112 n n CAR OAE DRW sing 113 n n CAS NAN DRW doub 114 n n CAS CAR DRW sing 115 n n CAT OAI DRW sing 116 n n CAT HAT DRW sing 117 n n CAU CAY DRW sing 118 n n CAU HAU DRW sing 119 n n CAV CAM DRW sing 120 n n CAV NAO DRW sing 121 n n CAV HAV DRW sing 122 n n CAW SAQ DRW sing 123 n n CAW HAW DRW sing 124 n n CAX CAJ DRW sing 125 n n CAX CAT DRW sing 126 n n CAX CAY DRW sing 127 n n CAX HAX DRW sing 128 n n CAY NAN DRW sing 129 n n CAY HAY DRW sing 130 n n CAZ SAQ DRW sing 131 n n CAZ CAS DRW sing 132 n n CAZ CAU DRW sing 133 n n CAZ HAZ DRW sing 134 n n SBA OAF DRW doub 135 n n SBA NAP DRW sing 136 n n # _atom_sites.entry_id 5DVP _atom_sites.fract_transf_matrix[1][1] 0.01643 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000836 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010746 _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] 0.013313 _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 DRW A 1 501 1 DRW T06 . D 3 SO4 A 1 502 1 SO4 SO4 . E 4 POA A 1 503 1 POA POA . F 2 DRW B 1 501 2 DRW T06 . G 4 POA B 1 502 2 POA POA . H 5 HOH A 1 601 198 HOH HOH . H 5 HOH A 2 602 140 HOH HOH . H 5 HOH A 3 603 104 HOH HOH . H 5 HOH A 4 604 53 HOH HOH . H 5 HOH A 5 605 214 HOH HOH . H 5 HOH A 6 606 171 HOH HOH . H 5 HOH A 7 607 19 HOH HOH . H 5 HOH A 8 608 80 HOH HOH . H 5 HOH A 9 609 127 HOH HOH . H 5 HOH A 10 610 182 HOH HOH . H 5 HOH A 11 611 234 HOH HOH . H 5 HOH A 12 612 184 HOH HOH . H 5 HOH A 13 613 116 HOH HOH . H 5 HOH A 14 614 11 HOH HOH . H 5 HOH A 15 615 29 HOH HOH . H 5 HOH A 16 616 197 HOH HOH . H 5 HOH A 17 617 13 HOH HOH . H 5 HOH A 18 618 149 HOH HOH . H 5 HOH A 19 619 47 HOH HOH . H 5 HOH A 20 620 31 HOH HOH . H 5 HOH A 21 621 42 HOH HOH . H 5 HOH A 22 622 93 HOH HOH . H 5 HOH A 23 623 215 HOH HOH . H 5 HOH A 24 624 46 HOH HOH . H 5 HOH A 25 625 79 HOH HOH . H 5 HOH A 26 626 73 HOH HOH . H 5 HOH A 27 627 220 HOH HOH . H 5 HOH A 28 628 209 HOH HOH . H 5 HOH A 29 629 164 HOH HOH . H 5 HOH A 30 630 9 HOH HOH . H 5 HOH A 31 631 177 HOH HOH . H 5 HOH A 32 632 16 HOH HOH . H 5 HOH A 33 633 10 HOH HOH . H 5 HOH A 34 634 211 HOH HOH . H 5 HOH A 35 635 108 HOH HOH . H 5 HOH A 36 636 43 HOH HOH . H 5 HOH A 37 637 100 HOH HOH . H 5 HOH A 38 638 226 HOH HOH . H 5 HOH A 39 639 17 HOH HOH . H 5 HOH A 40 640 219 HOH HOH . H 5 HOH A 41 641 122 HOH HOH . H 5 HOH A 42 642 24 HOH HOH . H 5 HOH A 43 643 18 HOH HOH . H 5 HOH A 44 644 147 HOH HOH . H 5 HOH A 45 645 69 HOH HOH . H 5 HOH A 46 646 67 HOH HOH . H 5 HOH A 47 647 12 HOH HOH . H 5 HOH A 48 648 167 HOH HOH . H 5 HOH A 49 649 128 HOH HOH . H 5 HOH A 50 650 115 HOH HOH . H 5 HOH A 51 651 39 HOH HOH . H 5 HOH A 52 652 102 HOH HOH . H 5 HOH A 53 653 49 HOH HOH . H 5 HOH A 54 654 101 HOH HOH . H 5 HOH A 55 655 151 HOH HOH . H 5 HOH A 56 656 165 HOH HOH . H 5 HOH A 57 657 84 HOH HOH . H 5 HOH A 58 658 188 HOH HOH . H 5 HOH A 59 659 56 HOH HOH . H 5 HOH A 60 660 216 HOH HOH . H 5 HOH A 61 661 131 HOH HOH . H 5 HOH A 62 662 74 HOH HOH . H 5 HOH A 63 663 85 HOH HOH . H 5 HOH A 64 664 137 HOH HOH . H 5 HOH A 65 665 189 HOH HOH . H 5 HOH A 66 666 5 HOH HOH . H 5 HOH A 67 667 20 HOH HOH . H 5 HOH A 68 668 129 HOH HOH . H 5 HOH A 69 669 123 HOH HOH . H 5 HOH A 70 670 190 HOH HOH . H 5 HOH A 71 671 50 HOH HOH . H 5 HOH A 72 672 120 HOH HOH . H 5 HOH A 73 673 32 HOH HOH . H 5 HOH A 74 674 96 HOH HOH . H 5 HOH A 75 675 224 HOH HOH . H 5 HOH A 76 676 82 HOH HOH . H 5 HOH A 77 677 94 HOH HOH . H 5 HOH A 78 678 191 HOH HOH . H 5 HOH A 79 679 57 HOH HOH . H 5 HOH A 80 680 199 HOH HOH . H 5 HOH A 81 681 175 HOH HOH . H 5 HOH A 82 682 87 HOH HOH . H 5 HOH A 83 683 173 HOH HOH . H 5 HOH A 84 684 40 HOH HOH . H 5 HOH A 85 685 88 HOH HOH . H 5 HOH A 86 686 160 HOH HOH . H 5 HOH A 87 687 222 HOH HOH . H 5 HOH A 88 688 194 HOH HOH . H 5 HOH A 89 689 202 HOH HOH . H 5 HOH A 90 690 132 HOH HOH . H 5 HOH A 91 691 232 HOH HOH . H 5 HOH A 92 692 14 HOH HOH . H 5 HOH A 93 693 233 HOH HOH . H 5 HOH A 94 694 205 HOH HOH . H 5 HOH A 95 695 72 HOH HOH . H 5 HOH A 96 696 38 HOH HOH . H 5 HOH A 97 697 15 HOH HOH . H 5 HOH A 98 698 125 HOH HOH . H 5 HOH A 99 699 138 HOH HOH . H 5 HOH A 100 700 133 HOH HOH . H 5 HOH A 101 701 97 HOH HOH . H 5 HOH A 102 702 136 HOH HOH . H 5 HOH A 103 703 212 HOH HOH . H 5 HOH A 104 704 227 HOH HOH . H 5 HOH A 105 705 195 HOH HOH . H 5 HOH A 106 706 223 HOH HOH . H 5 HOH A 107 707 90 HOH HOH . H 5 HOH A 108 708 225 HOH HOH . H 5 HOH A 109 709 59 HOH HOH . I 5 HOH B 1 601 4 HOH HOH . I 5 HOH B 2 602 106 HOH HOH . I 5 HOH B 3 603 92 HOH HOH . I 5 HOH B 4 604 71 HOH HOH . I 5 HOH B 5 605 148 HOH HOH . I 5 HOH B 6 606 217 HOH HOH . I 5 HOH B 7 607 52 HOH HOH . I 5 HOH B 8 608 135 HOH HOH . I 5 HOH B 9 609 111 HOH HOH . I 5 HOH B 10 610 119 HOH HOH . I 5 HOH B 11 611 235 HOH HOH . I 5 HOH B 12 612 35 HOH HOH . I 5 HOH B 13 613 60 HOH HOH . I 5 HOH B 14 614 3 HOH HOH . I 5 HOH B 15 615 68 HOH HOH . I 5 HOH B 16 616 41 HOH HOH . I 5 HOH B 17 617 36 HOH HOH . I 5 HOH B 18 618 145 HOH HOH . I 5 HOH B 19 619 2 HOH HOH . I 5 HOH B 20 620 146 HOH HOH . I 5 HOH B 21 621 33 HOH HOH . I 5 HOH B 22 622 200 HOH HOH . I 5 HOH B 23 623 98 HOH HOH . I 5 HOH B 24 624 45 HOH HOH . I 5 HOH B 25 625 91 HOH HOH . I 5 HOH B 26 626 51 HOH HOH . I 5 HOH B 27 627 110 HOH HOH . I 5 HOH B 28 628 150 HOH HOH . I 5 HOH B 29 629 44 HOH HOH . I 5 HOH B 30 630 54 HOH HOH . I 5 HOH B 31 631 86 HOH HOH . I 5 HOH B 32 632 126 HOH HOH . I 5 HOH B 33 633 78 HOH HOH . I 5 HOH B 34 634 23 HOH HOH . I 5 HOH B 35 635 8 HOH HOH . I 5 HOH B 36 636 166 HOH HOH . I 5 HOH B 37 637 25 HOH HOH . I 5 HOH B 38 638 113 HOH HOH . I 5 HOH B 39 639 181 HOH HOH . I 5 HOH B 40 640 117 HOH HOH . I 5 HOH B 41 641 143 HOH HOH . I 5 HOH B 42 642 26 HOH HOH . I 5 HOH B 43 643 58 HOH HOH . I 5 HOH B 44 644 61 HOH HOH . I 5 HOH B 45 645 112 HOH HOH . I 5 HOH B 46 646 210 HOH HOH . I 5 HOH B 47 647 153 HOH HOH . I 5 HOH B 48 648 231 HOH HOH . I 5 HOH B 49 649 22 HOH HOH . I 5 HOH B 50 650 187 HOH HOH . I 5 HOH B 51 651 7 HOH HOH . I 5 HOH B 52 652 103 HOH HOH . I 5 HOH B 53 653 63 HOH HOH . I 5 HOH B 54 654 142 HOH HOH . I 5 HOH B 55 655 83 HOH HOH . I 5 HOH B 56 656 218 HOH HOH . I 5 HOH B 57 657 174 HOH HOH . I 5 HOH B 58 658 34 HOH HOH . I 5 HOH B 59 659 55 HOH HOH . I 5 HOH B 60 660 1 HOH HOH . I 5 HOH B 61 661 64 HOH HOH . I 5 HOH B 62 662 130 HOH HOH . I 5 HOH B 63 663 28 HOH HOH . I 5 HOH B 64 664 118 HOH HOH . I 5 HOH B 65 665 236 HOH HOH . I 5 HOH B 66 666 154 HOH HOH . I 5 HOH B 67 667 172 HOH HOH . I 5 HOH B 68 668 70 HOH HOH . I 5 HOH B 69 669 81 HOH HOH . I 5 HOH B 70 670 139 HOH HOH . I 5 HOH B 71 671 158 HOH HOH . I 5 HOH B 72 672 37 HOH HOH . I 5 HOH B 73 673 152 HOH HOH . I 5 HOH B 74 674 114 HOH HOH . I 5 HOH B 75 675 183 HOH HOH . I 5 HOH B 76 676 155 HOH HOH . I 5 HOH B 77 677 105 HOH HOH . I 5 HOH B 78 678 27 HOH HOH . I 5 HOH B 79 679 179 HOH HOH . I 5 HOH B 80 680 141 HOH HOH . I 5 HOH B 81 681 185 HOH HOH . I 5 HOH B 82 682 176 HOH HOH . I 5 HOH B 83 683 89 HOH HOH . I 5 HOH B 84 684 206 HOH HOH . I 5 HOH B 85 685 75 HOH HOH . I 5 HOH B 86 686 192 HOH HOH . I 5 HOH B 87 687 213 HOH HOH . I 5 HOH B 88 688 6 HOH HOH . I 5 HOH B 89 689 76 HOH HOH . I 5 HOH B 90 690 124 HOH HOH . I 5 HOH B 91 691 95 HOH HOH . I 5 HOH B 92 692 77 HOH HOH . I 5 HOH B 93 693 48 HOH HOH . I 5 HOH B 94 694 30 HOH HOH . I 5 HOH B 95 695 66 HOH HOH . I 5 HOH B 96 696 186 HOH HOH . I 5 HOH B 97 697 21 HOH HOH . I 5 HOH B 98 698 121 HOH HOH . I 5 HOH B 99 699 134 HOH HOH . I 5 HOH B 100 700 65 HOH HOH . I 5 HOH B 101 701 161 HOH HOH . I 5 HOH B 102 702 196 HOH HOH . I 5 HOH B 103 703 156 HOH HOH . I 5 HOH B 104 704 178 HOH HOH . I 5 HOH B 105 705 99 HOH HOH . I 5 HOH B 106 706 203 HOH HOH . I 5 HOH B 107 707 169 HOH HOH . I 5 HOH B 108 708 162 HOH HOH . I 5 HOH B 109 709 193 HOH HOH . I 5 HOH B 110 710 170 HOH HOH . I 5 HOH B 111 711 180 HOH HOH . I 5 HOH B 112 712 163 HOH HOH . I 5 HOH B 113 713 109 HOH HOH . I 5 HOH B 114 714 201 HOH HOH . I 5 HOH B 115 715 207 HOH HOH . I 5 HOH B 116 716 107 HOH HOH . I 5 HOH B 117 717 168 HOH HOH . I 5 HOH B 118 718 204 HOH HOH . I 5 HOH B 119 719 157 HOH HOH . I 5 HOH B 120 720 62 HOH HOH . I 5 HOH B 121 721 144 HOH HOH . I 5 HOH B 122 722 159 HOH HOH . I 5 HOH B 123 723 208 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 CAB DRW . . . C 2 -27.781 -98.314 21.875 1 40.21 ? CAB DRW 501 A 1 HETATM 2 O OAD DRW . . . C 2 -24.805 -100.62 18.419 1 33.5 ? OAD DRW 501 A 1 HETATM 3 C CAJ DRW . . . C 2 -25.055 -99.979 19.437 1 32.68 ? CAJ DRW 501 A 1 HETATM 4 N NAN DRW . . . C 2 -26.805 -101.432 22.433 1 39.42 ? NAN DRW 501 A 1 HETATM 5 C CAS DRW . . . C 2 -27.286 -101.044 23.621 1 33.04 ? CAS DRW 501 A 1 HETATM 6 C CAU DRW . . . C 2 -26.78 -99.263 22.515 1 32.91 ? CAU DRW 501 A 1 HETATM 7 C CAX DRW . . . C 2 -26.337 -100.244 20.268 1 36.72 ? CAX DRW 501 A 1 HETATM 8 C CAY DRW . . . C 2 -26.123 -100.268 21.799 0.18 31.97 ? CAY DRW 501 A 1 HETATM 9 C CAZ DRW . . . C 2 -27.044 -99.742 23.742 1 32.83 ? CAZ DRW 501 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 9 #