data_3JDW # _model_server_result.job_id Fqt32fhQN5pJf8YQM87QIw _model_server_result.datetime_utc '2024-11-08 10:05:20' _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 3jdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 3JDW # _exptl.entry_id 3JDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 132.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description L-ornithine _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 90 _cell.entry_id 3JDW _cell.length_a 83.76 _cell.length_b 83.76 _cell.length_c 199.65 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JDW _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C5 H12 N2 O2' _chem_comp.formula_weight 132.161 _chem_comp.id ORN _chem_comp.mon_nstd_flag n _chem_comp.name L-ornithine _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms ? # 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 N CA ORN sing 237 n n N H ORN sing 238 n n N H2 ORN sing 239 n n CA CB ORN sing 240 n n CA C ORN sing 241 n n CA HA ORN sing 242 n n CB CG ORN sing 243 n n CB HB2 ORN sing 244 n n CB HB3 ORN sing 245 n n CG CD ORN sing 246 n n CG HG2 ORN sing 247 n n CG HG3 ORN sing 248 n n CD NE ORN sing 249 n n CD HD2 ORN sing 250 n n CD HD3 ORN sing 251 n n NE HE1 ORN sing 252 n n NE HE2 ORN sing 253 n n C O ORN doub 254 n n C OXT ORN sing 255 n n OXT HXT ORN sing 256 n n # _atom_sites.entry_id 3JDW _atom_sites.fract_transf_matrix[1][1] 0.011939 _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] 0.011939 _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] 0.005009 _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 ORN A 1 500 500 ORN ORN . C 3 HOH A 1 501 1 HOH HOH . C 3 HOH A 2 502 2 HOH HOH . C 3 HOH A 3 503 3 HOH HOH . C 3 HOH A 4 504 4 HOH HOH . C 3 HOH A 5 505 5 HOH HOH . C 3 HOH A 6 506 6 HOH HOH . C 3 HOH A 7 507 7 HOH HOH . C 3 HOH A 8 508 8 HOH HOH . C 3 HOH A 9 509 9 HOH HOH . C 3 HOH A 10 510 10 HOH HOH . C 3 HOH A 11 511 11 HOH HOH . C 3 HOH A 12 512 12 HOH HOH . C 3 HOH A 13 513 13 HOH HOH . C 3 HOH A 14 514 14 HOH HOH . C 3 HOH A 15 515 15 HOH HOH . C 3 HOH A 16 516 16 HOH HOH . C 3 HOH A 17 517 17 HOH HOH . C 3 HOH A 18 518 18 HOH HOH . C 3 HOH A 19 519 19 HOH HOH . C 3 HOH A 20 520 20 HOH HOH . C 3 HOH A 21 521 21 HOH HOH . C 3 HOH A 22 522 22 HOH HOH . C 3 HOH A 23 523 23 HOH HOH . C 3 HOH A 24 524 24 HOH HOH . C 3 HOH A 25 525 25 HOH HOH . C 3 HOH A 26 526 26 HOH HOH . C 3 HOH A 27 527 27 HOH HOH . C 3 HOH A 28 528 28 HOH HOH . C 3 HOH A 29 529 29 HOH HOH . C 3 HOH A 30 530 30 HOH HOH . C 3 HOH A 31 531 31 HOH HOH . C 3 HOH A 32 532 32 HOH HOH . C 3 HOH A 33 533 33 HOH HOH . C 3 HOH A 34 534 34 HOH HOH . C 3 HOH A 35 535 35 HOH HOH . C 3 HOH A 36 536 36 HOH HOH . C 3 HOH A 37 537 37 HOH HOH . C 3 HOH A 38 538 38 HOH HOH . C 3 HOH A 39 539 39 HOH HOH . C 3 HOH A 40 540 40 HOH HOH . C 3 HOH A 41 541 41 HOH HOH . C 3 HOH A 42 542 43 HOH HOH . C 3 HOH A 43 543 44 HOH HOH . C 3 HOH A 44 544 45 HOH HOH . C 3 HOH A 45 545 46 HOH HOH . C 3 HOH A 46 546 47 HOH HOH . C 3 HOH A 47 547 48 HOH HOH . C 3 HOH A 48 548 49 HOH HOH . C 3 HOH A 49 549 51 HOH HOH . C 3 HOH A 50 550 52 HOH HOH . C 3 HOH A 51 551 53 HOH HOH . C 3 HOH A 52 552 54 HOH HOH . C 3 HOH A 53 553 55 HOH HOH . C 3 HOH A 54 554 56 HOH HOH . C 3 HOH A 55 555 57 HOH HOH . C 3 HOH A 56 556 58 HOH HOH . C 3 HOH A 57 557 59 HOH HOH . C 3 HOH A 58 558 60 HOH HOH . C 3 HOH A 59 559 61 HOH HOH . C 3 HOH A 60 560 62 HOH HOH . C 3 HOH A 61 561 63 HOH HOH . C 3 HOH A 62 562 64 HOH HOH . C 3 HOH A 63 563 65 HOH HOH . C 3 HOH A 64 564 66 HOH HOH . C 3 HOH A 65 565 67 HOH HOH . C 3 HOH A 66 566 68 HOH HOH . C 3 HOH A 67 567 69 HOH HOH . C 3 HOH A 68 568 70 HOH HOH . C 3 HOH A 69 569 71 HOH HOH . C 3 HOH A 70 570 72 HOH HOH . C 3 HOH A 71 571 73 HOH HOH . C 3 HOH A 72 572 74 HOH HOH . C 3 HOH A 73 573 75 HOH HOH . C 3 HOH A 74 574 76 HOH HOH . C 3 HOH A 75 575 77 HOH HOH . C 3 HOH A 76 576 78 HOH HOH . C 3 HOH A 77 577 79 HOH HOH . C 3 HOH A 78 578 80 HOH HOH . C 3 HOH A 79 579 81 HOH HOH . C 3 HOH A 80 580 82 HOH HOH . C 3 HOH A 81 581 83 HOH HOH . C 3 HOH A 82 582 84 HOH HOH . C 3 HOH A 83 583 85 HOH HOH . C 3 HOH A 84 584 86 HOH HOH . C 3 HOH A 85 585 87 HOH HOH . C 3 HOH A 86 587 89 HOH HOH . C 3 HOH A 87 588 90 HOH HOH . C 3 HOH A 88 589 91 HOH HOH . C 3 HOH A 89 590 92 HOH HOH . C 3 HOH A 90 591 93 HOH HOH . C 3 HOH A 91 592 95 HOH HOH . C 3 HOH A 92 593 97 HOH HOH . C 3 HOH A 93 594 98 HOH HOH . C 3 HOH A 94 595 99 HOH HOH . C 3 HOH A 95 596 100 HOH HOH . C 3 HOH A 96 597 101 HOH HOH . C 3 HOH A 97 598 102 HOH HOH . C 3 HOH A 98 599 103 HOH HOH . C 3 HOH A 99 600 104 HOH HOH . C 3 HOH A 100 601 105 HOH HOH . C 3 HOH A 101 602 106 HOH HOH . C 3 HOH A 102 603 107 HOH HOH . C 3 HOH A 103 604 108 HOH HOH . C 3 HOH A 104 605 109 HOH HOH . C 3 HOH A 105 606 110 HOH HOH . C 3 HOH A 106 607 111 HOH HOH . C 3 HOH A 107 608 112 HOH HOH . C 3 HOH A 108 609 113 HOH HOH . C 3 HOH A 109 610 114 HOH HOH . C 3 HOH A 110 611 115 HOH HOH . C 3 HOH A 111 612 116 HOH HOH . C 3 HOH A 112 613 117 HOH HOH . C 3 HOH A 113 614 118 HOH HOH . C 3 HOH A 114 615 119 HOH HOH . C 3 HOH A 115 616 120 HOH HOH . C 3 HOH A 116 617 121 HOH HOH . C 3 HOH A 117 618 122 HOH HOH . C 3 HOH A 118 619 123 HOH HOH . C 3 HOH A 119 620 124 HOH HOH . C 3 HOH A 120 621 125 HOH HOH . C 3 HOH A 121 622 126 HOH HOH . C 3 HOH A 122 623 127 HOH HOH . C 3 HOH A 123 624 130 HOH HOH . C 3 HOH A 124 625 131 HOH HOH . C 3 HOH A 125 626 132 HOH HOH . C 3 HOH A 126 627 134 HOH HOH . C 3 HOH A 127 628 135 HOH HOH . C 3 HOH A 128 629 136 HOH HOH . C 3 HOH A 129 630 137 HOH HOH . C 3 HOH A 130 631 139 HOH HOH . C 3 HOH A 131 632 140 HOH HOH . C 3 HOH A 132 633 141 HOH HOH . C 3 HOH A 133 634 142 HOH HOH . C 3 HOH A 134 635 143 HOH HOH . C 3 HOH A 135 636 144 HOH HOH . C 3 HOH A 136 637 146 HOH HOH . C 3 HOH A 137 638 147 HOH HOH . C 3 HOH A 138 639 148 HOH HOH . C 3 HOH A 139 640 150 HOH HOH . C 3 HOH A 140 641 151 HOH HOH . C 3 HOH A 141 642 152 HOH HOH . C 3 HOH A 142 643 153 HOH HOH . C 3 HOH A 143 644 154 HOH HOH . C 3 HOH A 144 645 156 HOH HOH . C 3 HOH A 145 646 157 HOH HOH . C 3 HOH A 146 647 158 HOH HOH . C 3 HOH A 147 648 159 HOH HOH . C 3 HOH A 148 649 160 HOH HOH . C 3 HOH A 149 650 161 HOH HOH . C 3 HOH A 150 651 164 HOH HOH . C 3 HOH A 151 652 165 HOH HOH . C 3 HOH A 152 653 166 HOH HOH . C 3 HOH A 153 654 167 HOH HOH . C 3 HOH A 154 655 168 HOH HOH . C 3 HOH A 155 656 169 HOH HOH . C 3 HOH A 156 657 170 HOH HOH . C 3 HOH A 157 658 172 HOH HOH . C 3 HOH A 158 659 173 HOH HOH . C 3 HOH A 159 660 174 HOH HOH . C 3 HOH A 160 661 175 HOH HOH . C 3 HOH A 161 662 176 HOH HOH . C 3 HOH A 162 663 177 HOH HOH . C 3 HOH A 163 664 178 HOH HOH . C 3 HOH A 164 665 179 HOH HOH . C 3 HOH A 165 666 182 HOH HOH . C 3 HOH A 166 667 183 HOH HOH . C 3 HOH A 167 668 184 HOH HOH . C 3 HOH A 168 669 185 HOH HOH . C 3 HOH A 169 670 186 HOH HOH . C 3 HOH A 170 671 187 HOH HOH . C 3 HOH A 171 672 190 HOH HOH . C 3 HOH A 172 673 191 HOH HOH . C 3 HOH A 173 674 192 HOH HOH . C 3 HOH A 174 675 193 HOH HOH . C 3 HOH A 175 676 196 HOH HOH . C 3 HOH A 176 677 197 HOH HOH . C 3 HOH A 177 678 198 HOH HOH . C 3 HOH A 178 679 200 HOH HOH . C 3 HOH A 179 680 202 HOH HOH . C 3 HOH A 180 681 205 HOH HOH . C 3 HOH A 181 682 206 HOH HOH . C 3 HOH A 182 683 208 HOH HOH . C 3 HOH A 183 684 209 HOH HOH . C 3 HOH A 184 685 210 HOH HOH . C 3 HOH A 185 686 211 HOH HOH . C 3 HOH A 186 687 213 HOH HOH . C 3 HOH A 187 688 215 HOH HOH . C 3 HOH A 188 689 216 HOH HOH . C 3 HOH A 189 690 217 HOH HOH . C 3 HOH A 190 691 218 HOH HOH . C 3 HOH A 191 692 220 HOH HOH . C 3 HOH A 192 693 221 HOH HOH . C 3 HOH A 193 694 224 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 N N ORN . . . B 2 45.346 72.949 15.145 1 31.1 ? N ORN 500 A 1 HETATM 2 C CA ORN . . . B 2 44.315 72.538 16.14 1 30.42 ? CA ORN 500 A 1 HETATM 3 C CB ORN . . . B 2 44.657 71.18 16.798 1 30.46 ? CB ORN 500 A 1 HETATM 4 C CG ORN . . . B 2 46.129 70.825 17.011 1 27.73 ? CG ORN 500 A 1 HETATM 5 C CD ORN . . . B 2 46.263 69.289 17.156 1 28.03 ? CD ORN 500 A 1 HETATM 6 N NE ORN . . . B 2 47.688 68.731 17.032 1 30.19 ? NE ORN 500 A 1 HETATM 7 C C ORN . . . B 2 44.06 73.623 17.185 1 30.43 ? C ORN 500 A 1 HETATM 8 O O ORN . . . B 2 43.152 73.431 18.017 1 31.22 ? O ORN 500 A 1 HETATM 9 O OXT ORN . . . B 2 44.715 74.693 17.121 1 31.45 ? OXT ORN 500 A 1 HETATM 10 H H ORN . . . B 2 46.305 72.792 15.481 1 0 ? H ORN 500 A 1 HETATM 11 H HE1 ORN . . . B 2 48.188 69.084 17.876 1 0 ? HE1 ORN 500 A 1 HETATM 12 H HE2 ORN . . . B 2 48.224 69.175 16.26 1 0 ? HE2 ORN 500 A 1 HETATM 13 H HN2 ORN . . . B 2 45.206 73.98 15.168 1 0 ? HN2 ORN 500 A 1 HETATM 14 H HN3 ORN . . . B 2 45.149 72.562 14.202 1 0 ? HN3 ORN 500 A 1 HETATM 15 H HE3 ORN . . . B 2 47.736 67.7 17.02 1 0 ? HE3 ORN 500 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 382 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 15 #