data_5RCB # _model_server_result.job_id mcGfLXZdEllAVcAJRYP9rQ _model_server_result.datetime_utc '2024-11-24 13:35:10' _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 5rcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5RCB # _exptl.entry_id 5RCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.32 _cell.angle_gamma 90 _cell.entry_id 5RCB _cell.length_a 45.204 _cell.length_b 73.125 _cell.length_c 52.644 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5RCB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 B N N ? 2 E N N ? 2 G 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 344 A CYS 255 1_555 A SG CYS 379 A CYS 290 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 344 A CYS 255 1_555 A SG CYS 379 A CYS 290 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.02 ? disulf ? disulf3 A SG CYS 344 A CYS 255 1_555 A SG CYS 379 A CYS 290 1_555 ? ? ? ? C ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 A SG CYS 344 A CYS 255 1_555 A SG CYS 379 A CYS 290 1_555 ? ? ? ? D ? ? ? ? ? ? ? 2.04 ? metalc ? metalc1 K O2 PG4 . A PG4 410 1_555 L NA NA . A NA 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.035 ? metalc ? metalc2 K O4 PG4 . A PG4 410 1_555 L NA NA . A NA 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.179 ? metalc ? metalc3 K O5 PG4 . A PG4 410 1_555 L NA NA . A NA 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 144 n n C1 C2 GOL sing 145 n n C1 H11 GOL sing 146 n n C1 H12 GOL sing 147 n n O1 HO1 GOL sing 148 n n C2 O2 GOL sing 149 n n C2 C3 GOL sing 150 n n C2 H2 GOL sing 151 n n O2 HO2 GOL sing 152 n n C3 O3 GOL sing 153 n n C3 H31 GOL sing 154 n n C3 H32 GOL sing 155 n n O3 HO3 GOL sing 156 n n # _atom_sites.entry_id 5RCB _atom_sites.fract_transf_matrix[1][1] 0.022122 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007757 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013675 _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] 0.020129 _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 GOL A 1 401 401 GOL GOL . C 3 ACT A 1 402 501 ACT ACT . D 4 DMS A 1 403 601 DMS DMS . E 2 GOL A 1 404 701 GOL GOL . F 5 RDM A 1 405 401 RDM XXX . G 2 GOL A 1 406 401 GOL GOL . H 2 GOL A 1 407 402 GOL GOL . I 2 GOL A 1 408 403 GOL GOL . J 3 ACT A 1 409 405 ACT ACT . K 6 PG4 A 1 410 407 PG4 PG4 . L 7 NA A 1 411 408 NA NA . M 8 HOH A 1 501 217 HOH HOH . M 8 HOH A 2 502 62 HOH HOH . M 8 HOH A 3 503 248 HOH HOH . M 8 HOH A 4 504 147 HOH HOH . M 8 HOH A 5 505 173 HOH HOH . M 8 HOH A 6 506 114 HOH HOH . M 8 HOH A 7 507 150 HOH HOH . M 8 HOH A 8 508 159 HOH HOH . M 8 HOH A 9 509 189 HOH HOH . M 8 HOH A 10 510 43 HOH HOH . M 8 HOH A 11 511 141 HOH HOH . M 8 HOH A 12 512 210 HOH HOH . M 8 HOH A 13 513 168 HOH HOH . M 8 HOH A 14 514 52 HOH HOH . M 8 HOH A 15 515 193 HOH HOH . M 8 HOH A 16 516 133 HOH HOH . M 8 HOH A 17 517 205 HOH HOH . M 8 HOH A 18 518 90 HOH HOH . M 8 HOH A 19 519 229 HOH HOH . M 8 HOH A 20 520 18 HOH HOH . M 8 HOH A 21 521 15 HOH HOH . M 8 HOH A 22 522 30 HOH HOH . M 8 HOH A 23 523 117 HOH HOH . M 8 HOH A 24 524 196 HOH HOH . M 8 HOH A 25 525 136 HOH HOH . M 8 HOH A 26 526 240 HOH HOH . M 8 HOH A 27 527 264 HOH HOH . M 8 HOH A 28 528 275 HOH HOH . M 8 HOH A 29 529 14 HOH HOH . M 8 HOH A 30 530 48 HOH HOH . M 8 HOH A 31 531 26 HOH HOH . M 8 HOH A 32 532 154 HOH HOH . M 8 HOH A 33 533 22 HOH HOH . M 8 HOH A 34 534 151 HOH HOH . M 8 HOH A 35 535 68 HOH HOH . M 8 HOH A 36 536 60 HOH HOH . M 8 HOH A 37 537 55 HOH HOH . M 8 HOH A 38 538 225 HOH HOH . M 8 HOH A 39 539 46 HOH HOH . M 8 HOH A 40 540 71 HOH HOH . M 8 HOH A 41 541 111 HOH HOH . M 8 HOH A 42 542 2 HOH HOH . M 8 HOH A 43 543 37 HOH HOH . M 8 HOH A 44 544 230 HOH HOH . M 8 HOH A 45 545 5 HOH HOH . M 8 HOH A 46 546 42 HOH HOH . M 8 HOH A 47 547 39 HOH HOH . M 8 HOH A 48 548 258 HOH HOH . M 8 HOH A 49 549 227 HOH HOH . M 8 HOH A 50 550 49 HOH HOH . M 8 HOH A 51 551 252 HOH HOH . M 8 HOH A 52 552 167 HOH HOH . M 8 HOH A 53 553 209 HOH HOH . M 8 HOH A 54 554 21 HOH HOH . M 8 HOH A 55 555 165 HOH HOH . M 8 HOH A 56 556 45 HOH HOH . M 8 HOH A 57 557 207 HOH HOH . M 8 HOH A 58 558 241 HOH HOH . M 8 HOH A 59 559 185 HOH HOH . M 8 HOH A 60 560 4 HOH HOH . M 8 HOH A 61 561 35 HOH HOH . M 8 HOH A 62 562 256 HOH HOH . M 8 HOH A 63 563 3 HOH HOH . M 8 HOH A 64 564 75 HOH HOH . M 8 HOH A 65 565 190 HOH HOH . M 8 HOH A 66 566 27 HOH HOH . M 8 HOH A 67 567 80 HOH HOH . M 8 HOH A 68 568 66 HOH HOH . M 8 HOH A 69 569 96 HOH HOH . M 8 HOH A 70 570 41 HOH HOH . M 8 HOH A 71 571 29 HOH HOH . M 8 HOH A 72 572 93 HOH HOH . M 8 HOH A 73 573 152 HOH HOH . M 8 HOH A 74 574 148 HOH HOH . M 8 HOH A 75 575 6 HOH HOH . M 8 HOH A 76 576 175 HOH HOH . M 8 HOH A 77 577 65 HOH HOH . M 8 HOH A 78 578 115 HOH HOH . M 8 HOH A 79 579 11 HOH HOH . M 8 HOH A 80 580 20 HOH HOH . M 8 HOH A 81 581 206 HOH HOH . M 8 HOH A 82 582 97 HOH HOH . M 8 HOH A 83 583 131 HOH HOH . M 8 HOH A 84 584 182 HOH HOH . M 8 HOH A 85 585 238 HOH HOH . M 8 HOH A 86 586 17 HOH HOH . M 8 HOH A 87 587 12 HOH HOH . M 8 HOH A 88 588 89 HOH HOH . M 8 HOH A 89 589 51 HOH HOH . M 8 HOH A 90 590 109 HOH HOH . M 8 HOH A 91 591 172 HOH HOH . M 8 HOH A 92 592 161 HOH HOH . M 8 HOH A 93 593 104 HOH HOH . M 8 HOH A 94 594 261 HOH HOH . M 8 HOH A 95 595 58 HOH HOH . M 8 HOH A 96 596 99 HOH HOH . M 8 HOH A 97 597 124 HOH HOH . M 8 HOH A 98 598 100 HOH HOH . M 8 HOH A 99 599 144 HOH HOH . M 8 HOH A 100 600 143 HOH HOH . M 8 HOH A 101 601 87 HOH HOH . M 8 HOH A 102 602 157 HOH HOH . M 8 HOH A 103 603 233 HOH HOH . M 8 HOH A 104 604 177 HOH HOH . M 8 HOH A 105 605 112 HOH HOH . M 8 HOH A 106 606 28 HOH HOH . M 8 HOH A 107 607 129 HOH HOH . M 8 HOH A 108 608 224 HOH HOH . M 8 HOH A 109 609 57 HOH HOH . M 8 HOH A 110 610 25 HOH HOH . M 8 HOH A 111 611 181 HOH HOH . M 8 HOH A 112 612 10 HOH HOH . M 8 HOH A 113 613 108 HOH HOH . M 8 HOH A 114 614 76 HOH HOH . M 8 HOH A 115 615 44 HOH HOH . M 8 HOH A 116 616 102 HOH HOH . M 8 HOH A 117 617 88 HOH HOH . M 8 HOH A 118 618 33 HOH HOH . M 8 HOH A 119 619 223 HOH HOH . M 8 HOH A 120 620 77 HOH HOH . M 8 HOH A 121 621 271 HOH HOH . M 8 HOH A 122 622 158 HOH HOH . M 8 HOH A 123 623 202 HOH HOH . M 8 HOH A 124 624 13 HOH HOH . M 8 HOH A 125 625 98 HOH HOH . M 8 HOH A 126 626 219 HOH HOH . M 8 HOH A 127 627 73 HOH HOH . M 8 HOH A 128 628 145 HOH HOH . M 8 HOH A 129 629 110 HOH HOH . M 8 HOH A 130 630 86 HOH HOH . M 8 HOH A 131 631 81 HOH HOH . M 8 HOH A 132 632 201 HOH HOH . M 8 HOH A 133 633 59 HOH HOH . M 8 HOH A 134 634 155 HOH HOH . M 8 HOH A 135 635 171 HOH HOH . M 8 HOH A 136 636 142 HOH HOH . M 8 HOH A 137 637 221 HOH HOH . M 8 HOH A 138 638 91 HOH HOH . M 8 HOH A 139 639 265 HOH HOH . M 8 HOH A 140 640 263 HOH HOH . M 8 HOH A 141 641 47 HOH HOH . M 8 HOH A 142 642 211 HOH HOH . M 8 HOH A 143 643 34 HOH HOH . M 8 HOH A 144 644 94 HOH HOH . M 8 HOH A 145 645 8 HOH HOH . M 8 HOH A 146 646 120 HOH HOH . M 8 HOH A 147 647 194 HOH HOH . M 8 HOH A 148 648 63 HOH HOH . M 8 HOH A 149 649 40 HOH HOH . M 8 HOH A 150 650 67 HOH HOH . M 8 HOH A 151 651 197 HOH HOH . M 8 HOH A 152 652 247 HOH HOH . M 8 HOH A 153 653 38 HOH HOH . M 8 HOH A 154 654 23 HOH HOH . M 8 HOH A 155 655 56 HOH HOH . M 8 HOH A 156 656 24 HOH HOH . M 8 HOH A 157 657 253 HOH HOH . M 8 HOH A 158 658 226 HOH HOH . M 8 HOH A 159 659 116 HOH HOH . M 8 HOH A 160 660 174 HOH HOH . M 8 HOH A 161 661 259 HOH HOH . M 8 HOH A 162 662 36 HOH HOH . M 8 HOH A 163 663 156 HOH HOH . M 8 HOH A 164 664 79 HOH HOH . M 8 HOH A 165 665 251 HOH HOH . M 8 HOH A 166 666 64 HOH HOH . M 8 HOH A 167 667 126 HOH HOH . M 8 HOH A 168 668 125 HOH HOH . M 8 HOH A 169 669 138 HOH HOH . M 8 HOH A 170 670 139 HOH HOH . M 8 HOH A 171 671 164 HOH HOH . M 8 HOH A 172 672 192 HOH HOH . M 8 HOH A 173 673 270 HOH HOH . M 8 HOH A 174 674 54 HOH HOH . M 8 HOH A 175 675 127 HOH HOH . M 8 HOH A 176 676 169 HOH HOH . M 8 HOH A 177 677 134 HOH HOH . M 8 HOH A 178 678 203 HOH HOH . M 8 HOH A 179 679 119 HOH HOH . M 8 HOH A 180 680 208 HOH HOH . M 8 HOH A 181 681 84 HOH HOH . M 8 HOH A 182 682 215 HOH HOH . M 8 HOH A 183 683 269 HOH HOH . M 8 HOH A 184 684 183 HOH HOH . M 8 HOH A 185 685 232 HOH HOH . M 8 HOH A 186 686 50 HOH HOH . M 8 HOH A 187 687 268 HOH HOH . M 8 HOH A 188 688 121 HOH HOH . M 8 HOH A 189 689 132 HOH HOH . M 8 HOH A 190 690 83 HOH HOH . M 8 HOH A 191 691 187 HOH HOH . M 8 HOH A 192 692 140 HOH HOH . M 8 HOH A 193 693 188 HOH HOH . M 8 HOH A 194 694 95 HOH HOH . M 8 HOH A 195 695 162 HOH HOH . M 8 HOH A 196 696 107 HOH HOH . M 8 HOH A 197 697 170 HOH HOH . M 8 HOH A 198 698 176 HOH HOH . M 8 HOH A 199 699 153 HOH HOH . M 8 HOH A 200 700 272 HOH HOH . M 8 HOH A 201 701 236 HOH HOH . M 8 HOH A 202 702 246 HOH HOH . M 8 HOH A 203 703 235 HOH HOH . M 8 HOH A 204 704 267 HOH HOH . M 8 HOH A 205 705 250 HOH HOH . M 8 HOH A 206 706 199 HOH HOH . M 8 HOH A 207 707 245 HOH HOH . M 8 HOH A 208 708 105 HOH HOH . M 8 HOH A 209 709 74 HOH HOH . M 8 HOH A 210 710 180 HOH HOH . M 8 HOH A 211 711 228 HOH HOH . M 8 HOH A 212 712 274 HOH HOH . M 8 HOH A 213 713 260 HOH HOH . M 8 HOH A 214 714 273 HOH HOH . M 8 HOH A 215 715 149 HOH HOH . M 8 HOH A 216 716 137 HOH HOH . M 8 HOH A 217 717 254 HOH HOH . M 8 HOH A 218 718 214 HOH HOH . M 8 HOH A 219 719 178 HOH HOH . M 8 HOH A 220 720 160 HOH HOH . M 8 HOH A 221 721 166 HOH HOH . M 8 HOH A 222 722 179 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 C1 GOL . A . B 2 5.555 5.472 41.5 0.25 23.25 ? C1 GOL 401 A 1 HETATM 2 C C1 GOL . B . B 2 5.549 5.457 41.485 0.25 23.24 ? C1 GOL 401 A 1 HETATM 3 O O1 GOL . A . B 2 5.633 4.266 40.749 0.25 24.68 ? O1 GOL 401 A 1 HETATM 4 O O1 GOL . B . B 2 5.618 4.242 40.747 0.25 24.88 ? O1 GOL 401 A 1 HETATM 5 C C2 GOL . A . B 2 4.991 5.264 42.893 0.25 22.14 ? C2 GOL 401 A 1 HETATM 6 C C2 GOL . B . B 2 4.998 5.265 42.885 0.25 22.06 ? C2 GOL 401 A 1 HETATM 7 O O2 GOL . A . B 2 5.116 3.897 43.315 0.25 13.88 ? O2 GOL 401 A 1 HETATM 8 O O2 GOL . B . B 2 5.116 3.901 43.317 0.25 13.87 ? O2 GOL 401 A 1 HETATM 9 C C3 GOL . A . B 2 5.61 6.247 43.877 0.25 22.69 ? C3 GOL 401 A 1 HETATM 10 C C3 GOL . B . B 2 5.639 6.252 43.853 0.25 22.54 ? C3 GOL 401 A 1 HETATM 11 O O3 GOL . A . B 2 5.877 5.693 45.161 0.25 25.82 ? O3 GOL 401 A 1 HETATM 12 O O3 GOL . B . B 2 5.739 5.77 45.19 0.25 25.37 ? O3 GOL 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 12 #