data_3IBD # _model_server_result.job_id kVIWKxfV2vu_rYAGjHvyqA _model_server_result.datetime_utc '2024-11-04 23:48:55' _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 3ibd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 3IBD # _exptl.entry_id 3IBD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 494.573 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE _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 96.51 _cell.angle_gamma 90 _cell.entry_id 3IBD _cell.length_a 89.573 _cell.length_b 55.74 _cell.length_c 99.09 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IBD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 _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 ? 4 D N N ? 4 E 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 metalc ? metalc1 A SG CYS 417 A CYS 436 1_555 B FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc2 B FE HEM . A HEM 500 1_555 C N1 CPZ . A CPZ 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? # _chem_comp.formula 'C23 H42 O11' _chem_comp.formula_weight 494.573 _chem_comp.id CM5 _chem_comp.mon_nstd_flag . _chem_comp.name 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE;CYMAL-5' # 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 C7 C8 CM5 sing 70 n n C7 C6 CM5 sing 71 n n C7 H71 CM5 sing 72 n n C7 H72 CM5 sing 73 n n C8 C9 CM5 sing 74 n n C8 H81 CM5 sing 75 n n C8 H82 CM5 sing 76 n n C9 C10 CM5 sing 77 n n C9 H91 CM5 sing 78 n n C9 H92 CM5 sing 79 n n C10 C11 CM5 sing 80 n n C10 H101 CM5 sing 81 n n C10 H102 CM5 sing 82 n n C11 C6 CM5 sing 83 n n C11 H111 CM5 sing 84 n n C11 H112 CM5 sing 85 n n C6 C5 CM5 sing 86 n n C6 H6 CM5 sing 87 n n C5 C4 CM5 sing 88 n n C5 H51 CM5 sing 89 n n C5 H52 CM5 sing 90 n n C4 C3 CM5 sing 91 n n C4 H41 CM5 sing 92 n n C4 H42 CM5 sing 93 n n C3 C2 CM5 sing 94 n n C3 H31A CM5 sing 95 n n C3 H32A CM5 sing 96 n n C2 C1 CM5 sing 97 n n C2 H21A CM5 sing 98 n n C2 H22A CM5 sing 99 n n C1 O12 CM5 sing 100 n n C1 H11 CM5 sing 101 n n C1 H12 CM5 sing 102 n n O12 C13 CM5 sing 103 n n C13 C18 CM5 sing 104 n n C13 O14 CM5 sing 105 n n C13 H13 CM5 sing 106 n n C18 O22 CM5 sing 107 n n C18 C17 CM5 sing 108 n n C18 H18 CM5 sing 109 n n O22 H22 CM5 sing 110 n n C17 O21 CM5 sing 111 n n C17 C16 CM5 sing 112 n n C17 H17 CM5 sing 113 n n O21 H21 CM5 sing 114 n n O14 C15 CM5 sing 115 n n C15 C19 CM5 sing 116 n n C15 C16 CM5 sing 117 n n C15 H15 CM5 sing 118 n n C19 O20 CM5 sing 119 n n C19 H191 CM5 sing 120 n n C19 H192 CM5 sing 121 n n O20 H20 CM5 sing 122 n n C16 O23 CM5 sing 123 n n C16 H16 CM5 sing 124 n n O23 C24 CM5 sing 125 n n C24 O25 CM5 sing 126 n n C24 C29 CM5 sing 127 n n C24 H24 CM5 sing 128 n n O25 C26 CM5 sing 129 n n C26 C30 CM5 sing 130 n n C26 C27 CM5 sing 131 n n C26 H26 CM5 sing 132 n n C30 O31 CM5 sing 133 n n C30 H301 CM5 sing 134 n n C30 H302 CM5 sing 135 n n O31 H31 CM5 sing 136 n n C27 O32 CM5 sing 137 n n C27 C28 CM5 sing 138 n n C27 H27 CM5 sing 139 n n O32 H32 CM5 sing 140 n n C28 O33 CM5 sing 141 n n C28 C29 CM5 sing 142 n n C28 H28 CM5 sing 143 n n O33 H33 CM5 sing 144 n n C29 O34 CM5 sing 145 n n C29 H29 CM5 sing 146 n n O34 H34 CM5 sing 147 n n # _atom_sites.entry_id 3IBD _atom_sites.fract_transf_matrix[1][1] 0.011164 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001274 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01794 _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] 0.010157 _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 HEM A 1 500 500 HEM HEM . C 3 CPZ A 1 501 501 CPZ CPZ . D 4 CM5 A 1 1001 1001 CM5 CM5 . E 4 CM5 A 1 1002 1002 CM5 CM5 . F 5 SCN A 1 1003 1003 SCN SCN . G 5 SCN A 1 1004 1004 SCN SCN . H 5 SCN A 1 1005 1005 SCN SCN . I 5 SCN A 1 1006 1006 SCN SCN . J 6 HOH A 1 3 3 HOH HOH . J 6 HOH A 2 4 4 HOH HOH . J 6 HOH A 3 5 5 HOH HOH . J 6 HOH A 4 6 6 HOH HOH . J 6 HOH A 5 7 7 HOH HOH . J 6 HOH A 6 8 8 HOH HOH . J 6 HOH A 7 9 9 HOH HOH . J 6 HOH A 8 10 10 HOH HOH . J 6 HOH A 9 11 11 HOH HOH . J 6 HOH A 10 12 12 HOH HOH . J 6 HOH A 11 13 13 HOH HOH . J 6 HOH A 12 14 14 HOH HOH . J 6 HOH A 13 15 15 HOH HOH . J 6 HOH A 14 16 16 HOH HOH . J 6 HOH A 15 17 17 HOH HOH . J 6 HOH A 16 18 18 HOH HOH . J 6 HOH A 17 19 19 HOH HOH . J 6 HOH A 18 496 496 HOH HOH . J 6 HOH A 19 497 497 HOH HOH . J 6 HOH A 20 498 498 HOH HOH . J 6 HOH A 21 499 499 HOH HOH . J 6 HOH A 22 502 502 HOH HOH . J 6 HOH A 23 503 503 HOH HOH . J 6 HOH A 24 504 504 HOH HOH . J 6 HOH A 25 505 505 HOH HOH . J 6 HOH A 26 506 506 HOH HOH . J 6 HOH A 27 507 507 HOH HOH . J 6 HOH A 28 508 508 HOH HOH . J 6 HOH A 29 509 509 HOH HOH . J 6 HOH A 30 510 510 HOH HOH . J 6 HOH A 31 511 511 HOH HOH . J 6 HOH A 32 512 512 HOH HOH . J 6 HOH A 33 513 513 HOH HOH . J 6 HOH A 34 514 514 HOH HOH . J 6 HOH A 35 515 515 HOH HOH . J 6 HOH A 36 516 516 HOH HOH . J 6 HOH A 37 517 517 HOH HOH . J 6 HOH A 38 518 518 HOH HOH . J 6 HOH A 39 519 519 HOH HOH . J 6 HOH A 40 520 520 HOH HOH . J 6 HOH A 41 521 521 HOH HOH . J 6 HOH A 42 522 522 HOH HOH . J 6 HOH A 43 523 523 HOH HOH . J 6 HOH A 44 524 524 HOH HOH . J 6 HOH A 45 525 525 HOH HOH . J 6 HOH A 46 526 526 HOH HOH . J 6 HOH A 47 527 527 HOH HOH . J 6 HOH A 48 528 528 HOH HOH . J 6 HOH A 49 529 529 HOH HOH . J 6 HOH A 50 530 530 HOH HOH . J 6 HOH A 51 531 531 HOH HOH . J 6 HOH A 52 532 532 HOH HOH . J 6 HOH A 53 533 533 HOH HOH . J 6 HOH A 54 534 534 HOH HOH . J 6 HOH A 55 535 535 HOH HOH . J 6 HOH A 56 536 536 HOH HOH . J 6 HOH A 57 537 537 HOH HOH . J 6 HOH A 58 538 538 HOH HOH . J 6 HOH A 59 539 539 HOH HOH . J 6 HOH A 60 540 540 HOH HOH . J 6 HOH A 61 541 541 HOH HOH . J 6 HOH A 62 542 542 HOH HOH . J 6 HOH A 63 543 543 HOH HOH . J 6 HOH A 64 544 544 HOH HOH . J 6 HOH A 65 545 545 HOH HOH . J 6 HOH A 66 546 546 HOH HOH . J 6 HOH A 67 547 547 HOH HOH . J 6 HOH A 68 548 548 HOH HOH . J 6 HOH A 69 549 549 HOH HOH . J 6 HOH A 70 550 550 HOH HOH . J 6 HOH A 71 551 551 HOH HOH . J 6 HOH A 72 552 552 HOH HOH . J 6 HOH A 73 553 553 HOH HOH . J 6 HOH A 74 554 554 HOH HOH . J 6 HOH A 75 555 555 HOH HOH . J 6 HOH A 76 556 556 HOH HOH . J 6 HOH A 77 557 557 HOH HOH . J 6 HOH A 78 558 558 HOH HOH . J 6 HOH A 79 559 559 HOH HOH . J 6 HOH A 80 560 560 HOH HOH . J 6 HOH A 81 561 561 HOH HOH . J 6 HOH A 82 562 562 HOH HOH . J 6 HOH A 83 563 563 HOH HOH . J 6 HOH A 84 564 564 HOH HOH . J 6 HOH A 85 565 565 HOH HOH . J 6 HOH A 86 566 566 HOH HOH . J 6 HOH A 87 567 567 HOH HOH . J 6 HOH A 88 568 568 HOH HOH . J 6 HOH A 89 569 569 HOH HOH . J 6 HOH A 90 570 570 HOH HOH . J 6 HOH A 91 571 571 HOH HOH . J 6 HOH A 92 572 572 HOH HOH . J 6 HOH A 93 573 573 HOH HOH . J 6 HOH A 94 574 574 HOH HOH . J 6 HOH A 95 575 575 HOH HOH . J 6 HOH A 96 576 576 HOH HOH . J 6 HOH A 97 577 577 HOH HOH . J 6 HOH A 98 578 578 HOH HOH . J 6 HOH A 99 579 579 HOH HOH . J 6 HOH A 100 580 580 HOH HOH . J 6 HOH A 101 581 581 HOH HOH . J 6 HOH A 102 582 582 HOH HOH . J 6 HOH A 103 583 583 HOH HOH . J 6 HOH A 104 584 584 HOH HOH . J 6 HOH A 105 585 585 HOH HOH . J 6 HOH A 106 586 586 HOH HOH . J 6 HOH A 107 587 587 HOH HOH . J 6 HOH A 108 588 588 HOH HOH . J 6 HOH A 109 589 589 HOH HOH . J 6 HOH A 110 590 590 HOH HOH . J 6 HOH A 111 591 591 HOH HOH . J 6 HOH A 112 592 592 HOH HOH . J 6 HOH A 113 593 593 HOH HOH . J 6 HOH A 114 594 594 HOH HOH . J 6 HOH A 115 595 595 HOH HOH . J 6 HOH A 116 596 596 HOH HOH . J 6 HOH A 117 597 597 HOH HOH . J 6 HOH A 118 598 598 HOH HOH . J 6 HOH A 119 599 599 HOH HOH . J 6 HOH A 120 600 600 HOH HOH . J 6 HOH A 121 601 601 HOH HOH . J 6 HOH A 122 602 602 HOH HOH . J 6 HOH A 123 603 603 HOH HOH . J 6 HOH A 124 604 604 HOH HOH . J 6 HOH A 125 605 605 HOH HOH . J 6 HOH A 126 606 606 HOH HOH . J 6 HOH A 127 607 607 HOH HOH . J 6 HOH A 128 608 608 HOH HOH . J 6 HOH A 129 609 609 HOH HOH . J 6 HOH A 130 610 610 HOH HOH . J 6 HOH A 131 611 611 HOH HOH . J 6 HOH A 132 612 612 HOH HOH . J 6 HOH A 133 613 613 HOH HOH . J 6 HOH A 134 614 614 HOH HOH . J 6 HOH A 135 615 615 HOH HOH . J 6 HOH A 136 616 616 HOH HOH . J 6 HOH A 137 617 617 HOH HOH . J 6 HOH A 138 618 618 HOH HOH . J 6 HOH A 139 619 619 HOH HOH . J 6 HOH A 140 620 620 HOH HOH . J 6 HOH A 141 621 621 HOH HOH . J 6 HOH A 142 622 622 HOH HOH . J 6 HOH A 143 623 623 HOH HOH . J 6 HOH A 144 624 624 HOH HOH . J 6 HOH A 145 625 625 HOH HOH . J 6 HOH A 146 626 626 HOH HOH . J 6 HOH A 147 627 627 HOH HOH . J 6 HOH A 148 628 628 HOH HOH . J 6 HOH A 149 629 629 HOH HOH . J 6 HOH A 150 630 630 HOH HOH . J 6 HOH A 151 631 631 HOH HOH . J 6 HOH A 152 632 632 HOH HOH . J 6 HOH A 153 633 633 HOH HOH . J 6 HOH A 154 634 634 HOH HOH . J 6 HOH A 155 635 635 HOH HOH . J 6 HOH A 156 636 636 HOH HOH . J 6 HOH A 157 637 637 HOH HOH . J 6 HOH A 158 638 638 HOH HOH . J 6 HOH A 159 639 639 HOH HOH . J 6 HOH A 160 640 640 HOH HOH . J 6 HOH A 161 641 641 HOH HOH . J 6 HOH A 162 642 642 HOH HOH . J 6 HOH A 163 643 643 HOH HOH . J 6 HOH A 164 644 644 HOH HOH . J 6 HOH A 165 645 645 HOH HOH . J 6 HOH A 166 646 646 HOH HOH . J 6 HOH A 167 647 647 HOH HOH . J 6 HOH A 168 648 648 HOH HOH . J 6 HOH A 169 649 649 HOH HOH . J 6 HOH A 170 650 650 HOH HOH . J 6 HOH A 171 651 651 HOH HOH . J 6 HOH A 172 652 652 HOH HOH . J 6 HOH A 173 653 653 HOH HOH . J 6 HOH A 174 654 654 HOH HOH . J 6 HOH A 175 655 1 HOH HOH . J 6 HOH A 176 656 2 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 C7 CM5 . . . D 4 32.935 5.729 14.935 1 48.45 ? C7 CM5 1001 A 1 HETATM 2 C C8 CM5 . . . D 4 32.356 6.468 16.174 1 48.73 ? C8 CM5 1001 A 1 HETATM 3 C C9 CM5 . . . D 4 31.195 5.709 16.818 1 49.1 ? C9 CM5 1001 A 1 HETATM 4 C C10 CM5 . . . D 4 31.564 4.239 17.02 1 48.08 ? C10 CM5 1001 A 1 HETATM 5 C C11 CM5 . . . D 4 31.972 3.619 15.679 1 47.97 ? C11 CM5 1001 A 1 HETATM 6 C C6 CM5 . . . D 4 33.308 4.238 15.192 1 47.49 ? C6 CM5 1001 A 1 HETATM 7 C C5 CM5 . . . D 4 34.044 3.446 14.017 1 47.64 ? C5 CM5 1001 A 1 HETATM 8 C C4 CM5 . . . D 4 34.931 2.17 14.353 1 45.31 ? C4 CM5 1001 A 1 HETATM 9 C C3 CM5 . . . D 4 35.594 1.236 13.237 1 45.74 ? C3 CM5 1001 A 1 HETATM 10 C C2 CM5 . . . D 4 37.083 1.472 12.687 1 44.06 ? C2 CM5 1001 A 1 HETATM 11 C C1 CM5 . . . D 4 38.258 1.914 13.691 1 46.47 ? C1 CM5 1001 A 1 HETATM 12 O O12 CM5 . . . D 4 39.307 0.931 13.905 1 46.91 ? O12 CM5 1001 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 12 #