data_3R5O # _model_server_result.job_id 2hNwKNlKJbM54BNo5e1Q0Q _model_server_result.datetime_utc '2024-11-24 09:03:02' _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 3r5o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":607}' # _entry.id 3R5O # _exptl.entry_id 3R5O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 126.904 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'IODIDE ION' _entity.pdbx_number_of_molecules 10 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.98 _cell.angle_gamma 90 _cell.entry_id 3R5O _cell.length_a 54.008 _cell.length_b 80.047 _cell.length_c 75.676 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3R5O _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,N,O,P,Q,R,S,T,U,V,W,X _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 ? 6 H N N ? 6 I N N ? 6 J N N ? 6 K N N ? 6 L N N ? 6 M N N ? 6 N N N ? 6 O N N ? 6 P N N ? 6 Q N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 601 NAG 2 n B NAG 2 B 2 NAG A 602 NAG # 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 6 A CYS 6 1_555 A SG CYS 167 A CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 15 A CYS 15 1_555 A SG CYS 28 A CYS 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 129 A CYS 129 1_555 A SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 133 A CYS 133 1_555 A SG CYS 157 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 237 A CYS 237 1_555 A SG CYS 248 A CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 456 A CYS 456 1_555 A SG CYS 513 A CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf7 A SG CYS 554 A CYS 554 1_555 A SG CYS 579 A CYS 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 95 A ASN 95 1_555 E C1 NAG . A NAG 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale2 A OD2 ASP 108 A ASP 108 1_555 D CMD HEM . A HEM 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.556 ? covale ? covale3 A C PRO 197 A PRO 197 1_555 A N SEP 198 A SEP 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale4 A C SEP 198 A SEP 198 1_555 A N LEU 199 A LEU 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A ND2 ASN 205 A ASN 205 1_555 F C1 NAG . A NAG 599 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale6 A ND2 ASN 241 A ASN 241 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 A OE2 GLU 258 A GLU 258 1_555 D CMB HEM . A HEM 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.557 ? covale ? covale8 A ND2 ASN 332 A ASN 332 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale9 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? metalc ? metalc1 A O ASP 110 A ASP 110 1_555 C CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc2 A OD1 ASP 110 A ASP 110 1_555 C CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc3 A O THR 184 A THR 184 1_555 C CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc4 A OG1 THR 184 A THR 184 1_555 C CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc5 A O PHE 186 A PHE 186 1_555 C CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc6 A OD1 ASP 188 A ASP 188 1_555 C CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc7 A OG SER 190 A SER 190 1_555 C CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc8 A NE2 HIS 351 A HIS 351 1_555 D FE HEM . A HEM 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc9 D FE HEM . A HEM 605 1_555 X O HOH . A HOH 753 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? # _chem_comp.formula 'I -1' _chem_comp.formula_weight 126.904 _chem_comp.id IOD _chem_comp.mon_nstd_flag . _chem_comp.name 'IODIDE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3R5O _atom_sites.fract_transf_matrix[1][1] 0.018516 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004268 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012493 _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] 0.013561 _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 3 CA A 1 606 606 CA CA . D 4 HEM A 1 605 605 HEM HEM . E 5 NAG A 1 596 596 NAG NAG . F 5 NAG A 1 599 599 NAG NAG . G 5 NAG A 1 604 604 NAG NAG . H 6 IOD A 1 607 607 IOD IOD . I 6 IOD A 1 608 608 IOD IOD . J 6 IOD A 1 609 609 IOD IOD . K 6 IOD A 1 611 611 IOD IOD . L 6 IOD A 1 612 612 IOD IOD . M 6 IOD A 1 614 614 IOD IOD . N 6 IOD A 1 621 621 IOD IOD . O 6 IOD A 1 622 622 IOD IOD . P 6 IOD A 1 623 623 IOD IOD . Q 6 IOD A 1 624 624 IOD IOD . R 7 EUG A 1 597 1 EUG EUG . S 8 MPD A 1 598 1 MPD MPD . T 9 SCN A 1 700 700 SCN SCN . U 10 EDO A 1 600 1 EDO EDO . V 10 EDO A 1 603 2 EDO EDO . W 11 GOL A 1 610 1 GOL GOL . X 12 HOH A 1 613 2 HOH HOH . X 12 HOH A 2 615 3 HOH HOH . X 12 HOH A 3 616 4 HOH HOH . X 12 HOH A 4 617 6 HOH HOH . X 12 HOH A 5 618 7 HOH HOH . X 12 HOH A 6 619 8 HOH HOH . X 12 HOH A 7 620 9 HOH HOH . X 12 HOH A 8 625 10 HOH HOH . X 12 HOH A 9 626 11 HOH HOH . X 12 HOH A 10 627 12 HOH HOH . X 12 HOH A 11 628 13 HOH HOH . X 12 HOH A 12 629 14 HOH HOH . X 12 HOH A 13 630 15 HOH HOH . X 12 HOH A 14 631 18 HOH HOH . X 12 HOH A 15 632 19 HOH HOH . X 12 HOH A 16 633 20 HOH HOH . X 12 HOH A 17 634 21 HOH HOH . X 12 HOH A 18 635 22 HOH HOH . X 12 HOH A 19 636 24 HOH HOH . X 12 HOH A 20 637 25 HOH HOH . X 12 HOH A 21 638 26 HOH HOH . X 12 HOH A 22 639 29 HOH HOH . X 12 HOH A 23 640 30 HOH HOH . X 12 HOH A 24 641 31 HOH HOH . X 12 HOH A 25 642 32 HOH HOH . X 12 HOH A 26 643 33 HOH HOH . X 12 HOH A 27 644 34 HOH HOH . X 12 HOH A 28 645 35 HOH HOH . X 12 HOH A 29 646 36 HOH HOH . X 12 HOH A 30 647 37 HOH HOH . X 12 HOH A 31 648 38 HOH HOH . X 12 HOH A 32 649 39 HOH HOH . X 12 HOH A 33 650 40 HOH HOH . X 12 HOH A 34 651 41 HOH HOH . X 12 HOH A 35 652 43 HOH HOH . X 12 HOH A 36 653 44 HOH HOH . X 12 HOH A 37 654 45 HOH HOH . X 12 HOH A 38 655 46 HOH HOH . X 12 HOH A 39 656 47 HOH HOH . X 12 HOH A 40 657 50 HOH HOH . X 12 HOH A 41 658 51 HOH HOH . X 12 HOH A 42 659 52 HOH HOH . X 12 HOH A 43 660 53 HOH HOH . X 12 HOH A 44 661 54 HOH HOH . X 12 HOH A 45 662 56 HOH HOH . X 12 HOH A 46 663 57 HOH HOH . X 12 HOH A 47 664 58 HOH HOH . X 12 HOH A 48 665 59 HOH HOH . X 12 HOH A 49 666 61 HOH HOH . X 12 HOH A 50 667 63 HOH HOH . X 12 HOH A 51 668 66 HOH HOH . X 12 HOH A 52 669 69 HOH HOH . X 12 HOH A 53 670 70 HOH HOH . X 12 HOH A 54 671 71 HOH HOH . X 12 HOH A 55 672 72 HOH HOH . X 12 HOH A 56 673 74 HOH HOH . X 12 HOH A 57 674 76 HOH HOH . X 12 HOH A 58 675 77 HOH HOH . X 12 HOH A 59 676 80 HOH HOH . X 12 HOH A 60 677 83 HOH HOH . X 12 HOH A 61 678 84 HOH HOH . X 12 HOH A 62 679 88 HOH HOH . X 12 HOH A 63 680 89 HOH HOH . X 12 HOH A 64 681 92 HOH HOH . X 12 HOH A 65 682 93 HOH HOH . X 12 HOH A 66 683 94 HOH HOH . X 12 HOH A 67 684 95 HOH HOH . X 12 HOH A 68 685 97 HOH HOH . X 12 HOH A 69 686 98 HOH HOH . X 12 HOH A 70 687 99 HOH HOH . X 12 HOH A 71 688 101 HOH HOH . X 12 HOH A 72 689 103 HOH HOH . X 12 HOH A 73 690 106 HOH HOH . X 12 HOH A 74 691 107 HOH HOH . X 12 HOH A 75 692 108 HOH HOH . X 12 HOH A 76 693 109 HOH HOH . X 12 HOH A 77 694 110 HOH HOH . X 12 HOH A 78 695 111 HOH HOH . X 12 HOH A 79 696 112 HOH HOH . X 12 HOH A 80 697 113 HOH HOH . X 12 HOH A 81 698 114 HOH HOH . X 12 HOH A 82 699 115 HOH HOH . X 12 HOH A 83 701 116 HOH HOH . X 12 HOH A 84 702 117 HOH HOH . X 12 HOH A 85 703 119 HOH HOH . X 12 HOH A 86 704 120 HOH HOH . X 12 HOH A 87 705 122 HOH HOH . X 12 HOH A 88 706 126 HOH HOH . X 12 HOH A 89 707 128 HOH HOH . X 12 HOH A 90 708 129 HOH HOH . X 12 HOH A 91 709 131 HOH HOH . X 12 HOH A 92 710 134 HOH HOH . X 12 HOH A 93 711 135 HOH HOH . X 12 HOH A 94 712 136 HOH HOH . X 12 HOH A 95 713 140 HOH HOH . X 12 HOH A 96 714 141 HOH HOH . X 12 HOH A 97 715 142 HOH HOH . X 12 HOH A 98 716 143 HOH HOH . X 12 HOH A 99 717 144 HOH HOH . X 12 HOH A 100 718 145 HOH HOH . X 12 HOH A 101 719 158 HOH HOH . X 12 HOH A 102 720 159 HOH HOH . X 12 HOH A 103 721 160 HOH HOH . X 12 HOH A 104 722 163 HOH HOH . X 12 HOH A 105 723 164 HOH HOH . X 12 HOH A 106 724 165 HOH HOH . X 12 HOH A 107 725 168 HOH HOH . X 12 HOH A 108 726 169 HOH HOH . X 12 HOH A 109 727 170 HOH HOH . X 12 HOH A 110 728 171 HOH HOH . X 12 HOH A 111 729 174 HOH HOH . X 12 HOH A 112 730 175 HOH HOH . X 12 HOH A 113 731 176 HOH HOH . X 12 HOH A 114 732 177 HOH HOH . X 12 HOH A 115 733 178 HOH HOH . X 12 HOH A 116 734 179 HOH HOH . X 12 HOH A 117 735 180 HOH HOH . X 12 HOH A 118 736 182 HOH HOH . X 12 HOH A 119 737 184 HOH HOH . X 12 HOH A 120 738 185 HOH HOH . X 12 HOH A 121 739 186 HOH HOH . X 12 HOH A 122 740 187 HOH HOH . X 12 HOH A 123 741 188 HOH HOH . X 12 HOH A 124 742 189 HOH HOH . X 12 HOH A 125 743 190 HOH HOH . X 12 HOH A 126 744 191 HOH HOH . X 12 HOH A 127 745 192 HOH HOH . X 12 HOH A 128 746 193 HOH HOH . X 12 HOH A 129 747 194 HOH HOH . X 12 HOH A 130 748 195 HOH HOH . X 12 HOH A 131 749 196 HOH HOH . X 12 HOH A 132 750 197 HOH HOH . X 12 HOH A 133 751 198 HOH HOH . X 12 HOH A 134 752 199 HOH HOH . X 12 HOH A 135 753 200 HOH HOH . X 12 HOH A 136 754 201 HOH HOH . X 12 HOH A 137 755 202 HOH HOH . X 12 HOH A 138 756 204 HOH HOH . X 12 HOH A 139 757 205 HOH HOH . X 12 HOH A 140 758 206 HOH HOH . X 12 HOH A 141 759 207 HOH HOH . X 12 HOH A 142 760 208 HOH HOH . X 12 HOH A 143 761 209 HOH HOH . X 12 HOH A 144 762 211 HOH HOH . X 12 HOH A 145 763 218 HOH HOH . X 12 HOH A 146 764 219 HOH HOH . X 12 HOH A 147 765 221 HOH HOH . X 12 HOH A 148 766 222 HOH HOH . X 12 HOH A 149 767 225 HOH HOH . X 12 HOH A 150 768 226 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol I _atom_site.label_atom_id I _atom_site.label_comp_id IOD _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id H _atom_site.label_entity_id 6 _atom_site.Cartn_x -15.212 _atom_site.Cartn_y -15.97 _atom_site.Cartn_z 28.812 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 56.26 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id I _atom_site.auth_comp_id IOD _atom_site.auth_seq_id 607 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #