data_4ZIB # _model_server_result.job_id J5lB9GTg2PmNTGJViZUVVw _model_server_result.datetime_utc '2025-01-11 16:00:21' _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 4zib # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":512}' # _entry.id 4ZIB # _exptl.entry_id 4ZIB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.276 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(1-benzothiophen-3-yl)-L-alanine _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 120 _cell.entry_id 4ZIB _cell.length_a 105.14 _cell.length_b 105.14 _cell.length_c 70.92 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZIB _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 52.57 91.053911 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id M _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OE2 GLU 233 A GLU 396 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc2 A OE1 GLU 233 A GLU 396 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc3 A OG SER 236 A SER 399 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc4 B MG MG . A MG 501 1_555 E O2G ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc5 B MG MG . A MG 501 1_555 E O2B ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc6 B MG MG . A MG 501 1_555 N O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc7 B MG MG . A MG 501 1_555 N O HOH . A HOH 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc8 B MG MG . A MG 501 1_555 N O HOH . A HOH 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc9 B MG MG . A MG 501 1_555 N O HOH . A HOH 693 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc10 C MG MG . A MG 502 1_555 E O1A ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc11 C MG MG . A MG 502 1_555 E O1B ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc12 C MG MG . A MG 502 1_555 N O HOH . A HOH 686 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc13 C MG MG . A MG 502 1_555 N O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc14 D MG MG . A MG 503 1_555 E O3G ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc15 D MG MG . A MG 503 1_555 E O1B ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc16 D MG MG . A MG 503 1_555 N O HOH . A HOH 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc17 D MG MG . A MG 503 1_555 N O HOH . A HOH 686 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc18 D MG MG . A MG 503 1_555 N O HOH . A HOH 726 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? # _chem_comp.formula 'C11 H11 N O2 S' _chem_comp.formula_weight 221.276 _chem_comp.id 4OG _chem_comp.mon_nstd_flag n _chem_comp.name 3-(1-benzothiophen-3-yl)-L-alanine _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 C6 C7 4OG sing 1 n y C6 C5 4OG doub 2 n y C7 C4 4OG doub 3 n y C5 C8 4OG sing 4 n y C4 S3 4OG sing 5 n y C4 C9 4OG sing 6 n y S3 C2 4OG sing 7 n y C8 C9 4OG doub 8 n y C9 C1 4OG sing 9 n y C2 C1 4OG doub 10 n y C1 CB 4OG sing 11 n n CB CA 4OG sing 12 n n O C 4OG doub 13 n n CA C 4OG sing 14 n n CA N 4OG sing 15 n n C OXT 4OG sing 16 n n C5 H1 4OG sing 17 n n C6 H5 4OG sing 18 n n C7 H3 4OG sing 19 n n C8 H4 4OG sing 20 n n N H 4OG sing 21 n n N H2 4OG sing 22 n n CA HA 4OG sing 23 n n CB H9 4OG sing 24 n n CB H10 4OG sing 25 n n C2 H11 4OG sing 26 n n OXT HXT 4OG sing 27 n n # _atom_sites.entry_id 4ZIB _atom_sites.fract_transf_matrix[1][1] 0.009511 _atom_sites.fract_transf_matrix[1][2] 0.005491 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010983 _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] 0.0141 _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 MG A 1 501 501 MG MG . C 2 MG A 1 502 502 MG MG . D 2 MG A 1 503 503 MG MG . E 3 ATP A 1 504 504 ATP ATP . F 4 EDO A 1 505 505 EDO EDO . G 4 EDO A 1 506 506 EDO EDO . H 4 EDO A 1 507 507 EDO EDO . I 4 EDO A 1 508 508 EDO EDO . J 4 EDO A 1 509 509 EDO EDO . K 4 EDO A 1 510 510 EDO EDO . L 4 EDO A 1 511 511 EDO EDO . M 5 4OG A 1 512 512 4OG 4OG . N 6 HOH A 1 601 603 HOH HOH . N 6 HOH A 2 602 602 HOH HOH . N 6 HOH A 3 603 604 HOH HOH . N 6 HOH A 4 604 606 HOH HOH . N 6 HOH A 5 605 608 HOH HOH . N 6 HOH A 6 606 601 HOH HOH . N 6 HOH A 7 607 607 HOH HOH . N 6 HOH A 8 608 615 HOH HOH . N 6 HOH A 9 609 610 HOH HOH . N 6 HOH A 10 610 616 HOH HOH . N 6 HOH A 11 611 618 HOH HOH . N 6 HOH A 12 612 620 HOH HOH . N 6 HOH A 13 613 626 HOH HOH . N 6 HOH A 14 614 609 HOH HOH . N 6 HOH A 15 615 614 HOH HOH . N 6 HOH A 16 616 613 HOH HOH . N 6 HOH A 17 617 605 HOH HOH . N 6 HOH A 18 618 617 HOH HOH . N 6 HOH A 19 619 612 HOH HOH . N 6 HOH A 20 620 621 HOH HOH . N 6 HOH A 21 621 640 HOH HOH . N 6 HOH A 22 622 633 HOH HOH . N 6 HOH A 23 623 629 HOH HOH . N 6 HOH A 24 624 641 HOH HOH . N 6 HOH A 25 625 632 HOH HOH . N 6 HOH A 26 626 634 HOH HOH . N 6 HOH A 27 627 636 HOH HOH . N 6 HOH A 28 628 619 HOH HOH . N 6 HOH A 29 629 651 HOH HOH . N 6 HOH A 30 630 644 HOH HOH . N 6 HOH A 31 631 665 HOH HOH . N 6 HOH A 32 632 623 HOH HOH . N 6 HOH A 33 633 625 HOH HOH . N 6 HOH A 34 634 638 HOH HOH . N 6 HOH A 35 635 628 HOH HOH . N 6 HOH A 36 636 631 HOH HOH . N 6 HOH A 37 637 639 HOH HOH . N 6 HOH A 38 638 611 HOH HOH . N 6 HOH A 39 639 652 HOH HOH . N 6 HOH A 40 640 661 HOH HOH . N 6 HOH A 41 641 646 HOH HOH . N 6 HOH A 42 642 630 HOH HOH . N 6 HOH A 43 643 685 HOH HOH . N 6 HOH A 44 644 624 HOH HOH . N 6 HOH A 45 645 655 HOH HOH . N 6 HOH A 46 646 645 HOH HOH . N 6 HOH A 47 647 649 HOH HOH . N 6 HOH A 48 648 643 HOH HOH . N 6 HOH A 49 649 622 HOH HOH . N 6 HOH A 50 650 642 HOH HOH . N 6 HOH A 51 651 635 HOH HOH . N 6 HOH A 52 652 627 HOH HOH . N 6 HOH A 53 653 650 HOH HOH . N 6 HOH A 54 654 654 HOH HOH . N 6 HOH A 55 655 647 HOH HOH . N 6 HOH A 56 656 668 HOH HOH . N 6 HOH A 57 657 690 HOH HOH . N 6 HOH A 58 658 667 HOH HOH . N 6 HOH A 59 659 660 HOH HOH . N 6 HOH A 60 660 672 HOH HOH . N 6 HOH A 61 661 657 HOH HOH . N 6 HOH A 62 662 658 HOH HOH . N 6 HOH A 63 663 681 HOH HOH . N 6 HOH A 64 664 678 HOH HOH . N 6 HOH A 65 665 662 HOH HOH . N 6 HOH A 66 666 671 HOH HOH . N 6 HOH A 67 667 674 HOH HOH . N 6 HOH A 68 668 637 HOH HOH . N 6 HOH A 69 669 679 HOH HOH . N 6 HOH A 70 670 659 HOH HOH . N 6 HOH A 71 671 648 HOH HOH . N 6 HOH A 72 672 653 HOH HOH . N 6 HOH A 73 673 656 HOH HOH . N 6 HOH A 74 674 673 HOH HOH . N 6 HOH A 75 675 663 HOH HOH . N 6 HOH A 76 676 670 HOH HOH . N 6 HOH A 77 677 664 HOH HOH . N 6 HOH A 78 678 666 HOH HOH . N 6 HOH A 79 679 683 HOH HOH . N 6 HOH A 80 680 669 HOH HOH . N 6 HOH A 81 681 677 HOH HOH . N 6 HOH A 82 682 695 HOH HOH . N 6 HOH A 83 683 675 HOH HOH . N 6 HOH A 84 684 682 HOH HOH . N 6 HOH A 85 685 702 HOH HOH . N 6 HOH A 86 686 688 HOH HOH . N 6 HOH A 87 687 701 HOH HOH . N 6 HOH A 88 688 698 HOH HOH . N 6 HOH A 89 689 704 HOH HOH . N 6 HOH A 90 690 691 HOH HOH . N 6 HOH A 91 691 684 HOH HOH . N 6 HOH A 92 692 686 HOH HOH . N 6 HOH A 93 693 689 HOH HOH . N 6 HOH A 94 694 693 HOH HOH . N 6 HOH A 95 695 694 HOH HOH . N 6 HOH A 96 696 676 HOH HOH . N 6 HOH A 97 697 699 HOH HOH . N 6 HOH A 98 698 696 HOH HOH . N 6 HOH A 99 699 687 HOH HOH . N 6 HOH A 100 700 692 HOH HOH . N 6 HOH A 101 701 706 HOH HOH . N 6 HOH A 102 702 697 HOH HOH . N 6 HOH A 103 703 680 HOH HOH . N 6 HOH A 104 704 700 HOH HOH . N 6 HOH A 105 705 707 HOH HOH . N 6 HOH A 106 706 703 HOH HOH . N 6 HOH A 107 707 705 HOH HOH . N 6 HOH A 108 708 710 HOH HOH . N 6 HOH A 109 709 711 HOH HOH . N 6 HOH A 110 710 708 HOH HOH . N 6 HOH A 111 711 715 HOH HOH . N 6 HOH A 112 712 709 HOH HOH . N 6 HOH A 113 713 712 HOH HOH . N 6 HOH A 114 714 717 HOH HOH . N 6 HOH A 115 715 713 HOH HOH . N 6 HOH A 116 716 714 HOH HOH . N 6 HOH A 117 717 720 HOH HOH . N 6 HOH A 118 718 719 HOH HOH . N 6 HOH A 119 719 722 HOH HOH . N 6 HOH A 120 720 725 HOH HOH . N 6 HOH A 121 721 721 HOH HOH . N 6 HOH A 122 722 718 HOH HOH . N 6 HOH A 123 723 727 HOH HOH . N 6 HOH A 124 724 723 HOH HOH . N 6 HOH A 125 725 726 HOH HOH . N 6 HOH A 126 726 724 HOH HOH . N 6 HOH A 127 727 728 HOH HOH . N 6 HOH A 128 728 729 HOH HOH . N 6 HOH A 129 729 735 HOH HOH . N 6 HOH A 130 730 716 HOH HOH . N 6 HOH A 131 731 730 HOH HOH . N 6 HOH A 132 732 732 HOH HOH . N 6 HOH A 133 733 734 HOH HOH . N 6 HOH A 134 734 733 HOH HOH . N 6 HOH A 135 735 731 HOH HOH . N 6 HOH A 136 736 736 HOH HOH . N 6 HOH A 137 737 737 HOH HOH . N 6 HOH A 138 738 738 HOH HOH . N 6 HOH A 139 739 739 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 C4 4OG . . . M 5 7.869 46.563 30.375 1 63.37 ? C4 4OG 512 A 1 HETATM 2 C C5 4OG . . . M 5 10.415 47.596 30.086 1 48.25 ? C5 4OG 512 A 1 HETATM 3 C C6 4OG . . . M 5 9.333 48.271 29.553 1 54.37 ? C6 4OG 512 A 1 HETATM 4 C C7 4OG . . . M 5 8.054 47.762 29.691 1 55.6 ? C7 4OG 512 A 1 HETATM 5 C C8 4OG . . . M 5 10.235 46.402 30.767 1 49.62 ? C8 4OG 512 A 1 HETATM 6 C C9 4OG . . . M 5 8.962 45.857 30.929 1 56.12 ? C9 4OG 512 A 1 HETATM 7 N N 4OG . . . M 5 8.546 44.172 34.535 1 57.63 ? N 4OG 512 A 1 HETATM 8 C CA 4OG . . . M 5 9.761 43.988 33.694 1 51.07 ? CA 4OG 512 A 1 HETATM 9 C CB 4OG . . . M 5 9.379 43.638 32.252 1 51.54 ? CB 4OG 512 A 1 HETATM 10 C C1 4OG . . . M 5 8.502 44.649 31.573 1 57.71 ? C1 4OG 512 A 1 HETATM 11 C C2 4OG . . . M 5 7.18 44.478 31.505 1 51.53 ? C2 4OG 512 A 1 HETATM 12 S S3 4OG . . . M 5 6.372 45.737 30.66 1 60.47 ? S3 4OG 512 A 1 HETATM 13 C C 4OG . . . M 5 10.633 45.248 33.768 1 67.47 ? C 4OG 512 A 1 HETATM 14 O O 4OG . . . M 5 11.762 45.207 33.226 1 52.86 ? O 4OG 512 A 1 HETATM 15 O OXT 4OG . . . M 5 10.155 46.231 34.376 1 62.02 ? OXT 4OG 512 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 15 #