data_1IJ8 # _model_server_result.job_id 0qbakCJTEoDX3v0BI-odMA _model_server_result.datetime_utc '2024-11-05 04:56:18' _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 1ij8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 1IJ8 # _exptl.entry_id 1IJ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 364.419 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE' _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 90 _cell.angle_gamma 90 _cell.entry_id 1IJ8 _cell.length_a 72.269 _cell.length_b 80.362 _cell.length_c 43.402 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1IJ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 80.362 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 4 A CYS 4 1_555 A SG CYS 83 A CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf2 B SG CYS 4 B CYS 204 1_555 B SG CYS 83 B CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 A ND2 ASN 17 A ASN 17 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 B ND2 ASN 17 B ASN 217 1_555 E C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _chem_comp.formula 'C16 H20 N4 O4 S' _chem_comp.formula_weight 364.419 _chem_comp.id BNI _chem_comp.mon_nstd_flag . _chem_comp.name '5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'BIOTINYL P-NITROANILINE' # 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 C10 BNI sing 70 n n C1 O2 BNI doub 71 n n C1 N17 BNI sing 72 n n C10 C9 BNI sing 73 n n C10 H101 BNI sing 74 n n C10 H102 BNI sing 75 n n C9 C8 BNI sing 76 n n C9 H91 BNI sing 77 n n C9 H92 BNI sing 78 n n C8 C7 BNI sing 79 n n C8 H81 BNI sing 80 n n C8 H82 BNI sing 81 n n C7 C2 BNI sing 82 n n C7 H71 BNI sing 83 n n C7 H72 BNI sing 84 n n C2 C4 BNI sing 85 n n C2 S1 BNI sing 86 n n C2 H21A BNI sing 87 n n C6 C5 BNI sing 88 n n C6 S1 BNI sing 89 n n C6 H61 BNI sing 90 n n C6 H62 BNI sing 91 n n C4 C5 BNI sing 92 n n C4 N2 BNI sing 93 n n C4 HC4 BNI sing 94 n n C5 N1 BNI sing 95 n n C5 HC5 BNI sing 96 n n C3 O3 BNI doub 97 n n C3 N1 BNI sing 98 n n C3 N2 BNI sing 99 n n N1 HN11 BNI sing 100 n n N2 HN21 BNI sing 101 n n N17 C18 BNI sing 102 n n N17 H171 BNI sing 103 n n C18 C20 BNI doub 104 n y C18 C24 BNI sing 105 n y C20 C21 BNI sing 106 n y C20 H20 BNI sing 107 n n C21 C22 BNI doub 108 n y C21 H21 BNI sing 109 n n C22 C23 BNI sing 110 n y C22 N25 BNI sing 111 n n C23 C24 BNI doub 112 n y C23 H23 BNI sing 113 n n C24 H24 BNI sing 114 n n N25 O26 BNI doub 115 n n N25 O27 BNI sing 116 n n # _atom_sites.entry_id 1IJ8 _atom_sites.fract_transf_matrix[1][1] 0.013837 _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] 0.012444 _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] 0.02304 _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 2 NAG A 1 401 401 NAG NAG . D 3 BNI A 1 501 501 BNI BNI . E 2 NAG B 1 402 402 NAG NAG . F 3 BNI B 1 502 502 BNI BNI . G 4 HOH A 1 601 601 HOH HOH . G 4 HOH A 2 602 602 HOH HOH . G 4 HOH A 3 604 604 HOH HOH . G 4 HOH A 4 606 606 HOH HOH . G 4 HOH A 5 613 613 HOH HOH . G 4 HOH A 6 614 614 HOH HOH . G 4 HOH A 7 615 615 HOH HOH . G 4 HOH A 8 622 622 HOH HOH . G 4 HOH A 9 623 623 HOH HOH . G 4 HOH A 10 625 625 HOH HOH . G 4 HOH A 11 627 627 HOH HOH . G 4 HOH A 12 628 628 HOH HOH . G 4 HOH A 13 630 630 HOH HOH . G 4 HOH A 14 631 631 HOH HOH . G 4 HOH A 15 632 632 HOH HOH . G 4 HOH A 16 635 635 HOH HOH . G 4 HOH A 17 636 636 HOH HOH . G 4 HOH A 18 638 638 HOH HOH . G 4 HOH A 19 639 639 HOH HOH . G 4 HOH A 20 641 641 HOH HOH . G 4 HOH A 21 644 644 HOH HOH . G 4 HOH A 22 645 645 HOH HOH . G 4 HOH A 23 646 646 HOH HOH . G 4 HOH A 24 648 648 HOH HOH . G 4 HOH A 25 654 654 HOH HOH . G 4 HOH A 26 655 655 HOH HOH . G 4 HOH A 27 656 656 HOH HOH . G 4 HOH A 28 659 659 HOH HOH . G 4 HOH A 29 661 661 HOH HOH . G 4 HOH A 30 662 662 HOH HOH . G 4 HOH A 31 665 665 HOH HOH . G 4 HOH A 32 668 668 HOH HOH . G 4 HOH A 33 670 670 HOH HOH . G 4 HOH A 34 673 673 HOH HOH . G 4 HOH A 35 675 675 HOH HOH . G 4 HOH A 36 676 676 HOH HOH . G 4 HOH A 37 677 677 HOH HOH . G 4 HOH A 38 680 680 HOH HOH . G 4 HOH A 39 682 682 HOH HOH . H 4 HOH B 1 603 603 HOH HOH . H 4 HOH B 2 605 605 HOH HOH . H 4 HOH B 3 607 607 HOH HOH . H 4 HOH B 4 608 608 HOH HOH . H 4 HOH B 5 609 609 HOH HOH . H 4 HOH B 6 610 610 HOH HOH . H 4 HOH B 7 611 611 HOH HOH . H 4 HOH B 8 612 612 HOH HOH . H 4 HOH B 9 616 616 HOH HOH . H 4 HOH B 10 617 617 HOH HOH . H 4 HOH B 11 618 618 HOH HOH . H 4 HOH B 12 619 619 HOH HOH . H 4 HOH B 13 620 620 HOH HOH . H 4 HOH B 14 621 621 HOH HOH . H 4 HOH B 15 624 624 HOH HOH . H 4 HOH B 16 626 626 HOH HOH . H 4 HOH B 17 629 629 HOH HOH . H 4 HOH B 18 633 633 HOH HOH . H 4 HOH B 19 634 634 HOH HOH . H 4 HOH B 20 637 637 HOH HOH . H 4 HOH B 21 640 640 HOH HOH . H 4 HOH B 22 642 642 HOH HOH . H 4 HOH B 23 643 643 HOH HOH . H 4 HOH B 24 647 647 HOH HOH . H 4 HOH B 25 649 649 HOH HOH . H 4 HOH B 26 650 650 HOH HOH . H 4 HOH B 27 651 651 HOH HOH . H 4 HOH B 28 652 652 HOH HOH . H 4 HOH B 29 653 653 HOH HOH . H 4 HOH B 30 657 657 HOH HOH . H 4 HOH B 31 658 658 HOH HOH . H 4 HOH B 32 660 660 HOH HOH . H 4 HOH B 33 663 663 HOH HOH . H 4 HOH B 34 664 664 HOH HOH . H 4 HOH B 35 666 666 HOH HOH . H 4 HOH B 36 667 667 HOH HOH . H 4 HOH B 37 669 669 HOH HOH . H 4 HOH B 38 671 671 HOH HOH . H 4 HOH B 39 672 672 HOH HOH . H 4 HOH B 40 674 674 HOH HOH . H 4 HOH B 41 678 678 HOH HOH . H 4 HOH B 42 679 679 HOH HOH . H 4 HOH B 43 681 681 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 BNI . . . D 3 -4.478 31.383 28.456 0.88 50.93 ? C1 BNI 501 A 1 HETATM 2 C C10 BNI . . . D 3 -4.981 29.983 27.917 0.88 49.95 ? C10 BNI 501 A 1 HETATM 3 C C9 BNI . . . D 3 -3.632 29.297 27.638 0.88 48.73 ? C9 BNI 501 A 1 HETATM 4 C C8 BNI . . . D 3 -3.269 28.56 26.384 0.88 47.97 ? C8 BNI 501 A 1 HETATM 5 C C7 BNI . . . D 3 -2.528 29.718 25.716 0.88 46.81 ? C7 BNI 501 A 1 HETATM 6 C C2 BNI . . . D 3 -1.826 29.778 24.335 0.88 46.23 ? C2 BNI 501 A 1 HETATM 7 C C6 BNI . . . D 3 -1.27 29.824 21.778 0.88 45.56 ? C6 BNI 501 A 1 HETATM 8 C C4 BNI . . . D 3 -0.682 28.722 23.987 0.88 45.95 ? C4 BNI 501 A 1 HETATM 9 C C5 BNI . . . D 3 -0.197 28.973 22.567 0.88 45.61 ? C5 BNI 501 A 1 HETATM 10 C C3 BNI . . . D 3 -0.427 26.715 22.885 0.88 45.39 ? C3 BNI 501 A 1 HETATM 11 O O2 BNI . . . D 3 -5.318 32.192 28.778 0.88 50.99 ? O2 BNI 501 A 1 HETATM 12 O O3 BNI . . . D 3 -0.406 25.521 22.629 0.88 44.97 ? O3 BNI 501 A 1 HETATM 13 N N1 BNI . . . D 3 -0.073 27.656 21.986 0.88 45.31 ? N1 BNI 501 A 1 HETATM 14 N N2 BNI . . . D 3 -0.803 27.264 24.087 0.88 45.43 ? N2 BNI 501 A 1 HETATM 15 S S1 BNI . . . D 3 -2.819 29.648 22.86 0.88 45.55 ? S1 BNI 501 A 1 HETATM 16 N N17 BNI . . . D 3 -3.126 31.585 28.515 0.88 52.13 ? N17 BNI 501 A 1 HETATM 17 C C18 BNI . . . D 3 -2.331 32.362 29.351 0.88 53.46 ? C18 BNI 501 A 1 HETATM 18 C C20 BNI . . . D 3 -2.531 33.768 29.6 0.88 54.1 ? C20 BNI 501 A 1 HETATM 19 C C21 BNI . . . D 3 -1.622 34.471 30.498 0.88 54.97 ? C21 BNI 501 A 1 HETATM 20 C C22 BNI . . . D 3 -0.511 33.756 31.144 0.88 55.56 ? C22 BNI 501 A 1 HETATM 21 C C23 BNI . . . D 3 -0.33 32.357 30.881 0.88 54.96 ? C23 BNI 501 A 1 HETATM 22 C C24 BNI . . . D 3 -1.226 31.676 30.001 0.88 54.03 ? C24 BNI 501 A 1 HETATM 23 N N25 BNI . . . D 3 0.465 34.468 32.096 0.88 56.23 ? N25 BNI 501 A 1 HETATM 24 O O26 BNI . . . D 3 0.363 35.64 32.355 0.88 56.81 ? O26 BNI 501 A 1 HETATM 25 O O27 BNI . . . D 3 1.369 33.871 32.616 0.88 56.48 ? O27 BNI 501 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #