data_7BFB # _model_server_result.job_id v3lWRmAnqdYQmmkVW90-_A _model_server_result.datetime_utc '2024-11-21 09:28:35' _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 7bfb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1005}' # _entry.id 7BFB # _exptl.entry_id 7BFB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 276.193 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-phenyl-2-selanylbenzamide _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 90 _cell.angle_gamma 90 _cell.entry_id 7BFB _cell.length_a 67.739 _cell.length_b 100.455 _cell.length_c 104.597 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BFB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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,O,P,Q,R _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 C N N ? 2 D N N ? 2 E N N ? 2 L N N ? 2 O 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 covale ? covale1 A SG CYS 44 A CYS 44 1_555 C SE1 9JT . A 9JT 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? covale ? covale2 A SG CYS 145 A CYS 145 1_555 D SE1 9JT . A 9JT 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? covale ? covale3 A SG CYS 156 A CYS 156 1_555 E SE1 9JT . A 9JT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? covale ? covale4 B SG CYS 156 B CYS 156 1_555 L SE1 9JT . B 9JT 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc1 A O ASN 221 A ASN 221 1_555 J NA NA . A NA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc2 A OD1 ASN 221 A ASN 221 1_555 J NA NA . A NA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc3 A O PHE 223 A PHE 223 1_555 J NA NA . A NA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc4 A O ASP 263 A ASP 263 1_555 J NA NA . A NA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc5 A OD1 ASP 263 A ASP 263 1_555 J NA NA . A NA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc6 B O ASN 221 B ASN 221 1_555 P NA NA . B NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc7 B OD1 ASN 221 B ASN 221 1_555 P NA NA . B NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc8 B O PHE 223 B PHE 223 1_555 P NA NA . B NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc9 B O ASP 263 B ASP 263 1_555 P NA NA . B NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc10 B OD1 ASP 263 B ASP 263 1_555 P NA NA . B NA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc11 P NA NA . B NA 1006 1_555 R O HOH . B HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? # _chem_comp.formula 'C13 H11 N O Se' _chem_comp.formula_weight 276.193 _chem_comp.id 9JT _chem_comp.mon_nstd_flag . _chem_comp.name N-phenyl-2-selanylbenzamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '~{N}-phenyl-2-selanyl-benzamide;Ebselen, bound form' # 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 C05 C04 9JT doub 1 n y C05 C06 9JT sing 2 n y C04 C03 9JT sing 3 n y C06 C07 9JT doub 4 n y C03 C02 9JT doub 5 n y C07 C02 9JT sing 6 n y C07 C08 9JT sing 7 n n C16 C15 9JT doub 8 n y C16 C11 9JT sing 9 n y C02 SE1 9JT sing 10 n n N10 C08 9JT sing 11 n n N10 C11 9JT sing 12 n n C15 C14 9JT sing 13 n y C08 O09 9JT doub 14 n n C11 C12 9JT doub 15 n y C14 C13 9JT doub 16 n y C12 C13 9JT sing 17 n y C12 H1 9JT sing 18 n n C13 H2 9JT sing 19 n n C14 H3 9JT sing 20 n n C15 H4 9JT sing 21 n n C06 H5 9JT sing 22 n n C05 H6 9JT sing 23 n n C04 H7 9JT sing 24 n n C03 H8 9JT sing 25 n n SE1 H9 9JT sing 26 n n N10 H10 9JT sing 27 n n C16 H11 9JT sing 28 n n # _atom_sites.entry_id 7BFB _atom_sites.fract_transf_matrix[1][1] 0.014763 _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] 0.009955 _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] 0.009561 _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 9JT A 1 401 401 9JT 9JT . D 2 9JT A 1 402 501 9JT 9JT . E 2 9JT A 1 403 601 9JT 9JT . F 3 EDO A 1 404 701 EDO EDO . G 3 EDO A 1 405 801 EDO EDO . H 3 EDO A 1 406 901 EDO EDO . I 3 EDO A 1 407 1101 EDO EDO . J 4 NA A 1 408 2 NA NA . K 3 EDO B 1 1001 1001 EDO EDO . L 2 9JT B 1 1002 401 9JT 9JT . M 3 EDO B 1 1003 501 EDO EDO . N 3 EDO B 1 1004 601 EDO EDO . O 2 9JT B 1 1005 701 9JT 9JT . P 4 NA B 1 1006 1 NA NA . Q 5 HOH A 1 501 90 HOH HOH . Q 5 HOH A 2 502 60 HOH HOH . Q 5 HOH A 3 503 44 HOH HOH . Q 5 HOH A 4 504 69 HOH HOH . Q 5 HOH A 5 505 92 HOH HOH . Q 5 HOH A 6 506 37 HOH HOH . Q 5 HOH A 7 507 74 HOH HOH . Q 5 HOH A 8 508 32 HOH HOH . Q 5 HOH A 9 509 110 HOH HOH . Q 5 HOH A 10 510 78 HOH HOH . Q 5 HOH A 11 511 116 HOH HOH . Q 5 HOH A 12 512 41 HOH HOH . Q 5 HOH A 13 513 23 HOH HOH . Q 5 HOH A 14 514 52 HOH HOH . Q 5 HOH A 15 515 11 HOH HOH . Q 5 HOH A 16 516 18 HOH HOH . Q 5 HOH A 17 517 46 HOH HOH . Q 5 HOH A 18 518 77 HOH HOH . Q 5 HOH A 19 519 30 HOH HOH . Q 5 HOH A 20 520 57 HOH HOH . Q 5 HOH A 21 521 31 HOH HOH . Q 5 HOH A 22 522 19 HOH HOH . Q 5 HOH A 23 523 88 HOH HOH . Q 5 HOH A 24 524 51 HOH HOH . Q 5 HOH A 25 525 36 HOH HOH . Q 5 HOH A 26 526 80 HOH HOH . Q 5 HOH A 27 527 6 HOH HOH . Q 5 HOH A 28 528 33 HOH HOH . Q 5 HOH A 29 529 149 HOH HOH . Q 5 HOH A 30 530 106 HOH HOH . Q 5 HOH A 31 531 40 HOH HOH . Q 5 HOH A 32 532 71 HOH HOH . Q 5 HOH A 33 533 76 HOH HOH . Q 5 HOH A 34 534 113 HOH HOH . Q 5 HOH A 35 535 65 HOH HOH . Q 5 HOH A 36 536 66 HOH HOH . Q 5 HOH A 37 537 58 HOH HOH . Q 5 HOH A 38 538 38 HOH HOH . Q 5 HOH A 39 539 14 HOH HOH . Q 5 HOH A 40 540 61 HOH HOH . Q 5 HOH A 41 541 70 HOH HOH . Q 5 HOH A 42 542 50 HOH HOH . Q 5 HOH A 43 543 93 HOH HOH . Q 5 HOH A 44 544 7 HOH HOH . Q 5 HOH A 45 545 99 HOH HOH . Q 5 HOH A 46 546 100 HOH HOH . Q 5 HOH A 47 547 75 HOH HOH . Q 5 HOH A 48 548 139 HOH HOH . Q 5 HOH A 49 549 39 HOH HOH . Q 5 HOH A 50 550 42 HOH HOH . Q 5 HOH A 51 551 63 HOH HOH . Q 5 HOH A 52 552 67 HOH HOH . Q 5 HOH A 53 553 26 HOH HOH . Q 5 HOH A 54 554 62 HOH HOH . Q 5 HOH A 55 555 24 HOH HOH . Q 5 HOH A 56 556 64 HOH HOH . Q 5 HOH A 57 557 126 HOH HOH . Q 5 HOH A 58 558 83 HOH HOH . Q 5 HOH A 59 559 133 HOH HOH . Q 5 HOH A 60 560 54 HOH HOH . Q 5 HOH A 61 561 47 HOH HOH . Q 5 HOH A 62 562 98 HOH HOH . Q 5 HOH A 63 563 122 HOH HOH . Q 5 HOH A 64 564 101 HOH HOH . Q 5 HOH A 65 565 84 HOH HOH . Q 5 HOH A 66 566 142 HOH HOH . Q 5 HOH A 67 567 141 HOH HOH . Q 5 HOH A 68 568 43 HOH HOH . Q 5 HOH A 69 569 102 HOH HOH . Q 5 HOH A 70 570 140 HOH HOH . Q 5 HOH A 71 571 129 HOH HOH . Q 5 HOH A 72 572 107 HOH HOH . Q 5 HOH A 73 573 148 HOH HOH . Q 5 HOH A 74 574 143 HOH HOH . Q 5 HOH A 75 575 79 HOH HOH . Q 5 HOH A 76 576 132 HOH HOH . Q 5 HOH A 77 577 123 HOH HOH . Q 5 HOH A 78 578 120 HOH HOH . Q 5 HOH A 79 579 86 HOH HOH . Q 5 HOH A 80 580 97 HOH HOH . Q 5 HOH A 81 581 146 HOH HOH . Q 5 HOH A 82 582 68 HOH HOH . Q 5 HOH A 83 583 111 HOH HOH . R 5 HOH B 1 1101 35 HOH HOH . R 5 HOH B 2 1102 15 HOH HOH . R 5 HOH B 3 1103 10 HOH HOH . R 5 HOH B 4 1104 20 HOH HOH . R 5 HOH B 5 1105 109 HOH HOH . R 5 HOH B 6 1106 124 HOH HOH . R 5 HOH B 7 1107 16 HOH HOH . R 5 HOH B 8 1108 34 HOH HOH . R 5 HOH B 9 1109 73 HOH HOH . R 5 HOH B 10 1110 13 HOH HOH . R 5 HOH B 11 1111 27 HOH HOH . R 5 HOH B 12 1112 115 HOH HOH . R 5 HOH B 13 1113 9 HOH HOH . R 5 HOH B 14 1114 48 HOH HOH . R 5 HOH B 15 1115 4 HOH HOH . R 5 HOH B 16 1116 2 HOH HOH . R 5 HOH B 17 1117 55 HOH HOH . R 5 HOH B 18 1118 91 HOH HOH . R 5 HOH B 19 1119 96 HOH HOH . R 5 HOH B 20 1120 89 HOH HOH . R 5 HOH B 21 1121 59 HOH HOH . R 5 HOH B 22 1122 72 HOH HOH . R 5 HOH B 23 1123 5 HOH HOH . R 5 HOH B 24 1124 87 HOH HOH . R 5 HOH B 25 1125 81 HOH HOH . R 5 HOH B 26 1126 94 HOH HOH . R 5 HOH B 27 1127 21 HOH HOH . R 5 HOH B 28 1128 56 HOH HOH . R 5 HOH B 29 1129 22 HOH HOH . R 5 HOH B 30 1130 17 HOH HOH . R 5 HOH B 31 1131 118 HOH HOH . R 5 HOH B 32 1132 53 HOH HOH . R 5 HOH B 33 1133 29 HOH HOH . R 5 HOH B 34 1134 95 HOH HOH . R 5 HOH B 35 1135 131 HOH HOH . R 5 HOH B 36 1136 82 HOH HOH . R 5 HOH B 37 1137 104 HOH HOH . R 5 HOH B 38 1138 45 HOH HOH . R 5 HOH B 39 1139 105 HOH HOH . R 5 HOH B 40 1140 145 HOH HOH . R 5 HOH B 41 1141 135 HOH HOH . R 5 HOH B 42 1142 147 HOH HOH . R 5 HOH B 43 1143 138 HOH HOH . R 5 HOH B 44 1144 134 HOH HOH . R 5 HOH B 45 1145 125 HOH HOH . R 5 HOH B 46 1146 136 HOH HOH . R 5 HOH B 47 1147 144 HOH HOH . R 5 HOH B 48 1148 128 HOH HOH . R 5 HOH B 49 1149 137 HOH HOH . R 5 HOH B 50 1150 130 HOH HOH . R 5 HOH B 51 1151 119 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 C07 9JT . . . O 2 13.42 16.256 -14.092 0.79 63.88 ? C07 9JT 1005 B 1 HETATM 2 C C06 9JT . . . O 2 13.057 17.016 -12.986 0.79 65.09 ? C06 9JT 1005 B 1 HETATM 3 C C05 9JT . . . O 2 11.789 17.583 -12.92 0.79 63.21 ? C05 9JT 1005 B 1 HETATM 4 C C04 9JT . . . O 2 10.883 17.393 -13.957 0.79 66.26 ? C04 9JT 1005 B 1 HETATM 5 C C03 9JT . . . O 2 11.245 16.634 -15.061 0.79 64.68 ? C03 9JT 1005 B 1 HETATM 6 C C02 9JT . . . O 2 12.512 16.067 -15.12 0.79 67.78 ? C02 9JT 1005 B 1 HETATM 7 SE SE1 9JT . . . O 2 13.013 15.008 -16.677 0.79 87.9 ? SE1 9JT 1005 B 1 HETATM 8 H H5 9JT . . . O 2 13.761 17.165 -12.176 0.79 78.1 ? H5 9JT 1005 B 1 HETATM 9 H H6 9JT . . . O 2 11.507 18.176 -12.059 0.79 75.85 ? H6 9JT 1005 B 1 HETATM 10 H H7 9JT . . . O 2 9.896 17.835 -13.902 0.79 79.52 ? H7 9JT 1005 B 1 HETATM 11 H H8 9JT . . . O 2 10.543 16.485 -15.872 0.79 77.61 ? H8 9JT 1005 B 1 HETATM 12 H H9 9JT . . . O 2 11.907 14.627 -16.983 0.79 105.48 ? H9 9JT 1005 B 1 HETATM 13 H H10 9JT . . . O 2 11.503 13.403 -14.934 0.79 0 ? H10 9JT 1005 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #