data_1XDQ # _model_server_result.job_id OnRbm4O6E7nGcVEQa5xPEg _model_server_result.datetime_utc '2025-04-13 10:23:18' _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 1xdq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":403}' # _entry.id 1XDQ # _exptl.entry_id 1XDQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 60.055 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description UREA _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 1XDQ _cell.length_a 110.345 _cell.length_b 165.064 _cell.length_c 181.447 _cell.Z_PDB 40 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XDQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,F,G,H,I,Z 1 1 B,J,K,L,M,AA 2 1 C,N,O,P,Q,BA 3 1 D,R,S,T,U,CA 4 1 E,V,W,X,Y,DA 5 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 F N N ? 2 J N N ? 2 N N N ? 2 R N N ? 2 V 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 102 A CYS 102 1_555 G MO MO . A MO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc2 I S1' MTE . A MTE 301 1_555 G MO MO . A MO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc3 I S2' MTE . A MTE 301 1_555 G MO MO . A MO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc4 G MO MO . A MO 501 1_555 H O O . A O 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.712 ? metalc ? metalc5 G MO MO . A MO 501 1_555 Z O HOH . A HOH 645 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc6 B SG CYS 102 B CYS 102 1_555 K MO MO . B MO 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc7 M S2' MTE . B MTE 302 1_555 K MO MO . B MO 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc8 M S1' MTE . B MTE 302 1_555 K MO MO . B MO 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc9 K MO MO . B MO 502 1_555 L O O . B O 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.705 ? metalc ? metalc10 K MO MO . B MO 502 1_555 AA O HOH . B HOH 628 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc11 C SG CYS 102 C CYS 102 1_555 O MO MO . C MO 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc12 Q S2' MTE . C MTE 303 1_555 O MO MO . C MO 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc13 Q S1' MTE . C MTE 303 1_555 O MO MO . C MO 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc14 O MO MO . C MO 503 1_555 P O O . C O 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.711 ? metalc ? metalc15 O MO MO . C MO 503 1_555 BA O HOH . C HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc16 D SG CYS 102 D CYS 102 1_555 S MO MO . D MO 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc17 U S2' MTE . D MTE 304 1_555 S MO MO . D MO 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc18 U S1' MTE . D MTE 304 1_555 S MO MO . D MO 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc19 S MO MO . D MO 504 1_555 T O O . D O 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.725 ? metalc ? metalc20 S MO MO . D MO 504 1_555 CA O HOH . D HOH 629 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc21 E SG CYS 102 E CYS 102 1_555 W MO MO . E MO 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc22 Y S2' MTE . E MTE 305 1_555 W MO MO . E MO 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc23 Y S1' MTE . E MTE 305 1_555 W MO MO . E MO 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc24 W MO MO . E MO 505 1_555 X O O . E O 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.723 ? metalc ? metalc25 W MO MO . E MO 505 1_555 DA O HOH . E HOH 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? # _chem_comp.formula 'C H4 N2 O' _chem_comp.formula_weight 60.055 _chem_comp.id URE _chem_comp.mon_nstd_flag . _chem_comp.name UREA _chem_comp.type non-polymer _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 C O URE doub 398 n n C N1 URE sing 399 n n C N2 URE sing 400 n n N1 HN11 URE sing 401 n n N1 HN12 URE sing 402 n n N2 HN21 URE sing 403 n n N2 HN22 URE sing 404 n n # _atom_sites.entry_id 1XDQ _atom_sites.fract_transf_matrix[1][1] 0.009062 _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] 0.006058 _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] 0.005511 _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 F 2 URE A 1 401 401 URE URE . G 3 MO A 1 501 501 MO MO . H 4 O A 1 601 601 O OXO . I 5 MTE A 1 301 301 MTE MTE . J 2 URE B 1 402 402 URE URE . K 3 MO B 1 502 502 MO MO . L 4 O B 1 602 602 O OXO . M 5 MTE B 1 302 302 MTE MTE . N 2 URE C 1 403 403 URE URE . O 3 MO C 1 503 503 MO MO . P 4 O C 1 603 603 O OXO . Q 5 MTE C 1 303 303 MTE MTE . R 2 URE D 1 404 404 URE URE . S 3 MO D 1 504 504 MO MO . T 4 O D 1 604 604 O OXO . U 5 MTE D 1 304 304 MTE MTE . V 2 URE E 1 405 405 URE URE . W 3 MO E 1 505 505 MO MO . X 4 O E 1 605 605 O OXO . Y 5 MTE E 1 305 305 MTE MTE . Z 6 HOH A 1 602 1 HOH HOH . Z 6 HOH A 2 603 2 HOH HOH . Z 6 HOH A 3 604 9 HOH HOH . Z 6 HOH A 4 605 11 HOH HOH . Z 6 HOH A 5 606 17 HOH HOH . Z 6 HOH A 6 607 22 HOH HOH . Z 6 HOH A 7 608 28 HOH HOH . Z 6 HOH A 8 609 30 HOH HOH . Z 6 HOH A 9 610 31 HOH HOH . Z 6 HOH A 10 611 32 HOH HOH . Z 6 HOH A 11 612 34 HOH HOH . Z 6 HOH A 12 613 35 HOH HOH . Z 6 HOH A 13 614 36 HOH HOH . Z 6 HOH A 14 615 37 HOH HOH . Z 6 HOH A 15 616 38 HOH HOH . Z 6 HOH A 16 617 39 HOH HOH . Z 6 HOH A 17 618 41 HOH HOH . Z 6 HOH A 18 619 42 HOH HOH . Z 6 HOH A 19 620 43 HOH HOH . Z 6 HOH A 20 621 44 HOH HOH . Z 6 HOH A 21 622 45 HOH HOH . Z 6 HOH A 22 623 46 HOH HOH . Z 6 HOH A 23 624 47 HOH HOH . Z 6 HOH A 24 625 48 HOH HOH . Z 6 HOH A 25 626 49 HOH HOH . Z 6 HOH A 26 627 50 HOH HOH . Z 6 HOH A 27 628 51 HOH HOH . Z 6 HOH A 28 629 53 HOH HOH . Z 6 HOH A 29 630 54 HOH HOH . Z 6 HOH A 30 631 55 HOH HOH . Z 6 HOH A 31 632 102 HOH HOH . Z 6 HOH A 32 633 103 HOH HOH . Z 6 HOH A 33 634 107 HOH HOH . Z 6 HOH A 34 635 108 HOH HOH . Z 6 HOH A 35 636 114 HOH HOH . Z 6 HOH A 36 637 115 HOH HOH . Z 6 HOH A 37 638 116 HOH HOH . Z 6 HOH A 38 639 117 HOH HOH . Z 6 HOH A 39 640 118 HOH HOH . Z 6 HOH A 40 641 123 HOH HOH . Z 6 HOH A 41 642 126 HOH HOH . Z 6 HOH A 42 643 127 HOH HOH . Z 6 HOH A 43 644 128 HOH HOH . Z 6 HOH A 44 645 135 HOH HOH . Z 6 HOH A 45 646 142 HOH HOH . Z 6 HOH A 46 647 143 HOH HOH . Z 6 HOH A 47 648 149 HOH HOH . Z 6 HOH A 48 649 150 HOH HOH . Z 6 HOH A 49 650 160 HOH HOH . AA 6 HOH B 1 603 7 HOH HOH . AA 6 HOH B 2 604 13 HOH HOH . AA 6 HOH B 3 605 15 HOH HOH . AA 6 HOH B 4 606 20 HOH HOH . AA 6 HOH B 5 607 21 HOH HOH . AA 6 HOH B 6 608 24 HOH HOH . AA 6 HOH B 7 609 33 HOH HOH . AA 6 HOH B 8 610 57 HOH HOH . AA 6 HOH B 9 611 58 HOH HOH . AA 6 HOH B 10 612 59 HOH HOH . AA 6 HOH B 11 613 60 HOH HOH . AA 6 HOH B 12 614 61 HOH HOH . AA 6 HOH B 13 615 63 HOH HOH . AA 6 HOH B 14 616 64 HOH HOH . AA 6 HOH B 15 617 65 HOH HOH . AA 6 HOH B 16 618 66 HOH HOH . AA 6 HOH B 17 619 72 HOH HOH . AA 6 HOH B 18 620 73 HOH HOH . AA 6 HOH B 19 621 74 HOH HOH . AA 6 HOH B 20 622 75 HOH HOH . AA 6 HOH B 21 623 104 HOH HOH . AA 6 HOH B 22 624 124 HOH HOH . AA 6 HOH B 23 625 130 HOH HOH . AA 6 HOH B 24 626 131 HOH HOH . AA 6 HOH B 25 627 132 HOH HOH . AA 6 HOH B 26 628 136 HOH HOH . BA 6 HOH C 1 604 5 HOH HOH . BA 6 HOH C 2 605 18 HOH HOH . BA 6 HOH C 3 606 25 HOH HOH . BA 6 HOH C 4 607 29 HOH HOH . BA 6 HOH C 5 608 40 HOH HOH . BA 6 HOH C 6 609 78 HOH HOH . BA 6 HOH C 7 610 80 HOH HOH . BA 6 HOH C 8 611 81 HOH HOH . BA 6 HOH C 9 612 82 HOH HOH . BA 6 HOH C 10 613 83 HOH HOH . BA 6 HOH C 11 614 84 HOH HOH . BA 6 HOH C 12 615 86 HOH HOH . BA 6 HOH C 13 616 87 HOH HOH . BA 6 HOH C 14 617 88 HOH HOH . BA 6 HOH C 15 618 112 HOH HOH . BA 6 HOH C 16 619 122 HOH HOH . BA 6 HOH C 17 620 133 HOH HOH . BA 6 HOH C 18 621 137 HOH HOH . BA 6 HOH C 19 622 139 HOH HOH . BA 6 HOH C 20 623 140 HOH HOH . BA 6 HOH C 21 624 146 HOH HOH . BA 6 HOH C 22 625 152 HOH HOH . BA 6 HOH C 23 626 153 HOH HOH . BA 6 HOH C 24 627 154 HOH HOH . BA 6 HOH C 25 628 161 HOH HOH . BA 6 HOH C 26 629 162 HOH HOH . BA 6 HOH C 27 630 164 HOH HOH . BA 6 HOH C 28 631 166 HOH HOH . CA 6 HOH D 1 605 4 HOH HOH . CA 6 HOH D 2 606 6 HOH HOH . CA 6 HOH D 3 607 8 HOH HOH . CA 6 HOH D 4 608 10 HOH HOH . CA 6 HOH D 5 609 16 HOH HOH . CA 6 HOH D 6 610 19 HOH HOH . CA 6 HOH D 7 611 23 HOH HOH . CA 6 HOH D 8 612 26 HOH HOH . CA 6 HOH D 9 613 52 HOH HOH . CA 6 HOH D 10 614 56 HOH HOH . CA 6 HOH D 11 615 71 HOH HOH . CA 6 HOH D 12 616 76 HOH HOH . CA 6 HOH D 13 617 89 HOH HOH . CA 6 HOH D 14 618 90 HOH HOH . CA 6 HOH D 15 619 91 HOH HOH . CA 6 HOH D 16 620 92 HOH HOH . CA 6 HOH D 17 621 93 HOH HOH . CA 6 HOH D 18 622 94 HOH HOH . CA 6 HOH D 19 623 105 HOH HOH . CA 6 HOH D 20 624 119 HOH HOH . CA 6 HOH D 21 625 120 HOH HOH . CA 6 HOH D 22 626 121 HOH HOH . CA 6 HOH D 23 627 125 HOH HOH . CA 6 HOH D 24 628 129 HOH HOH . CA 6 HOH D 25 629 138 HOH HOH . CA 6 HOH D 26 630 141 HOH HOH . CA 6 HOH D 27 631 144 HOH HOH . CA 6 HOH D 28 632 145 HOH HOH . CA 6 HOH D 29 633 148 HOH HOH . CA 6 HOH D 30 634 151 HOH HOH . CA 6 HOH D 31 635 155 HOH HOH . CA 6 HOH D 32 636 156 HOH HOH . CA 6 HOH D 33 637 157 HOH HOH . CA 6 HOH D 34 638 167 HOH HOH . CA 6 HOH D 35 639 168 HOH HOH . CA 6 HOH D 36 640 169 HOH HOH . DA 6 HOH E 1 606 3 HOH HOH . DA 6 HOH E 2 607 12 HOH HOH . DA 6 HOH E 3 608 14 HOH HOH . DA 6 HOH E 4 609 27 HOH HOH . DA 6 HOH E 5 610 62 HOH HOH . DA 6 HOH E 6 611 67 HOH HOH . DA 6 HOH E 7 612 68 HOH HOH . DA 6 HOH E 8 613 69 HOH HOH . DA 6 HOH E 9 614 70 HOH HOH . DA 6 HOH E 10 615 77 HOH HOH . DA 6 HOH E 11 616 79 HOH HOH . DA 6 HOH E 12 617 85 HOH HOH . DA 6 HOH E 13 618 95 HOH HOH . DA 6 HOH E 14 619 96 HOH HOH . DA 6 HOH E 15 620 97 HOH HOH . DA 6 HOH E 16 621 98 HOH HOH . DA 6 HOH E 17 622 99 HOH HOH . DA 6 HOH E 18 623 100 HOH HOH . DA 6 HOH E 19 624 101 HOH HOH . DA 6 HOH E 20 625 106 HOH HOH . DA 6 HOH E 21 626 109 HOH HOH . DA 6 HOH E 22 627 110 HOH HOH . DA 6 HOH E 23 628 111 HOH HOH . DA 6 HOH E 24 629 113 HOH HOH . DA 6 HOH E 25 630 134 HOH HOH . DA 6 HOH E 26 631 147 HOH HOH . DA 6 HOH E 27 632 158 HOH HOH . DA 6 HOH E 28 633 159 HOH HOH . DA 6 HOH E 29 634 163 HOH HOH . DA 6 HOH E 30 635 165 HOH HOH . DA 6 HOH E 31 636 170 HOH HOH . DA 6 HOH E 32 637 171 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 C URE . . . N 2 -77.619 -5.761 64.069 1 62.28 ? C URE 403 C 1 HETATM 2 O O URE . . . N 2 -77.963 -6.689 64.916 1 64.41 ? O URE 403 C 1 HETATM 3 N N1 URE . . . N 2 -76.365 -5.401 63.766 1 49.52 ? N1 URE 403 C 1 HETATM 4 N N2 URE . . . N 2 -78.651 -5.136 63.454 1 56.85 ? N2 URE 403 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 4 #