data_1YD4
#
_model_server_result.job_id            cihu8UBNvkuMScTvPYPKfg 
_model_server_result.datetime_utc      '2024-10-19 11:39:02' 
_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          1yd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1001}' 
#
_entry.id    1YD4 
#
_exptl.entry_id    1YD4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              54.938 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MANGANESE (II) ION' 
_entity.pdbx_number_of_molecules    3 
_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            1YD4 
_cell.length_a            54.949 
_cell.length_b            54.949 
_cell.length_c            109.187 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YD4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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 B N N 
? 2 C N N 
? 2 D 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 OE1 GLU 60 A GLU 60 1_555 D MN MN . A MN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc2 A OE2 GLU 62 A GLU 62 1_555 D MN MN . A MN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc3 A OE2 GLU 76 A GLU 76 1_555 B MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
metalc ? metalc4 B MN MN . A MN 1001 1_555 E O HOH . A HOH 1022 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc5 B MN MN . A MN 1001 1_555 E O HOH . A HOH 1034 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc6 B MN MN . A MN 1001 1_555 E O HOH . A HOH 1058 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc7 B MN MN . A MN 1001 1_555 E O HOH . A HOH 1059 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc8 B MN MN . A MN 1001 1_555 E O HOH . A HOH 1123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc9 D MN MN . A MN 1004 1_555 E O HOH . A HOH 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? 
#
_chem_comp.formula           'Mn 2' 
_chem_comp.formula_weight    54.938 
_chem_comp.id                MN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MANGANESE (II) ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     1YD4 
_atom_sites.fract_transf_matrix[1][1]    0.018199 
_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]    0.018199 
_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]    0.009159 
_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 MN A 1 1001 1 MN MN . 
C 2 MN A 1 1002 2 MN MN . 
D 2 MN A 1 1004 4 MN MN . 
E 3 HOH A 1 1005 1 HOH HOH . 
E 3 HOH A 2 1006 2 HOH HOH . 
E 3 HOH A 3 1007 3 HOH HOH . 
E 3 HOH A 4 1008 4 HOH HOH . 
E 3 HOH A 5 1009 5 HOH HOH . 
E 3 HOH A 6 1010 6 HOH HOH . 
E 3 HOH A 7 1011 7 HOH HOH . 
E 3 HOH A 8 1012 8 HOH HOH . 
E 3 HOH A 9 1013 9 HOH HOH . 
E 3 HOH A 10 1014 10 HOH HOH . 
E 3 HOH A 11 1015 11 HOH HOH . 
E 3 HOH A 12 1016 12 HOH HOH . 
E 3 HOH A 13 1017 13 HOH HOH . 
E 3 HOH A 14 1018 14 HOH HOH . 
E 3 HOH A 15 1019 15 HOH HOH . 
E 3 HOH A 16 1020 16 HOH HOH . 
E 3 HOH A 17 1021 17 HOH HOH . 
E 3 HOH A 18 1022 18 HOH HOH . 
E 3 HOH A 19 1023 19 HOH HOH . 
E 3 HOH A 20 1024 20 HOH HOH . 
E 3 HOH A 21 1025 21 HOH HOH . 
E 3 HOH A 22 1026 22 HOH HOH . 
E 3 HOH A 23 1027 23 HOH HOH . 
E 3 HOH A 24 1028 24 HOH HOH . 
E 3 HOH A 25 1029 25 HOH HOH . 
E 3 HOH A 26 1030 26 HOH HOH . 
E 3 HOH A 27 1031 27 HOH HOH . 
E 3 HOH A 28 1032 28 HOH HOH . 
E 3 HOH A 29 1033 29 HOH HOH . 
E 3 HOH A 30 1034 30 HOH HOH . 
E 3 HOH A 31 1035 31 HOH HOH . 
E 3 HOH A 32 1036 32 HOH HOH . 
E 3 HOH A 33 1037 33 HOH HOH . 
E 3 HOH A 34 1038 34 HOH HOH . 
E 3 HOH A 35 1039 35 HOH HOH . 
E 3 HOH A 36 1040 36 HOH HOH . 
E 3 HOH A 37 1041 37 HOH HOH . 
E 3 HOH A 38 1042 38 HOH HOH . 
E 3 HOH A 39 1043 39 HOH HOH . 
E 3 HOH A 40 1044 40 HOH HOH . 
E 3 HOH A 41 1045 41 HOH HOH . 
E 3 HOH A 42 1046 42 HOH HOH . 
E 3 HOH A 43 1047 43 HOH HOH . 
E 3 HOH A 44 1048 44 HOH HOH . 
E 3 HOH A 45 1049 45 HOH HOH . 
E 3 HOH A 46 1050 46 HOH HOH . 
E 3 HOH A 47 1051 47 HOH HOH . 
E 3 HOH A 48 1052 48 HOH HOH . 
E 3 HOH A 49 1053 49 HOH HOH . 
E 3 HOH A 50 1054 50 HOH HOH . 
E 3 HOH A 51 1055 51 HOH HOH . 
E 3 HOH A 52 1056 52 HOH HOH . 
E 3 HOH A 53 1057 53 HOH HOH . 
E 3 HOH A 54 1058 54 HOH HOH . 
E 3 HOH A 55 1059 55 HOH HOH . 
E 3 HOH A 56 1060 56 HOH HOH . 
E 3 HOH A 57 1061 57 HOH HOH . 
E 3 HOH A 58 1062 58 HOH HOH . 
E 3 HOH A 59 1063 59 HOH HOH . 
E 3 HOH A 60 1064 60 HOH HOH . 
E 3 HOH A 61 1065 61 HOH HOH . 
E 3 HOH A 62 1066 62 HOH HOH . 
E 3 HOH A 63 1067 63 HOH HOH . 
E 3 HOH A 64 1068 64 HOH HOH . 
E 3 HOH A 65 1069 65 HOH HOH . 
E 3 HOH A 66 1070 66 HOH HOH . 
E 3 HOH A 67 1071 67 HOH HOH . 
E 3 HOH A 68 1072 69 HOH HOH . 
E 3 HOH A 69 1073 72 HOH HOH . 
E 3 HOH A 70 1074 73 HOH HOH . 
E 3 HOH A 71 1075 74 HOH HOH . 
E 3 HOH A 72 1076 75 HOH HOH . 
E 3 HOH A 73 1077 76 HOH HOH . 
E 3 HOH A 74 1078 77 HOH HOH . 
E 3 HOH A 75 1079 78 HOH HOH . 
E 3 HOH A 76 1080 79 HOH HOH . 
E 3 HOH A 77 1081 80 HOH HOH . 
E 3 HOH A 78 1082 81 HOH HOH . 
E 3 HOH A 79 1083 82 HOH HOH . 
E 3 HOH A 80 1084 83 HOH HOH . 
E 3 HOH A 81 1085 85 HOH HOH . 
E 3 HOH A 82 1086 86 HOH HOH . 
E 3 HOH A 83 1087 87 HOH HOH . 
E 3 HOH A 84 1088 88 HOH HOH . 
E 3 HOH A 85 1089 89 HOH HOH . 
E 3 HOH A 86 1090 90 HOH HOH . 
E 3 HOH A 87 1091 91 HOH HOH . 
E 3 HOH A 88 1092 92 HOH HOH . 
E 3 HOH A 89 1093 93 HOH HOH . 
E 3 HOH A 90 1094 94 HOH HOH . 
E 3 HOH A 91 1095 95 HOH HOH . 
E 3 HOH A 92 1096 96 HOH HOH . 
E 3 HOH A 93 1097 97 HOH HOH . 
E 3 HOH A 94 1098 98 HOH HOH . 
E 3 HOH A 95 1099 99 HOH HOH . 
E 3 HOH A 96 1100 100 HOH HOH . 
E 3 HOH A 97 1101 101 HOH HOH . 
E 3 HOH A 98 1102 102 HOH HOH . 
E 3 HOH A 99 1103 103 HOH HOH . 
E 3 HOH A 100 1104 104 HOH HOH . 
E 3 HOH A 101 1105 106 HOH HOH . 
E 3 HOH A 102 1106 107 HOH HOH . 
E 3 HOH A 103 1107 108 HOH HOH . 
E 3 HOH A 104 1108 109 HOH HOH . 
E 3 HOH A 105 1109 110 HOH HOH . 
E 3 HOH A 106 1110 111 HOH HOH . 
E 3 HOH A 107 1111 112 HOH HOH . 
E 3 HOH A 108 1112 113 HOH HOH . 
E 3 HOH A 109 1113 114 HOH HOH . 
E 3 HOH A 110 1114 115 HOH HOH . 
E 3 HOH A 111 1115 116 HOH HOH . 
E 3 HOH A 112 1116 117 HOH HOH . 
E 3 HOH A 113 1117 118 HOH HOH . 
E 3 HOH A 114 1118 119 HOH HOH . 
E 3 HOH A 115 1119 121 HOH HOH . 
E 3 HOH A 116 1120 122 HOH HOH . 
E 3 HOH A 117 1121 124 HOH HOH . 
E 3 HOH A 118 1122 128 HOH HOH . 
E 3 HOH A 119 1123 143 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           MN 
_atom_site.label_atom_id         MN 
_atom_site.label_comp_id         MN 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         B 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               47.335 
_atom_site.Cartn_y               27.828 
_atom_site.Cartn_z               36.836 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        35.94 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          MN 
_atom_site.auth_comp_id          MN 
_atom_site.auth_seq_id           1001 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#