data_1P4D
#
_model_server_result.job_id            X4qoucZGcIDEJCp-VoLoPQ 
_model_server_result.datetime_utc      '2024-11-25 14:38:47' 
_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          1p4d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":608}' 
#
_entry.id    1P4D 
#
_exptl.entry_id    1P4D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    11 
_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            1P4D 
_cell.length_a            128.219 
_cell.length_b            128.219 
_cell.length_c            121.184 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1P4D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,I,R 1 1 
B,J,K,L,M,N,O,S 2 1 
C,P,Q,T 3 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
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 Q 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 ND1 HIS 146 A HIS 146 1_555 D MG MG . A MG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc2 A NE2 HIS 157 A HIS 157 1_555 D MG MG . A MG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc3 A NE2 HIS 159 A HIS 159 1_555 D MG MG . A MG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
metalc ? metalc4 D MG MG . A MG 900 1_555 R O HOH . A HOH 942 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc5 D MG MG . A MG 900 1_555 R O HOH . A HOH 956 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc6 D MG MG . A MG 900 1_555 R O HOH . A HOH 981 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc7 B ND1 HIS 146 B HIS 146 1_555 J MG MG . B MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc8 B NE2 HIS 157 B HIS 157 1_555 J MG MG . B MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? 
metalc ? metalc9 B NE2 HIS 159 B HIS 159 1_555 J MG MG . B MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? 
metalc ? metalc10 J MG MG . B MG 901 1_555 S O HOH . B HOH 934 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc11 C ND1 HIS 146 C HIS 146 1_555 P MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? 
metalc ? metalc12 C NE2 HIS 157 C HIS 157 1_555 P MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? 
metalc ? metalc13 C NE2 HIS 159 C HIS 159 1_555 P MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc14 P MG MG . C MG 902 1_555 T O HOH . C HOH 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
#
_chem_comp.formula           'C2 H6 O2' 
_chem_comp.formula_weight    62.068 
_chem_comp.id                EDO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-ETHANEDIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ETHYLENE GLYCOL' 
#
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 O1 EDO sing 70 n n 
C1 C2 EDO sing 71 n n 
C1 H11 EDO sing 72 n n 
C1 H12 EDO sing 73 n n 
O1 HO1 EDO sing 74 n n 
C2 O2 EDO sing 75 n n 
C2 H21 EDO sing 76 n n 
C2 H22 EDO sing 77 n n 
O2 HO2 EDO sing 78 n n 
#
_atom_sites.entry_id                     1P4D 
_atom_sites.fract_transf_matrix[1][1]    0.007799 
_atom_sites.fract_transf_matrix[1][2]    0.004503 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009006 
_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]    0.008252 
_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
D 2 MG A 1 900 900 MG MG . 
E 3 EDO A 1 600 600 EDO EGL . 
F 3 EDO A 1 601 601 EDO EGL . 
G 3 EDO A 1 606 606 EDO EGL . 
H 3 EDO A 1 608 608 EDO EGL . 
I 3 EDO A 1 612 612 EDO EGL . 
J 2 MG B 1 901 900 MG MG . 
K 3 EDO B 1 602 602 EDO EGL . 
L 3 EDO B 1 604 604 EDO EGL . 
M 3 EDO B 1 605 605 EDO EGL . 
N 3 EDO B 1 607 607 EDO EGL . 
O 3 EDO B 1 610 610 EDO EGL . 
P 2 MG C 1 902 900 MG MG . 
Q 3 EDO C 1 603 603 EDO EGL . 
R 4 HOH A 1 901 2 HOH TIP . 
R 4 HOH A 2 902 5 HOH TIP . 
R 4 HOH A 3 903 7 HOH TIP . 
R 4 HOH A 4 904 10 HOH TIP . 
R 4 HOH A 5 905 11 HOH TIP . 
R 4 HOH A 6 906 12 HOH TIP . 
R 4 HOH A 7 907 13 HOH TIP . 
R 4 HOH A 8 908 14 HOH TIP . 
R 4 HOH A 9 909 15 HOH TIP . 
R 4 HOH A 10 910 16 HOH TIP . 
R 4 HOH A 11 911 17 HOH TIP . 
R 4 HOH A 12 912 18 HOH TIP . 
R 4 HOH A 13 913 22 HOH TIP . 
R 4 HOH A 14 914 24 HOH TIP . 
R 4 HOH A 15 915 25 HOH TIP . 
R 4 HOH A 16 916 26 HOH TIP . 
R 4 HOH A 17 917 27 HOH TIP . 
R 4 HOH A 18 918 28 HOH TIP . 
R 4 HOH A 19 919 29 HOH TIP . 
R 4 HOH A 20 920 30 HOH TIP . 
R 4 HOH A 21 921 32 HOH TIP . 
R 4 HOH A 22 922 34 HOH TIP . 
R 4 HOH A 23 923 37 HOH TIP . 
R 4 HOH A 24 924 38 HOH TIP . 
R 4 HOH A 25 925 42 HOH TIP . 
R 4 HOH A 26 926 43 HOH TIP . 
R 4 HOH A 27 927 45 HOH TIP . 
R 4 HOH A 28 928 49 HOH TIP . 
R 4 HOH A 29 929 51 HOH TIP . 
R 4 HOH A 30 930 55 HOH TIP . 
R 4 HOH A 31 931 57 HOH TIP . 
R 4 HOH A 32 932 59 HOH TIP . 
R 4 HOH A 33 933 62 HOH TIP . 
R 4 HOH A 34 934 63 HOH TIP . 
R 4 HOH A 35 935 66 HOH TIP . 
R 4 HOH A 36 936 67 HOH TIP . 
R 4 HOH A 37 937 71 HOH TIP . 
R 4 HOH A 38 938 72 HOH TIP . 
R 4 HOH A 39 939 74 HOH TIP . 
R 4 HOH A 40 940 75 HOH TIP . 
R 4 HOH A 41 941 76 HOH TIP . 
R 4 HOH A 42 942 79 HOH TIP . 
R 4 HOH A 43 943 85 HOH TIP . 
R 4 HOH A 44 944 87 HOH TIP . 
R 4 HOH A 45 945 88 HOH TIP . 
R 4 HOH A 46 946 90 HOH TIP . 
R 4 HOH A 47 947 91 HOH TIP . 
R 4 HOH A 48 948 93 HOH TIP . 
R 4 HOH A 49 949 95 HOH TIP . 
R 4 HOH A 50 950 98 HOH TIP . 
R 4 HOH A 51 951 104 HOH TIP . 
R 4 HOH A 52 952 110 HOH TIP . 
R 4 HOH A 53 953 111 HOH TIP . 
R 4 HOH A 54 954 112 HOH TIP . 
R 4 HOH A 55 955 113 HOH TIP . 
R 4 HOH A 56 956 114 HOH TIP . 
R 4 HOH A 57 957 116 HOH TIP . 
R 4 HOH A 58 958 118 HOH TIP . 
R 4 HOH A 59 959 119 HOH TIP . 
R 4 HOH A 60 960 124 HOH TIP . 
R 4 HOH A 61 961 127 HOH TIP . 
R 4 HOH A 62 962 128 HOH TIP . 
R 4 HOH A 63 963 133 HOH TIP . 
R 4 HOH A 64 964 137 HOH TIP . 
R 4 HOH A 65 965 140 HOH TIP . 
R 4 HOH A 66 966 148 HOH TIP . 
R 4 HOH A 67 967 151 HOH TIP . 
R 4 HOH A 68 968 152 HOH TIP . 
R 4 HOH A 69 969 153 HOH TIP . 
R 4 HOH A 70 970 155 HOH TIP . 
R 4 HOH A 71 971 159 HOH TIP . 
R 4 HOH A 72 972 160 HOH TIP . 
R 4 HOH A 73 973 161 HOH TIP . 
R 4 HOH A 74 974 163 HOH TIP . 
R 4 HOH A 75 975 167 HOH TIP . 
R 4 HOH A 76 976 168 HOH TIP . 
R 4 HOH A 77 977 169 HOH TIP . 
R 4 HOH A 78 978 170 HOH TIP . 
R 4 HOH A 79 979 172 HOH TIP . 
R 4 HOH A 80 980 173 HOH TIP . 
R 4 HOH A 81 981 174 HOH TIP . 
S 4 HOH B 1 902 1 HOH TIP . 
S 4 HOH B 2 903 3 HOH TIP . 
S 4 HOH B 3 904 4 HOH TIP . 
S 4 HOH B 4 905 8 HOH TIP . 
S 4 HOH B 5 906 9 HOH TIP . 
S 4 HOH B 6 907 19 HOH TIP . 
S 4 HOH B 7 908 20 HOH TIP . 
S 4 HOH B 8 909 21 HOH TIP . 
S 4 HOH B 9 910 23 HOH TIP . 
S 4 HOH B 10 911 33 HOH TIP . 
S 4 HOH B 11 912 35 HOH TIP . 
S 4 HOH B 12 913 36 HOH TIP . 
S 4 HOH B 13 914 39 HOH TIP . 
S 4 HOH B 14 915 40 HOH TIP . 
S 4 HOH B 15 916 41 HOH TIP . 
S 4 HOH B 16 917 44 HOH TIP . 
S 4 HOH B 17 918 46 HOH TIP . 
S 4 HOH B 18 919 47 HOH TIP . 
S 4 HOH B 19 920 48 HOH TIP . 
S 4 HOH B 20 921 50 HOH TIP . 
S 4 HOH B 21 922 52 HOH TIP . 
S 4 HOH B 22 923 53 HOH TIP . 
S 4 HOH B 23 924 54 HOH TIP . 
S 4 HOH B 24 925 56 HOH TIP . 
S 4 HOH B 25 926 58 HOH TIP . 
S 4 HOH B 26 927 61 HOH TIP . 
S 4 HOH B 27 928 64 HOH TIP . 
S 4 HOH B 28 929 65 HOH TIP . 
S 4 HOH B 29 930 68 HOH TIP . 
S 4 HOH B 30 931 69 HOH TIP . 
S 4 HOH B 31 932 70 HOH TIP . 
S 4 HOH B 32 933 77 HOH TIP . 
S 4 HOH B 33 934 78 HOH TIP . 
S 4 HOH B 34 935 80 HOH TIP . 
S 4 HOH B 35 936 82 HOH TIP . 
S 4 HOH B 36 937 83 HOH TIP . 
S 4 HOH B 37 938 84 HOH TIP . 
S 4 HOH B 38 939 86 HOH TIP . 
S 4 HOH B 39 940 89 HOH TIP . 
S 4 HOH B 40 941 97 HOH TIP . 
S 4 HOH B 41 942 99 HOH TIP . 
S 4 HOH B 42 943 102 HOH TIP . 
S 4 HOH B 43 944 103 HOH TIP . 
S 4 HOH B 44 945 106 HOH TIP . 
S 4 HOH B 45 946 107 HOH TIP . 
S 4 HOH B 46 947 108 HOH TIP . 
S 4 HOH B 47 948 109 HOH TIP . 
S 4 HOH B 48 949 117 HOH TIP . 
S 4 HOH B 49 950 121 HOH TIP . 
S 4 HOH B 50 951 122 HOH TIP . 
S 4 HOH B 51 952 123 HOH TIP . 
S 4 HOH B 52 953 126 HOH TIP . 
S 4 HOH B 53 954 129 HOH TIP . 
S 4 HOH B 54 955 130 HOH TIP . 
S 4 HOH B 55 956 134 HOH TIP . 
S 4 HOH B 56 957 135 HOH TIP . 
S 4 HOH B 57 958 136 HOH TIP . 
S 4 HOH B 58 959 139 HOH TIP . 
S 4 HOH B 59 960 141 HOH TIP . 
S 4 HOH B 60 961 142 HOH TIP . 
S 4 HOH B 61 962 143 HOH TIP . 
S 4 HOH B 62 963 145 HOH TIP . 
S 4 HOH B 63 964 146 HOH TIP . 
S 4 HOH B 64 965 147 HOH TIP . 
S 4 HOH B 65 966 149 HOH TIP . 
S 4 HOH B 66 967 154 HOH TIP . 
S 4 HOH B 67 968 157 HOH TIP . 
S 4 HOH B 68 969 162 HOH TIP . 
S 4 HOH B 69 970 164 HOH TIP . 
S 4 HOH B 70 971 165 HOH TIP . 
S 4 HOH B 71 972 166 HOH TIP . 
S 4 HOH B 72 973 171 HOH TIP . 
T 4 HOH C 1 903 31 HOH TIP . 
T 4 HOH C 2 904 60 HOH TIP . 
T 4 HOH C 3 905 92 HOH TIP . 
T 4 HOH C 4 906 94 HOH TIP . 
T 4 HOH C 5 907 125 HOH TIP . 
T 4 HOH C 6 908 138 HOH TIP . 
T 4 HOH C 7 909 144 HOH TIP . 
T 4 HOH C 8 910 156 HOH TIP . 
T 4 HOH C 9 911 158 HOH TIP . 
#
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 EDO . . . H 3 58.185 66.325 100.824 1 78.19 ? C1 EDO 608 A 1 
HETATM 2 O O1 EDO . . . H 3 56.776 66.549 100.721 1 75.45 ? O1 EDO 608 A 1 
HETATM 3 C C2 EDO . . . H 3 58.582 66.072 102.297 1 78.02 ? C2 EDO 608 A 1 
HETATM 4 O O2 EDO . . . H 3 57.426 66.13 103.153 1 78.9 ? O2 EDO 608 A 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           4 
#