data_2ONY
#
_model_server_result.job_id            qszLNKrQ18GhPxSHTccbCQ 
_model_server_result.datetime_utc      '2025-02-17 18:34:55' 
_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          2ony 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":3001}' 
#
_entry.id    2ONY 
#
_exptl.entry_id    2ONY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              384.411 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYL-L-HOMOCYSTEINE 
_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            2ONY 
_cell.length_a            93.96 
_cell.length_b            93.96 
_cell.length_c            188.03 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2ONY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PQS monomeric 1 author_and_software_defined_assembly 1 
PQS monomeric 1 author_and_software_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 1 
A,B,C,D,E,F,G,H 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
? 2 C N N 
? 2 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 48 A CYS 48 1_555 B SG CYS 139 B CYS 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
#
_chem_comp.formula           'C14 H20 N6 O5 S' 
_chem_comp.formula_weight    384.411 
_chem_comp.id                SAH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              S-ADENOSYL-L-HOMOCYSTEINE 
_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
N CA SAH sing 281 n n 
N HN1 SAH sing 282 n n 
N HN2 SAH sing 283 n n 
CA CB SAH sing 284 n n 
CA C SAH sing 285 n n 
CA HA SAH sing 286 n n 
CB CG SAH sing 287 n n 
CB HB1 SAH sing 288 n n 
CB HB2 SAH sing 289 n n 
CG SD SAH sing 290 n n 
CG HG1 SAH sing 291 n n 
CG HG2 SAH sing 292 n n 
SD C5' SAH sing 293 n n 
C O SAH doub 294 n n 
C OXT SAH sing 295 n n 
OXT HXT SAH sing 296 n n 
C5' C4' SAH sing 297 n n 
C5' "H5'1" SAH sing 298 n n 
C5' "H5'2" SAH sing 299 n n 
C4' O4' SAH sing 300 n n 
C4' C3' SAH sing 301 n n 
C4' H4' SAH sing 302 n n 
O4' C1' SAH sing 303 n n 
C3' O3' SAH sing 304 n n 
C3' C2' SAH sing 305 n n 
C3' H3' SAH sing 306 n n 
O3' HO3' SAH sing 307 n n 
C2' O2' SAH sing 308 n n 
C2' C1' SAH sing 309 n n 
C2' H2' SAH sing 310 n n 
O2' HO2' SAH sing 311 n n 
C1' N9 SAH sing 312 n n 
C1' H1' SAH sing 313 n n 
N9 C8 SAH sing 314 n y 
N9 C4 SAH sing 315 n y 
C8 N7 SAH doub 316 n y 
C8 H8 SAH sing 317 n n 
N7 C5 SAH sing 318 n y 
C5 C6 SAH sing 319 n y 
C5 C4 SAH doub 320 n y 
C6 N6 SAH sing 321 n n 
C6 N1 SAH doub 322 n y 
N6 HN61 SAH sing 323 n n 
N6 HN62 SAH sing 324 n n 
N1 C2 SAH sing 325 n y 
C2 N3 SAH doub 326 n y 
C2 H2 SAH sing 327 n n 
N3 C4 SAH sing 328 n y 
#
_atom_sites.entry_id                     2ONY 
_atom_sites.fract_transf_matrix[1][1]    0.010643 
_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]    0.010643 
_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]    0.005318 
_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 SAH A 1 3001 3001 SAH SAH . 
D 3 TMJ A 1 2001 2001 TMJ TMC . 
E 4 PO4 B 1 4001 4001 PO4 PO4 . 
F 2 SAH B 1 3002 3002 SAH SAH . 
G 5 HOH A 1 3002 1001 HOH HOH . 
G 5 HOH A 2 3003 1002 HOH HOH . 
G 5 HOH A 3 3004 1003 HOH HOH . 
G 5 HOH A 4 3005 1004 HOH HOH . 
G 5 HOH A 5 3006 1005 HOH HOH . 
G 5 HOH A 6 3007 1006 HOH HOH . 
G 5 HOH A 7 3008 1007 HOH HOH . 
G 5 HOH A 8 3009 1008 HOH HOH . 
G 5 HOH A 9 3010 1009 HOH HOH . 
G 5 HOH A 10 3011 1010 HOH HOH . 
G 5 HOH A 11 3012 1011 HOH HOH . 
G 5 HOH A 12 3013 1012 HOH HOH . 
G 5 HOH A 13 3014 1013 HOH HOH . 
G 5 HOH A 14 3015 1014 HOH HOH . 
G 5 HOH A 15 3016 1015 HOH HOH . 
G 5 HOH A 16 3017 1016 HOH HOH . 
G 5 HOH A 17 3018 1017 HOH HOH . 
G 5 HOH A 18 3019 1018 HOH HOH . 
G 5 HOH A 19 3020 1019 HOH HOH . 
G 5 HOH A 20 3021 1020 HOH HOH . 
G 5 HOH A 21 3022 1022 HOH HOH . 
G 5 HOH A 22 3023 1023 HOH HOH . 
G 5 HOH A 23 3024 1024 HOH HOH . 
G 5 HOH A 24 3025 1025 HOH HOH . 
G 5 HOH A 25 3026 1026 HOH HOH . 
G 5 HOH A 26 3027 1027 HOH HOH . 
G 5 HOH A 27 3028 1031 HOH HOH . 
G 5 HOH A 28 3029 1044 HOH HOH . 
G 5 HOH A 29 3030 1065 HOH HOH . 
G 5 HOH A 30 3031 1066 HOH HOH . 
G 5 HOH A 31 3032 1068 HOH HOH . 
G 5 HOH A 32 3033 1073 HOH HOH . 
G 5 HOH A 33 3034 1074 HOH HOH . 
G 5 HOH A 34 3035 1077 HOH HOH . 
G 5 HOH A 35 3036 1082 HOH HOH . 
G 5 HOH A 36 3037 1084 HOH HOH . 
G 5 HOH A 37 3038 1085 HOH HOH . 
G 5 HOH A 38 3039 1086 HOH HOH . 
G 5 HOH A 39 3040 1087 HOH HOH . 
G 5 HOH A 40 3041 1088 HOH HOH . 
G 5 HOH A 41 3042 1089 HOH HOH . 
G 5 HOH A 42 3043 1090 HOH HOH . 
G 5 HOH A 43 3044 1091 HOH HOH . 
G 5 HOH A 44 3045 1092 HOH HOH . 
G 5 HOH A 45 3046 1094 HOH HOH . 
G 5 HOH A 46 3047 1095 HOH HOH . 
G 5 HOH A 47 3048 1096 HOH HOH . 
G 5 HOH A 48 3049 1097 HOH HOH . 
G 5 HOH A 49 3050 1098 HOH HOH . 
G 5 HOH A 50 3051 1099 HOH HOH . 
G 5 HOH A 51 3052 1100 HOH HOH . 
G 5 HOH A 52 3053 1101 HOH HOH . 
G 5 HOH A 53 3054 1115 HOH HOH . 
G 5 HOH A 54 3055 1121 HOH HOH . 
G 5 HOH A 55 3056 1122 HOH HOH . 
G 5 HOH A 56 3057 1127 HOH HOH . 
G 5 HOH A 57 3058 1128 HOH HOH . 
G 5 HOH A 58 3059 1139 HOH HOH . 
G 5 HOH A 59 3060 1141 HOH HOH . 
G 5 HOH A 60 3061 1142 HOH HOH . 
G 5 HOH A 61 3062 1143 HOH HOH . 
G 5 HOH A 62 3063 1144 HOH HOH . 
G 5 HOH A 63 3064 1145 HOH HOH . 
G 5 HOH A 64 3065 1146 HOH HOH . 
G 5 HOH A 65 3066 1147 HOH HOH . 
G 5 HOH A 66 3067 1148 HOH HOH . 
G 5 HOH A 67 3068 1149 HOH HOH . 
G 5 HOH A 68 3069 1150 HOH HOH . 
G 5 HOH A 69 3070 1151 HOH HOH . 
G 5 HOH A 70 3071 1152 HOH HOH . 
G 5 HOH A 71 3072 1153 HOH HOH . 
G 5 HOH A 72 3073 1154 HOH HOH . 
G 5 HOH A 73 3074 1155 HOH HOH . 
G 5 HOH A 74 3075 1156 HOH HOH . 
H 5 HOH B 1 4002 1021 HOH HOH . 
H 5 HOH B 2 4003 1028 HOH HOH . 
H 5 HOH B 3 4004 1029 HOH HOH . 
H 5 HOH B 4 4005 1030 HOH HOH . 
H 5 HOH B 5 4006 1032 HOH HOH . 
H 5 HOH B 6 4007 1033 HOH HOH . 
H 5 HOH B 7 4008 1034 HOH HOH . 
H 5 HOH B 8 4009 1035 HOH HOH . 
H 5 HOH B 9 4010 1036 HOH HOH . 
H 5 HOH B 10 4011 1037 HOH HOH . 
H 5 HOH B 11 4012 1038 HOH HOH . 
H 5 HOH B 12 4013 1039 HOH HOH . 
H 5 HOH B 13 4014 1040 HOH HOH . 
H 5 HOH B 14 4015 1041 HOH HOH . 
H 5 HOH B 15 4016 1042 HOH HOH . 
H 5 HOH B 16 4017 1043 HOH HOH . 
H 5 HOH B 17 4018 1045 HOH HOH . 
H 5 HOH B 18 4019 1046 HOH HOH . 
H 5 HOH B 19 4020 1047 HOH HOH . 
H 5 HOH B 20 4021 1048 HOH HOH . 
H 5 HOH B 21 4022 1049 HOH HOH . 
H 5 HOH B 22 4023 1050 HOH HOH . 
H 5 HOH B 23 4024 1051 HOH HOH . 
H 5 HOH B 24 4025 1052 HOH HOH . 
H 5 HOH B 25 4026 1053 HOH HOH . 
H 5 HOH B 26 4027 1054 HOH HOH . 
H 5 HOH B 27 4028 1055 HOH HOH . 
H 5 HOH B 28 4029 1056 HOH HOH . 
H 5 HOH B 29 4030 1057 HOH HOH . 
H 5 HOH B 30 4031 1058 HOH HOH . 
H 5 HOH B 31 4032 1059 HOH HOH . 
H 5 HOH B 32 4033 1060 HOH HOH . 
H 5 HOH B 33 4034 1061 HOH HOH . 
H 5 HOH B 34 4035 1062 HOH HOH . 
H 5 HOH B 35 4036 1063 HOH HOH . 
H 5 HOH B 36 4037 1064 HOH HOH . 
H 5 HOH B 37 4038 1067 HOH HOH . 
H 5 HOH B 38 4039 1069 HOH HOH . 
H 5 HOH B 39 4040 1070 HOH HOH . 
H 5 HOH B 40 4041 1071 HOH HOH . 
H 5 HOH B 41 4042 1072 HOH HOH . 
H 5 HOH B 42 4043 1075 HOH HOH . 
H 5 HOH B 43 4044 1076 HOH HOH . 
H 5 HOH B 44 4045 1078 HOH HOH . 
H 5 HOH B 45 4046 1079 HOH HOH . 
H 5 HOH B 46 4047 1080 HOH HOH . 
H 5 HOH B 47 4048 1081 HOH HOH . 
H 5 HOH B 48 4049 1083 HOH HOH . 
H 5 HOH B 49 4050 1093 HOH HOH . 
H 5 HOH B 50 4051 1102 HOH HOH . 
H 5 HOH B 51 4052 1103 HOH HOH . 
H 5 HOH B 52 4053 1104 HOH HOH . 
H 5 HOH B 53 4054 1105 HOH HOH . 
H 5 HOH B 54 4055 1106 HOH HOH . 
H 5 HOH B 55 4056 1107 HOH HOH . 
H 5 HOH B 56 4057 1108 HOH HOH . 
H 5 HOH B 57 4058 1109 HOH HOH . 
H 5 HOH B 58 4059 1110 HOH HOH . 
H 5 HOH B 59 4060 1111 HOH HOH . 
H 5 HOH B 60 4061 1112 HOH HOH . 
H 5 HOH B 61 4062 1113 HOH HOH . 
H 5 HOH B 62 4063 1114 HOH HOH . 
H 5 HOH B 63 4064 1116 HOH HOH . 
H 5 HOH B 64 4065 1117 HOH HOH . 
H 5 HOH B 65 4066 1118 HOH HOH . 
H 5 HOH B 66 4067 1119 HOH HOH . 
H 5 HOH B 67 4068 1120 HOH HOH . 
H 5 HOH B 68 4069 1123 HOH HOH . 
H 5 HOH B 69 4070 1124 HOH HOH . 
H 5 HOH B 70 4071 1125 HOH HOH . 
H 5 HOH B 71 4072 1126 HOH HOH . 
H 5 HOH B 72 4073 1129 HOH HOH . 
H 5 HOH B 73 4074 1130 HOH HOH . 
H 5 HOH B 74 4075 1131 HOH HOH . 
H 5 HOH B 75 4076 1132 HOH HOH . 
H 5 HOH B 76 4077 1133 HOH HOH . 
H 5 HOH B 77 4078 1134 HOH HOH . 
H 5 HOH B 78 4079 1135 HOH HOH . 
H 5 HOH B 79 4080 1136 HOH HOH . 
H 5 HOH B 80 4081 1137 HOH HOH . 
H 5 HOH B 81 4082 1138 HOH HOH . 
H 5 HOH B 82 4083 1140 HOH HOH . 
H 5 HOH B 83 4084 1157 HOH HOH . 
H 5 HOH B 84 4085 1158 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 N N SAH . . . C 2 26.515 52.808 18.374 1 64.55 ? N SAH 3001 A 1 
HETATM 2 C CA SAH . . . C 2 27.677 52.328 17.646 1 64.51 ? CA SAH 3001 A 1 
HETATM 3 C CB SAH . . . C 2 28.801 51.985 18.64 1 65.35 ? CB SAH 3001 A 1 
HETATM 4 C CG SAH . . . C 2 28.437 51.019 19.759 1 66.28 ? CG SAH 3001 A 1 
HETATM 5 S SD SAH . . . C 2 29.855 50.692 20.817 1 65.73 ? SD SAH 3001 A 1 
HETATM 6 C C SAH . . . C 2 27.335 51.142 16.741 1 65.29 ? C SAH 3001 A 1 
HETATM 7 O O SAH . . . C 2 28.251 50.367 16.389 1 65.1 ? O SAH 3001 A 1 
HETATM 8 O OXT SAH . . . C 2 26.15 51.026 16.356 1 65.38 ? OXT SAH 3001 A 1 
HETATM 9 C C5' SAH . . . C 2 29.343 51.482 22.379 1 70.48 ? C5' SAH 3001 A 1 
HETATM 10 C C4' SAH . . . C 2 29.644 52.963 22.373 1 72.72 ? C4' SAH 3001 A 1 
HETATM 11 O O4' SAH . . . C 2 29.209 53.616 23.598 1 73.99 ? O4' SAH 3001 A 1 
HETATM 12 C C3' SAH . . . C 2 31.103 53.351 22.159 1 74.83 ? C3' SAH 3001 A 1 
HETATM 13 O O3' SAH . . . C 2 31.211 54.26 21.066 1 74.99 ? O3' SAH 3001 A 1 
HETATM 14 C C2' SAH . . . C 2 31.519 53.934 23.509 1 75.32 ? C2' SAH 3001 A 1 
HETATM 15 O O2' SAH . . . C 2 32.539 54.912 23.421 1 78.74 ? O2' SAH 3001 A 1 
HETATM 16 C C1' SAH . . . C 2 30.205 54.535 24.007 1 74.17 ? C1' SAH 3001 A 1 
HETATM 17 N N9 SAH . . . C 2 30.112 54.727 25.46 1 72.68 ? N9 SAH 3001 A 1 
HETATM 18 C C8 SAH . . . C 2 30.973 54.237 26.491 1 72.1 ? C8 SAH 3001 A 1 
HETATM 19 N N7 SAH . . . C 2 30.608 54.613 27.693 1 72.24 ? N7 SAH 3001 A 1 
HETATM 20 C C5 SAH . . . C 2 29.47 55.372 27.46 1 73.11 ? C5 SAH 3001 A 1 
HETATM 21 C C6 SAH . . . C 2 28.642 56.051 28.393 1 74.85 ? C6 SAH 3001 A 1 
HETATM 22 N N6 SAH . . . C 2 28.844 56.048 29.716 1 73.75 ? N6 SAH 3001 A 1 
HETATM 23 N N1 SAH . . . C 2 27.575 56.744 27.895 1 75.17 ? N1 SAH 3001 A 1 
HETATM 24 C C2 SAH . . . C 2 27.375 56.741 26.549 1 73.69 ? C2 SAH 3001 A 1 
HETATM 25 N N3 SAH . . . C 2 28.104 56.129 25.581 1 72.6 ? N3 SAH 3001 A 1 
HETATM 26 C C4 SAH . . . C 2 29.147 55.454 26.113 1 72.18 ? C4 SAH 3001 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#