data_2H4J
#
_model_server_result.job_id            TDFnVAaWi26we79D2aeDyQ 
_model_server_result.datetime_utc      '2024-12-03 19:47:12' 
_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          2h4j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1003}' 
#
_entry.id    2H4J 
#
_exptl.entry_id    2H4J 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              601.352 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE" 
_entity.pdbx_number_of_molecules    1 
_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            2H4J 
_cell.length_a            46.049 
_cell.length_b            59.683 
_cell.length_c            107.35 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2H4J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 124 A CYS 124 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc2 A SG CYS 127 A CYS 127 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc3 A SG CYS 148 A CYS 148 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc4 A SG CYS 151 A CYS 151 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
#
_chem_comp.formula           'C17 H25 N5 O15 P2' 
_chem_comp.formula_weight    601.352 
_chem_comp.id                OAD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE" 
_chem_comp.type              'rna linking' 
_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
PA O1A OAD doub 252 n n 
PA O2A OAD sing 253 n n 
PA O5' OAD sing 254 n n 
PA O3A OAD sing 255 n n 
O2A HOA2 OAD sing 256 n n 
O5' C5' OAD sing 257 n n 
C5' C4' OAD sing 258 n n 
C5' "H5'1" OAD sing 259 n n 
C5' "H5'2" OAD sing 260 n n 
C4' O4' OAD sing 261 n n 
C4' C3' OAD sing 262 n n 
C4' "H'4" OAD sing 263 n n 
O4' C1' OAD sing 264 n n 
C3' O3' OAD sing 265 n n 
C3' C2' OAD sing 266 n n 
C3' "H'3" OAD sing 267 n n 
O3' "HO'3" OAD sing 268 n n 
C2' O2' OAD sing 269 n n 
C2' C1' OAD sing 270 n n 
C2' "H'2" OAD sing 271 n n 
O2' "HO'2" OAD sing 272 n n 
C1' N9 OAD sing 273 n n 
C1' "H'1" OAD sing 274 n n 
N9 C8 OAD sing 275 n y 
N9 C4 OAD sing 276 n y 
C8 N7 OAD doub 277 n y 
C8 H8 OAD sing 278 n n 
N7 C5 OAD sing 279 n y 
C5 C6 OAD doub 280 n y 
C5 C4 OAD sing 281 n y 
C6 N6 OAD sing 282 n n 
C6 N1 OAD sing 283 n y 
N6 H61 OAD sing 284 n n 
N6 H62 OAD sing 285 n n 
N1 C2 OAD doub 286 n y 
C2 N3 OAD sing 287 n y 
C2 H2 OAD sing 288 n n 
N3 C4 OAD doub 289 n y 
O3A PB OAD sing 290 n n 
PB O1B OAD doub 291 n n 
PB O2B OAD sing 292 n n 
PB O5D OAD sing 293 n n 
O2B HOB2 OAD sing 294 n n 
O2D C2D OAD sing 295 n n 
O2D C6D OAD sing 296 n n 
O5D C5D OAD sing 297 n n 
C5D C4D OAD sing 298 n n 
C5D H5R1 OAD sing 299 n n 
C5D H5R2 OAD sing 300 n n 
C4D O4D OAD sing 301 n n 
C4D C3D OAD sing 302 n n 
C4D "HR'4" OAD sing 303 n n 
O4D C1D OAD sing 304 n n 
C3D O3D OAD sing 305 n n 
C3D C2D OAD sing 306 n n 
C3D "HR'3" OAD sing 307 n n 
O3D HOR3 OAD sing 308 n n 
C2D C1D OAD sing 309 n n 
C2D "HR'2" OAD sing 310 n n 
C1D O1D OAD sing 311 n n 
C1D "HR'1" OAD sing 312 n n 
O1D HOR1 OAD sing 313 n n 
C6D O6D OAD doub 314 n n 
C6D C7D OAD sing 315 n n 
C7D H7R1 OAD sing 316 n n 
C7D H7R2 OAD sing 317 n n 
C7D H7R3 OAD sing 318 n n 
#
_atom_sites.entry_id                     2H4J 
_atom_sites.fract_transf_matrix[1][1]    0.021716 
_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]    0.016755 
_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]    0.009315 
_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 3 ZN A 1 1001 1001 ZN ZN . 
D 4 NCA A 1 1002 1 NCA NCA . 
E 5 OAD A 1 1003 2 OAD OAD . 
F 6 HOH A 1 1004 3 HOH HOH . 
F 6 HOH A 2 1005 5 HOH HOH . 
F 6 HOH A 3 1006 6 HOH HOH . 
F 6 HOH A 4 1007 7 HOH HOH . 
F 6 HOH A 5 1008 8 HOH HOH . 
F 6 HOH A 6 1009 9 HOH HOH . 
F 6 HOH A 7 1010 10 HOH HOH . 
F 6 HOH A 8 1011 11 HOH HOH . 
F 6 HOH A 9 1012 12 HOH HOH . 
F 6 HOH A 10 1013 13 HOH HOH . 
F 6 HOH A 11 1014 14 HOH HOH . 
F 6 HOH A 12 1015 15 HOH HOH . 
F 6 HOH A 13 1016 17 HOH HOH . 
F 6 HOH A 14 1017 20 HOH HOH . 
F 6 HOH A 15 1018 21 HOH HOH . 
F 6 HOH A 16 1019 22 HOH HOH . 
F 6 HOH A 17 1020 23 HOH HOH . 
F 6 HOH A 18 1021 25 HOH HOH . 
F 6 HOH A 19 1022 27 HOH HOH . 
F 6 HOH A 20 1023 28 HOH HOH . 
F 6 HOH A 21 1024 30 HOH HOH . 
F 6 HOH A 22 1025 34 HOH HOH . 
F 6 HOH A 23 1026 35 HOH HOH . 
F 6 HOH A 24 1027 36 HOH HOH . 
F 6 HOH A 25 1028 37 HOH HOH . 
F 6 HOH A 26 1029 38 HOH HOH . 
F 6 HOH A 27 1030 41 HOH HOH . 
F 6 HOH A 28 1031 42 HOH HOH . 
F 6 HOH A 29 1032 43 HOH HOH . 
F 6 HOH A 30 1033 47 HOH HOH . 
F 6 HOH A 31 1034 48 HOH HOH . 
F 6 HOH A 32 1035 49 HOH HOH . 
F 6 HOH A 33 1036 50 HOH HOH . 
F 6 HOH A 34 1037 51 HOH HOH . 
F 6 HOH A 35 1038 52 HOH HOH . 
F 6 HOH A 36 1039 53 HOH HOH . 
F 6 HOH A 37 1040 56 HOH HOH . 
F 6 HOH A 38 1041 57 HOH HOH . 
F 6 HOH A 39 1042 59 HOH HOH . 
F 6 HOH A 40 1043 60 HOH HOH . 
F 6 HOH A 41 1044 61 HOH HOH . 
F 6 HOH A 42 1045 64 HOH HOH . 
F 6 HOH A 43 1046 68 HOH HOH . 
F 6 HOH A 44 1047 72 HOH HOH . 
F 6 HOH A 45 1048 79 HOH HOH . 
F 6 HOH A 46 1049 80 HOH HOH . 
F 6 HOH A 47 1050 83 HOH HOH . 
F 6 HOH A 48 1051 88 HOH HOH . 
F 6 HOH A 49 1052 89 HOH HOH . 
F 6 HOH A 50 1053 92 HOH HOH . 
F 6 HOH A 51 1054 94 HOH HOH . 
F 6 HOH A 52 1055 97 HOH HOH . 
F 6 HOH A 53 1056 98 HOH HOH . 
F 6 HOH A 54 1057 99 HOH HOH . 
F 6 HOH A 55 1058 101 HOH HOH . 
F 6 HOH A 56 1059 105 HOH HOH . 
F 6 HOH A 57 1060 106 HOH HOH . 
F 6 HOH A 58 1061 108 HOH HOH . 
F 6 HOH A 59 1062 109 HOH HOH . 
F 6 HOH A 60 1063 110 HOH HOH . 
F 6 HOH A 61 1064 113 HOH HOH . 
F 6 HOH A 62 1065 114 HOH HOH . 
F 6 HOH A 63 1066 117 HOH HOH . 
F 6 HOH A 64 1067 118 HOH HOH . 
F 6 HOH A 65 1068 119 HOH HOH . 
F 6 HOH A 66 1069 121 HOH HOH . 
F 6 HOH A 67 1070 122 HOH HOH . 
F 6 HOH A 68 1071 125 HOH HOH . 
F 6 HOH A 69 1072 126 HOH HOH . 
F 6 HOH A 70 1073 131 HOH HOH . 
F 6 HOH A 71 1074 132 HOH HOH . 
F 6 HOH A 72 1075 136 HOH HOH . 
F 6 HOH A 73 1076 137 HOH HOH . 
F 6 HOH A 74 1077 138 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 P PA OAD . . . E 5 10.9 20.769 13.319 1 80.99 ? PA OAD 1003 A 1 
HETATM 2 O O1A OAD . . . E 5 10.457 22.082 12.722 1 82.68 ? O1A OAD 1003 A 1 
HETATM 3 O O2A OAD . . . E 5 11.91 20.906 14.443 1 84.03 ? O2A OAD 1003 A 1 
HETATM 4 O O5' OAD . . . E 5 11.5 19.675 12.23 1 81.37 ? O5' OAD 1003 A 1 
HETATM 5 C C5' OAD . . . E 5 10.844 18.93 11.165 1 74.91 ? C5' OAD 1003 A 1 
HETATM 6 C C4' OAD . . . E 5 11.727 17.919 10.404 1 73.43 ? C4' OAD 1003 A 1 
HETATM 7 O O4' OAD . . . E 5 11.127 17.568 9.134 1 70.81 ? O4' OAD 1003 A 1 
HETATM 8 C C3' OAD . . . E 5 13.203 18.334 10.152 1 72.33 ? C3' OAD 1003 A 1 
HETATM 9 O O3' OAD . . . E 5 14.167 17.426 10.74 1 70.81 ? O3' OAD 1003 A 1 
HETATM 10 C C2' OAD . . . E 5 13.315 18.327 8.634 1 72.57 ? C2' OAD 1003 A 1 
HETATM 11 O O2' OAD . . . E 5 14.582 17.909 8.109 1 70.72 ? O2' OAD 1003 A 1 
HETATM 12 C C1' OAD . . . E 5 12.198 17.376 8.207 1 65.86 ? C1' OAD 1003 A 1 
HETATM 13 N N9 OAD . . . E 5 11.85 17.626 6.795 1 68.88 ? N9 OAD 1003 A 1 
HETATM 14 C C8 OAD . . . E 5 11.857 18.819 6.157 1 67.71 ? C8 OAD 1003 A 1 
HETATM 15 N N7 OAD . . . E 5 11.499 18.683 4.859 1 67.08 ? N7 OAD 1003 A 1 
HETATM 16 C C5 OAD . . . E 5 11.265 17.364 4.646 1 68.42 ? C5 OAD 1003 A 1 
HETATM 17 C C6 OAD . . . E 5 10.835 16.513 3.492 1 69 ? C6 OAD 1003 A 1 
HETATM 18 N N6 OAD . . . E 5 10.605 17.052 2.271 1 69.09 ? N6 OAD 1003 A 1 
HETATM 19 N N1 OAD . . . E 5 10.691 15.196 3.705 1 67.36 ? N1 OAD 1003 A 1 
HETATM 20 C C2 OAD . . . E 5 10.953 14.641 4.921 1 68.82 ? C2 OAD 1003 A 1 
HETATM 21 N N3 OAD . . . E 5 11.333 15.315 6.02 1 65.14 ? N3 OAD 1003 A 1 
HETATM 22 C C4 OAD . . . E 5 11.506 16.666 5.939 1 67.8 ? C4 OAD 1003 A 1 
HETATM 23 O O3A OAD . . . E 5 9.587 20.059 13.961 1 82.39 ? O3A OAD 1003 A 1 
HETATM 24 P PB OAD . . . E 5 8.338 19.787 13.012 1 80.74 ? PB OAD 1003 A 1 
HETATM 25 O O1B OAD . . . E 5 7.106 20.109 13.804 1 80.87 ? O1B OAD 1003 A 1 
HETATM 26 O O2B OAD . . . E 5 8.551 18.402 12.489 1 80.26 ? O2B OAD 1003 A 1 
HETATM 27 O O2D OAD . . . E 5 12.3 23.057 7.451 1 85.87 ? O2D OAD 1003 A 1 
HETATM 28 O O5D OAD . . . E 5 8.633 20.923 11.854 1 84.09 ? O5D OAD 1003 A 1 
HETATM 29 C C5D OAD . . . E 5 9.393 20.762 10.604 1 85.59 ? C5D OAD 1003 A 1 
HETATM 30 C C4D OAD . . . E 5 10.212 21.963 10.02 1 85.9 ? C4D OAD 1003 A 1 
HETATM 31 O O4D OAD . . . E 5 11.558 22.045 10.537 1 85.79 ? O4D OAD 1003 A 1 
HETATM 32 C C3D OAD . . . E 5 10.381 21.922 8.49 1 85.62 ? C3D OAD 1003 A 1 
HETATM 33 O O3D OAD . . . E 5 9.732 23.053 7.877 1 84.89 ? O3D OAD 1003 A 1 
HETATM 34 C C2D OAD . . . E 5 11.88 21.893 8.177 1 85.94 ? C2D OAD 1003 A 1 
HETATM 35 C C1D OAD . . . E 5 12.572 21.799 9.537 1 85.95 ? C1D OAD 1003 A 1 
HETATM 36 O O1D OAD . . . E 5 13.702 22.69 9.668 1 86.44 ? O1D OAD 1003 A 1 
HETATM 37 C C6D OAD . . . E 5 12.27 22.923 5.993 1 84.68 ? C6D OAD 1003 A 1 
HETATM 38 O O6D OAD . . . E 5 12.617 21.849 5.507 1 86.2 ? O6D OAD 1003 A 1 
HETATM 39 C C7D OAD . . . E 5 11.833 24.099 5.147 1 85.07 ? C7D OAD 1003 A 1 
#
_model_server_stats.io_time_ms              66 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#