data_2AZ3 # _model_server_result.job_id xBuEOPrZrqGu7zz3HxQvuA _model_server_result.datetime_utc '2024-10-19 01:38:32' _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 2az3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":1800}' # _entry.id 2AZ3 # _exptl.entry_id 2AZ3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 9 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.53 _cell.angle_gamma 90 _cell.entry_id 2AZ3 _cell.length_a 124.37 _cell.length_b 71.52 _cell.length_c 157.99 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2AZ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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 ? hexameric 6 author_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,J,K,L,M,N,U,V,W 1 1,2 D,E,F,G,H,I,O,P,Q,R,S,T,X,Y,Z,AA,BA,CA 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 K N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 T 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 OE2 GLU 58 A GLU 55 1_555 J MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc2 J MG MG . A MG 201 1_555 K O1A CDP . A CDP 1100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc3 B OE1 GLU 58 B GLU 55 1_555 L MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc4 L MG MG . B MG 202 1_555 M O1A CDP . B CDP 1200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? # _chem_comp.formula 'C9 H15 N3 O11 P2' _chem_comp.formula_weight 403.176 _chem_comp.id CDP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-DIPHOSPHATE" _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 O3B PB CDP sing 70 n n PB O1B CDP doub 71 n n PB O2B CDP sing 72 n n PB O3A CDP sing 73 n n O3A PA CDP sing 74 n n PA O1A CDP doub 75 n n PA O2A CDP sing 76 n n PA O5' CDP sing 77 n n O5' C5' CDP sing 78 n n C5' C4' CDP sing 79 n n C5' "H5'1" CDP sing 80 n n C5' "H5'2" CDP sing 81 n n C4' O4' CDP sing 82 n n C4' C3' CDP sing 83 n n C4' H4' CDP sing 84 n n O4' C1' CDP sing 85 n n C3' O3' CDP sing 86 n n C3' C2' CDP sing 87 n n C3' H3' CDP sing 88 n n O3' HA CDP sing 89 n n C2' O2' CDP sing 90 n n C2' C1' CDP sing 91 n n C2' H2' CDP sing 92 n n O2' HB CDP sing 93 n n C1' N1 CDP sing 94 n n C1' H1' CDP sing 95 n n N1 C2 CDP sing 96 n n N1 C6 CDP sing 97 n n C2 O2 CDP doub 98 n n C2 N3 CDP sing 99 n n N3 C4 CDP doub 100 n n C4 N4 CDP sing 101 n n C4 C5 CDP sing 102 n n N4 H4N1 CDP sing 103 n n N4 H4N2 CDP sing 104 n n C5 C6 CDP doub 105 n n C5 H5 CDP sing 106 n n C6 H6 CDP sing 107 n n HO1 O2A CDP sing 108 n n HO2 O2B CDP sing 109 n n HO3 O3B CDP sing 110 n n # _atom_sites.entry_id 2AZ3 _atom_sites.fract_transf_matrix[1][1] 0.008041 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000779 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013982 _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] 0.006359 _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 J 2 MG A 1 201 1 MG MG . K 3 CDP A 1 1100 1100 CDP CDP . L 2 MG B 1 202 2 MG MG . M 3 CDP B 1 1200 1200 CDP CDP . N 3 CDP C 1 1300 1300 CDP CDP . O 3 CDP D 1 1400 1400 CDP CDP . P 3 CDP E 1 1500 1500 CDP CDP . Q 3 CDP F 1 1600 1600 CDP CDP . R 3 CDP G 1 1700 1700 CDP CDP . S 3 CDP H 1 1800 1800 CDP CDP . T 3 CDP I 1 1900 1900 CDP CDP . U 4 HOH A 1 1101 2 HOH WAT . U 4 HOH A 2 1102 11 HOH WAT . U 4 HOH A 3 1103 12 HOH WAT . U 4 HOH A 4 1104 18 HOH WAT . U 4 HOH A 5 1105 19 HOH WAT . U 4 HOH A 6 1106 24 HOH WAT . U 4 HOH A 7 1107 25 HOH WAT . U 4 HOH A 8 1108 27 HOH WAT . U 4 HOH A 9 1109 31 HOH WAT . U 4 HOH A 10 1110 40 HOH WAT . U 4 HOH A 11 1111 41 HOH WAT . U 4 HOH A 12 1112 67 HOH WAT . U 4 HOH A 13 1113 68 HOH WAT . U 4 HOH A 14 1114 79 HOH WAT . U 4 HOH A 15 1115 88 HOH WAT . U 4 HOH A 16 1116 90 HOH WAT . U 4 HOH A 17 1117 98 HOH WAT . U 4 HOH A 18 1118 100 HOH WAT . U 4 HOH A 19 1119 103 HOH WAT . U 4 HOH A 20 1120 106 HOH WAT . U 4 HOH A 21 1121 109 HOH WAT . U 4 HOH A 22 1122 121 HOH WAT . U 4 HOH A 23 1123 122 HOH WAT . U 4 HOH A 24 1124 126 HOH WAT . U 4 HOH A 25 1125 137 HOH WAT . V 4 HOH B 1 1201 5 HOH WAT . V 4 HOH B 2 1202 20 HOH WAT . V 4 HOH B 3 1203 21 HOH WAT . V 4 HOH B 4 1204 29 HOH WAT . V 4 HOH B 5 1205 32 HOH WAT . V 4 HOH B 6 1206 45 HOH WAT . V 4 HOH B 7 1207 46 HOH WAT . V 4 HOH B 8 1208 61 HOH WAT . V 4 HOH B 9 1209 62 HOH WAT . V 4 HOH B 10 1210 65 HOH WAT . V 4 HOH B 11 1211 69 HOH WAT . V 4 HOH B 12 1212 82 HOH WAT . V 4 HOH B 13 1213 83 HOH WAT . V 4 HOH B 14 1214 101 HOH WAT . V 4 HOH B 15 1215 115 HOH WAT . V 4 HOH B 16 1216 116 HOH WAT . V 4 HOH B 17 1217 117 HOH WAT . V 4 HOH B 18 1218 123 HOH WAT . V 4 HOH B 19 1219 130 HOH WAT . W 4 HOH C 1 1301 1 HOH WAT . W 4 HOH C 2 1302 9 HOH WAT . W 4 HOH C 3 1303 13 HOH WAT . W 4 HOH C 4 1304 14 HOH WAT . W 4 HOH C 5 1305 28 HOH WAT . W 4 HOH C 6 1306 36 HOH WAT . W 4 HOH C 7 1307 37 HOH WAT . W 4 HOH C 8 1308 39 HOH WAT . W 4 HOH C 9 1309 43 HOH WAT . W 4 HOH C 10 1310 55 HOH WAT . W 4 HOH C 11 1311 70 HOH WAT . W 4 HOH C 12 1312 74 HOH WAT . W 4 HOH C 13 1313 77 HOH WAT . W 4 HOH C 14 1314 89 HOH WAT . W 4 HOH C 15 1315 99 HOH WAT . W 4 HOH C 16 1316 107 HOH WAT . W 4 HOH C 17 1317 125 HOH WAT . W 4 HOH C 18 1318 128 HOH WAT . W 4 HOH C 19 1319 136 HOH WAT . X 4 HOH D 1 1401 7 HOH WAT . X 4 HOH D 2 1402 15 HOH WAT . X 4 HOH D 3 1403 26 HOH WAT . X 4 HOH D 4 1404 38 HOH WAT . X 4 HOH D 5 1405 49 HOH WAT . X 4 HOH D 6 1406 51 HOH WAT . X 4 HOH D 7 1407 64 HOH WAT . X 4 HOH D 8 1408 81 HOH WAT . X 4 HOH D 9 1409 86 HOH WAT . X 4 HOH D 10 1410 91 HOH WAT . X 4 HOH D 11 1411 92 HOH WAT . X 4 HOH D 12 1412 97 HOH WAT . X 4 HOH D 13 1413 114 HOH WAT . X 4 HOH D 14 1414 124 HOH WAT . X 4 HOH D 15 1415 139 HOH WAT . Y 4 HOH E 1 1501 8 HOH WAT . Y 4 HOH E 2 1502 22 HOH WAT . Y 4 HOH E 3 1503 42 HOH WAT . Y 4 HOH E 4 1504 52 HOH WAT . Y 4 HOH E 5 1505 54 HOH WAT . Y 4 HOH E 6 1506 57 HOH WAT . Y 4 HOH E 7 1507 63 HOH WAT . Y 4 HOH E 8 1508 75 HOH WAT . Y 4 HOH E 9 1509 78 HOH WAT . Y 4 HOH E 10 1510 87 HOH WAT . Y 4 HOH E 11 1511 95 HOH WAT . Y 4 HOH E 12 1512 102 HOH WAT . Z 4 HOH F 1 1601 3 HOH WAT . Z 4 HOH F 2 1602 10 HOH WAT . Z 4 HOH F 3 1603 33 HOH WAT . Z 4 HOH F 4 1604 47 HOH WAT . Z 4 HOH F 5 1605 53 HOH WAT . Z 4 HOH F 6 1606 72 HOH WAT . Z 4 HOH F 7 1607 76 HOH WAT . Z 4 HOH F 8 1608 96 HOH WAT . Z 4 HOH F 9 1609 108 HOH WAT . Z 4 HOH F 10 1610 120 HOH WAT . Z 4 HOH F 11 1611 134 HOH WAT . Z 4 HOH F 12 1612 135 HOH WAT . Z 4 HOH F 13 1613 140 HOH WAT . AA 4 HOH G 1 1701 6 HOH WAT . AA 4 HOH G 2 1702 23 HOH WAT . AA 4 HOH G 3 1703 35 HOH WAT . AA 4 HOH G 4 1704 60 HOH WAT . AA 4 HOH G 5 1705 71 HOH WAT . AA 4 HOH G 6 1706 85 HOH WAT . AA 4 HOH G 7 1707 111 HOH WAT . AA 4 HOH G 8 1708 112 HOH WAT . AA 4 HOH G 9 1709 113 HOH WAT . AA 4 HOH G 10 1710 118 HOH WAT . AA 4 HOH G 11 1711 133 HOH WAT . BA 4 HOH H 1 1801 4 HOH WAT . BA 4 HOH H 2 1802 30 HOH WAT . BA 4 HOH H 3 1803 34 HOH WAT . BA 4 HOH H 4 1804 44 HOH WAT . BA 4 HOH H 5 1805 48 HOH WAT . BA 4 HOH H 6 1806 50 HOH WAT . BA 4 HOH H 7 1807 56 HOH WAT . BA 4 HOH H 8 1808 58 HOH WAT . BA 4 HOH H 9 1809 59 HOH WAT . BA 4 HOH H 10 1810 66 HOH WAT . BA 4 HOH H 11 1811 84 HOH WAT . BA 4 HOH H 12 1812 93 HOH WAT . BA 4 HOH H 13 1813 94 HOH WAT . BA 4 HOH H 14 1814 110 HOH WAT . BA 4 HOH H 15 1815 119 HOH WAT . BA 4 HOH H 16 1816 131 HOH WAT . BA 4 HOH H 17 1817 132 HOH WAT . CA 4 HOH I 1 1901 16 HOH WAT . CA 4 HOH I 2 1902 17 HOH WAT . CA 4 HOH I 3 1903 73 HOH WAT . CA 4 HOH I 4 1904 80 HOH WAT . CA 4 HOH I 5 1905 104 HOH WAT . CA 4 HOH I 6 1906 105 HOH WAT . CA 4 HOH I 7 1907 127 HOH WAT . CA 4 HOH I 8 1908 129 HOH WAT . CA 4 HOH I 9 1909 138 HOH WAT . # 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 O O3B CDP . . . S 3 25.232 -54.764 70.153 1 72.42 ? O3B CDP 1800 H 1 HETATM 2 P PB CDP . . . S 3 25.433 -54.291 71.667 1 73.54 ? PB CDP 1800 H 1 HETATM 3 O O1B CDP . . . S 3 26.999 -54.272 71.972 1 70.23 ? O1B CDP 1800 H 1 HETATM 4 O O2B CDP . . . S 3 24.789 -52.837 71.805 1 73.4 ? O2B CDP 1800 H 1 HETATM 5 O O3A CDP . . . S 3 24.707 -55.273 72.788 1 73.15 ? O3A CDP 1800 H 1 HETATM 6 P PA CDP . . . S 3 25.263 -56.64 73.528 1 71.03 ? PA CDP 1800 H 1 HETATM 7 O O1A CDP . . . S 3 26.85 -56.79 73.46 1 70.72 ? O1A CDP 1800 H 1 HETATM 8 O O2A CDP . . . S 3 24.756 -56.821 75.042 1 68.99 ? O2A CDP 1800 H 1 HETATM 9 O O5' CDP . . . S 3 24.521 -57.812 72.71 1 68.31 ? O5' CDP 1800 H 1 HETATM 10 C C5' CDP . . . S 3 24.629 -57.881 71.306 1 65.93 ? C5' CDP 1800 H 1 HETATM 11 C C4' CDP . . . S 3 23.289 -57.716 70.573 1 64.44 ? C4' CDP 1800 H 1 HETATM 12 O O4' CDP . . . S 3 22.265 -58.662 70.965 1 64.99 ? O4' CDP 1800 H 1 HETATM 13 C C3' CDP . . . S 3 22.632 -56.314 70.481 1 63.34 ? C3' CDP 1800 H 1 HETATM 14 O O3' CDP . . . S 3 23.009 -55.514 69.346 1 62.11 ? O3' CDP 1800 H 1 HETATM 15 C C2' CDP . . . S 3 21.135 -56.568 70.637 1 62.54 ? C2' CDP 1800 H 1 HETATM 16 O O2' CDP . . . S 3 20.346 -56.323 69.498 1 59.31 ? O2' CDP 1800 H 1 HETATM 17 C C1' CDP . . . S 3 20.963 -58.056 70.895 1 64 ? C1' CDP 1800 H 1 HETATM 18 N N1 CDP . . . S 3 20 -58.238 71.997 1 65.54 ? N1 CDP 1800 H 1 HETATM 19 C C2 CDP . . . S 3 18.741 -58.806 71.644 1 67.08 ? C2 CDP 1800 H 1 HETATM 20 O O2 CDP . . . S 3 18.497 -59.171 70.458 1 68.94 ? O2 CDP 1800 H 1 HETATM 21 N N3 CDP . . . S 3 17.797 -58.969 72.582 1 64.51 ? N3 CDP 1800 H 1 HETATM 22 C C4 CDP . . . S 3 18.041 -58.576 73.841 1 64.44 ? C4 CDP 1800 H 1 HETATM 23 N N4 CDP . . . S 3 17.073 -58.769 74.753 1 65.08 ? N4 CDP 1800 H 1 HETATM 24 C C5 CDP . . . S 3 19.254 -58.007 74.214 1 64.39 ? C5 CDP 1800 H 1 HETATM 25 C C6 CDP . . . S 3 20.235 -57.823 73.251 1 63.98 ? C6 CDP 1800 H 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #