data_4RPH # _model_server_result.job_id dZqG5BoTivCJjXGLQZQlBg _model_server_result.datetime_utc '2024-11-24 15:45:51' _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 4rph # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":402}' # _entry.id 4RPH # _exptl.entry_id 4RPH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _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 110.17 _cell.angle_gamma 90 _cell.entry_id 4RPH _cell.length_a 171.73 _cell.length_b 99.47 _cell.length_c 100.24 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RPH _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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,J 1 1,2 B,C,F,G,H,I,K,L 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_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 171.73 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 E N N ? 3 G N N ? 3 I N N # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id GDU _chem_comp.mon_nstd_flag . _chem_comp.name "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms UDP-D-GALACTOPYRANOSE # 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 N1 C2 GDU sing 161 n n N1 C6 GDU sing 162 n n N1 C1D GDU sing 163 n n C2 N3 GDU sing 164 n n C2 O2 GDU doub 165 n n N3 C4 GDU sing 166 n n N3 HN3 GDU sing 167 n n C4 C5 GDU sing 168 n n C4 O4 GDU doub 169 n n C5 C6 GDU doub 170 n n C5 H5 GDU sing 171 n n C6 H6 GDU sing 172 n n C1D C2D GDU sing 173 n n C1D O4D GDU sing 174 n n C1D H1D GDU sing 175 n n C2D O2D GDU sing 176 n n C2D C3D GDU sing 177 n n C2D H2D GDU sing 178 n n O2D HO2' GDU sing 179 n n C3D C4D GDU sing 180 n n C3D O3D GDU sing 181 n n C3D H3D GDU sing 182 n n C4D O4D GDU sing 183 n n C4D C5D GDU sing 184 n n C4D H4D GDU sing 185 n n O3D HO3' GDU sing 186 n n C5D O5D GDU sing 187 n n C5D "H5'1" GDU sing 188 n n C5D "H5'2" GDU sing 189 n n O5D PA GDU sing 190 n n PA O1A GDU doub 191 n n PA O2A GDU sing 192 n n PA O3A GDU sing 193 n n O2A HOA2 GDU sing 194 n n O3A PB GDU sing 195 n n PB O1B GDU doub 196 n n PB O2B GDU sing 197 n n PB O3B GDU sing 198 n n O2B HOB2 GDU sing 199 n n O3B C1' GDU sing 200 n n C1' C2' GDU sing 201 n n C1' O5' GDU sing 202 n n C1' H1' GDU sing 203 n n C2' C3' GDU sing 204 n n C2' O2' GDU sing 205 n n C2' H2' GDU sing 206 n n C3' C4' GDU sing 207 n n C3' O3' GDU sing 208 n n C3' H3' GDU sing 209 n n C4' C5' GDU sing 210 n n C4' O4' GDU sing 211 n n C4' H4' GDU sing 212 n n C5' C6' GDU sing 213 n n C5' O5' GDU sing 214 n n C5' H5' GDU sing 215 n n C6' O6' GDU sing 216 n n C6' "H6'1" GDU sing 217 n n C6' "H6'2" GDU sing 218 n n O2' HO2A GDU sing 219 n n O3' HO3A GDU sing 220 n n O4' HO4' GDU sing 221 n n O6' HO6' GDU sing 222 n n # _atom_sites.entry_id 4RPH _atom_sites.fract_transf_matrix[1][1] 0.005823 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002139 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010053 _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] 0.010628 _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 FAD B 1 401 602 FAD FAD . E 3 GDU B 1 402 500 GDU GDU . F 2 FAD A 1 401 602 FAD FAD . G 3 GDU A 1 402 500 GDU GDU . H 2 FAD C 1 401 602 FAD FAD . I 3 GDU C 1 402 500 GDU GDU . J 4 HOH B 1 501 2 HOH HOH . J 4 HOH B 2 502 5 HOH HOH . J 4 HOH B 3 503 7 HOH HOH . J 4 HOH B 4 504 8 HOH HOH . J 4 HOH B 5 505 10 HOH HOH . J 4 HOH B 6 506 12 HOH HOH . J 4 HOH B 7 507 13 HOH HOH . J 4 HOH B 8 508 14 HOH HOH . J 4 HOH B 9 509 15 HOH HOH . J 4 HOH B 10 510 16 HOH HOH . J 4 HOH B 11 511 17 HOH HOH . J 4 HOH B 12 512 19 HOH HOH . J 4 HOH B 13 513 22 HOH HOH . J 4 HOH B 14 514 30 HOH HOH . J 4 HOH B 15 515 31 HOH HOH . J 4 HOH B 16 516 32 HOH HOH . J 4 HOH B 17 517 33 HOH HOH . J 4 HOH B 18 518 35 HOH HOH . J 4 HOH B 19 519 36 HOH HOH . J 4 HOH B 20 520 43 HOH HOH . J 4 HOH B 21 521 45 HOH HOH . J 4 HOH B 22 522 48 HOH HOH . J 4 HOH B 23 523 50 HOH HOH . J 4 HOH B 24 524 51 HOH HOH . J 4 HOH B 25 525 52 HOH HOH . J 4 HOH B 26 526 53 HOH HOH . J 4 HOH B 27 527 57 HOH HOH . J 4 HOH B 28 528 59 HOH HOH . J 4 HOH B 29 529 62 HOH HOH . J 4 HOH B 30 530 63 HOH HOH . J 4 HOH B 31 531 65 HOH HOH . J 4 HOH B 32 532 69 HOH HOH . J 4 HOH B 33 533 70 HOH HOH . J 4 HOH B 34 534 74 HOH HOH . J 4 HOH B 35 535 77 HOH HOH . J 4 HOH B 36 536 78 HOH HOH . J 4 HOH B 37 537 85 HOH HOH . J 4 HOH B 38 538 87 HOH HOH . J 4 HOH B 39 539 88 HOH HOH . J 4 HOH B 40 540 90 HOH HOH . J 4 HOH B 41 541 94 HOH HOH . J 4 HOH B 42 542 95 HOH HOH . J 4 HOH B 43 543 98 HOH HOH . J 4 HOH B 44 544 102 HOH HOH . J 4 HOH B 45 545 104 HOH HOH . J 4 HOH B 46 546 106 HOH HOH . J 4 HOH B 47 547 110 HOH HOH . J 4 HOH B 48 548 112 HOH HOH . J 4 HOH B 49 549 113 HOH HOH . J 4 HOH B 50 550 114 HOH HOH . J 4 HOH B 51 551 115 HOH HOH . J 4 HOH B 52 552 116 HOH HOH . J 4 HOH B 53 553 122 HOH HOH . J 4 HOH B 54 554 123 HOH HOH . J 4 HOH B 55 555 124 HOH HOH . J 4 HOH B 56 556 136 HOH HOH . J 4 HOH B 57 557 138 HOH HOH . J 4 HOH B 58 558 139 HOH HOH . J 4 HOH B 59 559 140 HOH HOH . J 4 HOH B 60 560 142 HOH HOH . K 4 HOH A 1 501 9 HOH HOH . K 4 HOH A 2 502 23 HOH HOH . K 4 HOH A 3 503 26 HOH HOH . K 4 HOH A 4 504 28 HOH HOH . K 4 HOH A 5 505 29 HOH HOH . K 4 HOH A 6 506 34 HOH HOH . K 4 HOH A 7 507 37 HOH HOH . K 4 HOH A 8 508 39 HOH HOH . K 4 HOH A 9 509 46 HOH HOH . K 4 HOH A 10 510 55 HOH HOH . K 4 HOH A 11 511 56 HOH HOH . K 4 HOH A 12 512 58 HOH HOH . K 4 HOH A 13 513 60 HOH HOH . K 4 HOH A 14 514 67 HOH HOH . K 4 HOH A 15 515 75 HOH HOH . K 4 HOH A 16 516 76 HOH HOH . K 4 HOH A 17 517 79 HOH HOH . K 4 HOH A 18 518 82 HOH HOH . K 4 HOH A 19 519 86 HOH HOH . K 4 HOH A 20 520 91 HOH HOH . K 4 HOH A 21 521 92 HOH HOH . K 4 HOH A 22 522 96 HOH HOH . K 4 HOH A 23 523 99 HOH HOH . K 4 HOH A 24 524 100 HOH HOH . K 4 HOH A 25 525 107 HOH HOH . K 4 HOH A 26 526 109 HOH HOH . K 4 HOH A 27 527 111 HOH HOH . K 4 HOH A 28 528 117 HOH HOH . K 4 HOH A 29 529 118 HOH HOH . K 4 HOH A 30 530 119 HOH HOH . K 4 HOH A 31 531 120 HOH HOH . K 4 HOH A 32 532 121 HOH HOH . K 4 HOH A 33 533 125 HOH HOH . K 4 HOH A 34 534 126 HOH HOH . K 4 HOH A 35 535 127 HOH HOH . K 4 HOH A 36 536 128 HOH HOH . K 4 HOH A 37 537 135 HOH HOH . K 4 HOH A 38 538 141 HOH HOH . L 4 HOH C 1 501 1 HOH HOH . L 4 HOH C 2 502 3 HOH HOH . L 4 HOH C 3 503 4 HOH HOH . L 4 HOH C 4 504 6 HOH HOH . L 4 HOH C 5 505 11 HOH HOH . L 4 HOH C 6 506 20 HOH HOH . L 4 HOH C 7 507 21 HOH HOH . L 4 HOH C 8 508 25 HOH HOH . L 4 HOH C 9 509 27 HOH HOH . L 4 HOH C 10 510 38 HOH HOH . L 4 HOH C 11 511 42 HOH HOH . L 4 HOH C 12 512 47 HOH HOH . L 4 HOH C 13 513 49 HOH HOH . L 4 HOH C 14 514 54 HOH HOH . L 4 HOH C 15 515 61 HOH HOH . L 4 HOH C 16 516 64 HOH HOH . L 4 HOH C 17 517 68 HOH HOH . L 4 HOH C 18 518 80 HOH HOH . L 4 HOH C 19 519 83 HOH HOH . L 4 HOH C 20 520 84 HOH HOH . L 4 HOH C 21 521 89 HOH HOH . L 4 HOH C 22 522 93 HOH HOH . L 4 HOH C 23 523 97 HOH HOH . L 4 HOH C 24 524 101 HOH HOH . L 4 HOH C 25 525 105 HOH HOH . L 4 HOH C 26 526 108 HOH HOH . L 4 HOH C 27 527 129 HOH HOH . L 4 HOH C 28 528 130 HOH HOH . L 4 HOH C 29 529 132 HOH HOH . L 4 HOH C 30 530 133 HOH HOH . L 4 HOH C 31 531 134 HOH HOH . L 4 HOH C 32 532 137 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 N1 GDU . . . I 3 24.043 -2.85 -18.228 1 79.34 ? N1 GDU 402 C 1 HETATM 2 C C2 GDU . . . I 3 22.857 -3.422 -17.988 1 83.55 ? C2 GDU 402 C 1 HETATM 3 N N3 GDU . . . I 3 22.164 -3.216 -16.847 1 80.65 ? N3 GDU 402 C 1 HETATM 4 C C4 GDU . . . I 3 22.661 -2.413 -15.907 1 73.81 ? C4 GDU 402 C 1 HETATM 5 C C5 GDU . . . I 3 23.884 -1.797 -16.111 1 72.6 ? C5 GDU 402 C 1 HETATM 6 C C6 GDU . . . I 3 24.576 -2.032 -17.3 1 73.83 ? C6 GDU 402 C 1 HETATM 7 O O2 GDU . . . I 3 22.385 -4.155 -18.826 1 83.77 ? O2 GDU 402 C 1 HETATM 8 O O4 GDU . . . I 3 21.983 -2.205 -14.78 1 68.46 ? O4 GDU 402 C 1 HETATM 9 C C1D GDU . . . I 3 24.788 -3.097 -19.511 1 81.3 ? C1D GDU 402 C 1 HETATM 10 C C2D GDU . . . I 3 24.311 -2.187 -20.588 1 83.77 ? C2D GDU 402 C 1 HETATM 11 O O2D GDU . . . I 3 23.96 -2.911 -21.712 1 90.11 ? O2D GDU 402 C 1 HETATM 12 C C3D GDU . . . I 3 25.419 -1.321 -20.878 1 91.15 ? C3D GDU 402 C 1 HETATM 13 C C4D GDU . . . I 3 26.595 -2.046 -20.429 1 95.45 ? C4D GDU 402 C 1 HETATM 14 O O4D GDU . . . I 3 26.144 -2.91 -19.372 1 91.31 ? O4D GDU 402 C 1 HETATM 15 O O3D GDU . . . I 3 25.498 -1.028 -22.254 1 86.65 ? O3D GDU 402 C 1 HETATM 16 C C5D GDU . . . I 3 27.554 -1.107 -19.861 1 97.58 ? C5D GDU 402 C 1 HETATM 17 O O5D GDU . . . I 3 27.206 -0.542 -18.637 1 95.39 ? O5D GDU 402 C 1 HETATM 18 P PA GDU . . . I 3 27.8 0.883 -18.233 1 82.61 ? PA GDU 402 C 1 HETATM 19 O O1A GDU . . . I 3 27.51 1.107 -16.727 1 72.63 ? O1A GDU 402 C 1 HETATM 20 O O2A GDU . . . I 3 29.309 0.962 -18.529 1 86.37 ? O2A GDU 402 C 1 HETATM 21 O O3A GDU . . . I 3 26.983 1.979 -19.073 1 89.66 ? O3A GDU 402 C 1 HETATM 22 P PB GDU . . . I 3 27.624 3.359 -19.317 1 88.45 ? PB GDU 402 C 1 HETATM 23 O O1B GDU . . . I 3 26.572 4.286 -19.733 1 80.17 ? O1B GDU 402 C 1 HETATM 24 O O2B GDU . . . I 3 28.707 3.277 -20.326 1 84.59 ? O2B GDU 402 C 1 HETATM 25 O O3B GDU . . . I 3 28.157 3.827 -18.002 1 82.02 ? O3B GDU 402 C 1 HETATM 26 C C1' GDU . . . I 3 28.612 5.126 -17.886 0.25 79.21 ? C1' GDU 402 C 1 HETATM 27 C C2' GDU . . . I 3 30.111 5.089 -17.704 0.29 78.71 ? C2' GDU 402 C 1 HETATM 28 C C3' GDU . . . I 3 30.467 4.236 -16.577 0.79 80.22 ? C3' GDU 402 C 1 HETATM 29 C C4' GDU . . . I 3 29.83 4.663 -15.362 0.75 74.33 ? C4' GDU 402 C 1 HETATM 30 C C5' GDU . . . I 3 28.379 5.036 -15.498 0.88 71.5 ? C5' GDU 402 C 1 HETATM 31 C C6' GDU . . . I 3 27.962 5.867 -14.357 1 76.27 ? C6' GDU 402 C 1 HETATM 32 O O2' GDU . . . I 3 30.777 4.691 -18.897 0.63 82.19 ? O2' GDU 402 C 1 HETATM 33 O O3' GDU . . . I 3 31.906 4.258 -16.411 0.75 78.93 ? O3' GDU 402 C 1 HETATM 34 O O4' GDU . . . I 3 30.583 5.733 -14.751 0.38 76.31 ? O4' GDU 402 C 1 HETATM 35 O O5' GDU . . . I 3 28.028 5.729 -16.771 0.46 79.15 ? O5' GDU 402 C 1 HETATM 36 O O6' GDU . . . I 3 27.361 5.212 -13.281 1 69.03 ? O6' GDU 402 C 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 768 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 36 #