data_4RPH
#
_model_server_result.job_id            xyHeuI_b0XLUHIKTtq1aOA 
_model_server_result.datetime_utc      '2024-11-14 18:10:15' 
_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":"G","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 . . . G 3 23.977 -2.502 18.469 1 65.55 ? N1 GDU 402 A 1 
HETATM 2 C C2 GDU . . . G 3 22.912 -3.289 18.266 1 69.15 ? C2 GDU 402 A 1 
HETATM 3 N N3 GDU . . . G 3 22.704 -3.951 17.108 1 70.11 ? N3 GDU 402 A 1 
HETATM 4 C C4 GDU . . . G 3 23.581 -3.837 16.111 1 60.17 ? C4 GDU 402 A 1 
HETATM 5 C C5 GDU . . . G 3 24.699 -3.037 16.274 1 56.92 ? C5 GDU 402 A 1 
HETATM 6 C C6 GDU . . . G 3 24.884 -2.364 17.483 1 59.66 ? C6 GDU 402 A 1 
HETATM 7 O O2 GDU . . . G 3 22.098 -3.412 19.152 1 66.51 ? O2 GDU 402 A 1 
HETATM 8 O O4 GDU . . . G 3 23.381 -4.489 14.967 1 61.12 ? O4 GDU 402 A 1 
HETATM 9 C C1D GDU . . . G 3 24.185 -1.778 19.772 1 53.62 ? C1D GDU 402 A 1 
HETATM 10 C C2D GDU . . . G 3 24.739 -2.692 20.809 1 60.19 ? C2D GDU 402 A 1 
HETATM 11 O O2D GDU . . . G 3 23.977 -2.633 21.962 1 62.05 ? O2D GDU 402 A 1 
HETATM 12 C C3D GDU . . . G 3 26.069 -2.223 21.07 1 63.94 ? C3D GDU 402 A 1 
HETATM 13 C C4D GDU . . . G 3 26.07 -0.831 20.653 1 69.05 ? C4D GDU 402 A 1 
HETATM 14 O O4D GDU . . . G 3 25.049 -0.715 19.647 1 65.09 ? O4D GDU 402 A 1 
HETATM 15 O O3D GDU . . . G 3 26.393 -2.34 22.436 1 62.98 ? O3D GDU 402 A 1 
HETATM 16 C C5D GDU . . . G 3 27.35 -0.522 20.028 1 68.79 ? C5D GDU 402 A 1 
HETATM 17 O O5D GDU . . . G 3 27.58 -1.12 18.792 1 72.93 ? O5D GDU 402 A 1 
HETATM 18 P PA GDU . . . G 3 29.078 -1.347 18.291 1 61.95 ? PA GDU 402 A 1 
HETATM 19 O O1A GDU . . . G 3 29.017 -1.74 16.793 1 61.56 ? O1A GDU 402 A 1 
HETATM 20 O O2A GDU . . . G 3 29.936 -0.087 18.504 1 62.52 ? O2A GDU 402 A 1 
HETATM 21 O O3A GDU . . . G 3 29.662 -2.596 19.111 1 67.1 ? O3A GDU 402 A 1 
HETATM 22 P PB GDU . . . G 3 31.173 -2.647 19.409 1 61.06 ? PB GDU 402 A 1 
HETATM 23 O O1B GDU . . . G 3 31.527 -4.026 19.742 1 63.15 ? O1B GDU 402 A 1 
HETATM 24 O O2B GDU . . . G 3 31.546 -1.712 20.498 1 56.99 ? O2B GDU 402 A 1 
HETATM 25 O O3B GDU . . . G 3 31.87 -2.282 18.139 1 65.44 ? O3B GDU 402 A 1 
HETATM 26 C C1' GDU . . . G 3 33.192 -2.641 17.968 0.31 63.38 ? C1' GDU 402 A 1 
HETATM 27 C C2' GDU . . . G 3 34.005 -1.375 17.834 0.52 65.17 ? C2' GDU 402 A 1 
HETATM 28 C C3' GDU . . . G 3 33.483 -0.531 16.765 0.59 63.28 ? C3' GDU 402 A 1 
HETATM 29 C C4' GDU . . . G 3 33.407 -1.231 15.51 0.58 63.89 ? C4' GDU 402 A 1 
HETATM 30 C C5' GDU . . . G 3 32.899 -2.645 15.589 0.74 61.8 ? C5' GDU 402 A 1 
HETATM 31 C C6' GDU . . . G 3 33.302 -3.398 14.39 1 60.42 ? C6' GDU 402 A 1 
HETATM 32 O O2' GDU . . . G 3 34.092 -0.675 19.072 0.35 66.31 ? O2' GDU 402 A 1 
HETATM 33 O O3' GDU . . . G 3 34.33 0.641 16.637 0.84 65.69 ? O3' GDU 402 A 1 
HETATM 34 O O4' GDU . . . G 3 34.674 -1.175 14.818 0.26 62.93 ? O4' GDU 402 A 1 
HETATM 35 O O5' GDU . . . G 3 33.324 -3.397 16.803 0.59 62.92 ? O5' GDU 402 A 1 
HETATM 36 O O6' GDU . . . G 3 32.375 -3.485 13.351 1 51.16 ? O6' GDU 402 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           36 
#