data_4EDF
#
_model_server_result.job_id            laCbPK1ZXykU5cwJCV1rXw 
_model_server_result.datetime_utc      '2024-11-07 19:50:57' 
_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          4edf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":501}' 
#
_entry.id    4EDF 
#
_exptl.entry_id    4EDF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              566.302 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE-GLUCOSE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          107.01 
_cell.angle_gamma         90 
_cell.entry_id            4EDF 
_cell.length_a            88.66 
_cell.length_b            151.07 
_cell.length_c            88.74 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4EDF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,D,E,H,I,L 1 1 
B,C,F,G,J,K 2 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 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_chem_comp.formula           'C15 H24 N2 O17 P2' 
_chem_comp.formula_weight    566.302 
_chem_comp.id                UPG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE-GLUCOSE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" 
#
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 UPG sing 358 n n 
N1 C6 UPG sing 359 n n 
N1 C1C UPG sing 360 n n 
C2 N3 UPG sing 361 n n 
C2 O2 UPG doub 362 n n 
N3 C4 UPG sing 363 n n 
N3 HN3 UPG sing 364 n n 
C4 C5 UPG sing 365 n n 
C4 O4 UPG doub 366 n n 
C5 C6 UPG doub 367 n n 
C5 H5 UPG sing 368 n n 
C6 H6 UPG sing 369 n n 
C1C C2C UPG sing 370 n n 
C1C O4C UPG sing 371 n n 
C1C H1C UPG sing 372 n n 
C2C O2C UPG sing 373 n n 
C2C C3C UPG sing 374 n n 
C2C H2C UPG sing 375 n n 
O2C HO2C UPG sing 376 n n 
C3C C4C UPG sing 377 n n 
C3C O3C UPG sing 378 n n 
C3C H3C UPG sing 379 n n 
C4C O4C UPG sing 380 n n 
C4C C5C UPG sing 381 n n 
C4C H4C UPG sing 382 n n 
O3C HO3C UPG sing 383 n n 
C5C O5C UPG sing 384 n n 
C5C H5C1 UPG sing 385 n n 
C5C H5C2 UPG sing 386 n n 
O5C PA UPG sing 387 n n 
PA O1A UPG doub 388 n n 
PA O2A UPG sing 389 n n 
PA O3A UPG sing 390 n n 
O2A HOA2 UPG sing 391 n n 
O3A PB UPG sing 392 n n 
PB O1B UPG doub 393 n n 
PB O2B UPG sing 394 n n 
PB O3B UPG sing 395 n n 
O2B HOB2 UPG sing 396 n n 
O3B C1' UPG sing 397 n n 
C1' C2' UPG sing 398 n n 
C1' O5' UPG sing 399 n n 
C1' H1' UPG sing 400 n n 
C2' C3' UPG sing 401 n n 
C2' O2' UPG sing 402 n n 
C2' H2' UPG sing 403 n n 
C3' C4' UPG sing 404 n n 
C3' O3' UPG sing 405 n n 
C3' H3' UPG sing 406 n n 
C4' C5' UPG sing 407 n n 
C4' O4' UPG sing 408 n n 
C4' H4' UPG sing 409 n n 
C5' C6' UPG sing 410 n n 
C5' O5' UPG sing 411 n n 
C5' H5' UPG sing 412 n n 
C6' O6' UPG sing 413 n n 
C6' "H6'1" UPG sing 414 n n 
C6' "H6'2" UPG sing 415 n n 
O2' HO2' UPG sing 416 n n 
O3' HO3' UPG sing 417 n n 
O4' HO4' UPG sing 418 n n 
O6' HO6' UPG sing 419 n n 
#
_atom_sites.entry_id                     4EDF 
_atom_sites.fract_transf_matrix[1][1]    0.011279 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003451 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006619 
_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]    0.011784 
_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
E 2 UPG A 1 501 501 UPG UPG . 
F 2 UPG B 1 501 501 UPG UPG . 
G 2 UPG C 1 501 501 UPG UPG . 
H 2 UPG D 1 501 501 UPG UPG . 
I 3 HOH A 1 601 2 HOH HOH . 
I 3 HOH A 2 602 3 HOH HOH . 
I 3 HOH A 3 603 6 HOH HOH . 
I 3 HOH A 4 604 8 HOH HOH . 
I 3 HOH A 5 605 11 HOH HOH . 
I 3 HOH A 6 606 13 HOH HOH . 
I 3 HOH A 7 607 15 HOH HOH . 
I 3 HOH A 8 608 16 HOH HOH . 
I 3 HOH A 9 609 19 HOH HOH . 
I 3 HOH A 10 610 20 HOH HOH . 
I 3 HOH A 11 611 26 HOH HOH . 
I 3 HOH A 12 612 30 HOH HOH . 
I 3 HOH A 13 613 35 HOH HOH . 
I 3 HOH A 14 614 37 HOH HOH . 
I 3 HOH A 15 615 49 HOH HOH . 
I 3 HOH A 16 616 50 HOH HOH . 
I 3 HOH A 17 617 51 HOH HOH . 
I 3 HOH A 18 618 52 HOH HOH . 
I 3 HOH A 19 619 55 HOH HOH . 
I 3 HOH A 20 620 56 HOH HOH . 
I 3 HOH A 21 621 59 HOH HOH . 
I 3 HOH A 22 622 69 HOH HOH . 
I 3 HOH A 23 623 74 HOH HOH . 
I 3 HOH A 24 624 89 HOH HOH . 
I 3 HOH A 25 625 90 HOH HOH . 
I 3 HOH A 26 626 93 HOH HOH . 
I 3 HOH A 27 627 96 HOH HOH . 
I 3 HOH A 28 628 97 HOH HOH . 
I 3 HOH A 29 629 99 HOH HOH . 
I 3 HOH A 30 630 110 HOH HOH . 
I 3 HOH A 31 631 117 HOH HOH . 
I 3 HOH A 32 632 125 HOH HOH . 
I 3 HOH A 33 633 131 HOH HOH . 
I 3 HOH A 34 634 134 HOH HOH . 
I 3 HOH A 35 635 143 HOH HOH . 
I 3 HOH A 36 636 153 HOH HOH . 
I 3 HOH A 37 637 157 HOH HOH . 
I 3 HOH A 38 638 165 HOH HOH . 
I 3 HOH A 39 639 166 HOH HOH . 
I 3 HOH A 40 640 169 HOH HOH . 
I 3 HOH A 41 641 176 HOH HOH . 
J 3 HOH B 1 601 4 HOH HOH . 
J 3 HOH B 2 602 12 HOH HOH . 
J 3 HOH B 3 603 29 HOH HOH . 
J 3 HOH B 4 604 33 HOH HOH . 
J 3 HOH B 5 605 36 HOH HOH . 
J 3 HOH B 6 606 39 HOH HOH . 
J 3 HOH B 7 607 44 HOH HOH . 
J 3 HOH B 8 608 45 HOH HOH . 
J 3 HOH B 9 609 61 HOH HOH . 
J 3 HOH B 10 610 62 HOH HOH . 
J 3 HOH B 11 611 64 HOH HOH . 
J 3 HOH B 12 612 66 HOH HOH . 
J 3 HOH B 13 613 67 HOH HOH . 
J 3 HOH B 14 614 82 HOH HOH . 
J 3 HOH B 15 615 85 HOH HOH . 
J 3 HOH B 16 616 91 HOH HOH . 
J 3 HOH B 17 617 92 HOH HOH . 
J 3 HOH B 18 618 103 HOH HOH . 
J 3 HOH B 19 619 105 HOH HOH . 
J 3 HOH B 20 620 113 HOH HOH . 
J 3 HOH B 21 621 118 HOH HOH . 
J 3 HOH B 22 622 120 HOH HOH . 
J 3 HOH B 23 623 129 HOH HOH . 
J 3 HOH B 24 624 132 HOH HOH . 
J 3 HOH B 25 625 150 HOH HOH . 
J 3 HOH B 26 626 151 HOH HOH . 
J 3 HOH B 27 627 152 HOH HOH . 
J 3 HOH B 28 628 159 HOH HOH . 
J 3 HOH B 29 629 161 HOH HOH . 
J 3 HOH B 30 630 164 HOH HOH . 
J 3 HOH B 31 631 171 HOH HOH . 
J 3 HOH B 32 632 174 HOH HOH . 
K 3 HOH C 1 601 17 HOH HOH . 
K 3 HOH C 2 602 18 HOH HOH . 
K 3 HOH C 3 603 21 HOH HOH . 
K 3 HOH C 4 604 24 HOH HOH . 
K 3 HOH C 5 605 25 HOH HOH . 
K 3 HOH C 6 606 28 HOH HOH . 
K 3 HOH C 7 607 31 HOH HOH . 
K 3 HOH C 8 608 34 HOH HOH . 
K 3 HOH C 9 609 43 HOH HOH . 
K 3 HOH C 10 610 47 HOH HOH . 
K 3 HOH C 11 611 58 HOH HOH . 
K 3 HOH C 12 612 63 HOH HOH . 
K 3 HOH C 13 613 65 HOH HOH . 
K 3 HOH C 14 614 70 HOH HOH . 
K 3 HOH C 15 615 78 HOH HOH . 
K 3 HOH C 16 616 80 HOH HOH . 
K 3 HOH C 17 617 81 HOH HOH . 
K 3 HOH C 18 618 87 HOH HOH . 
K 3 HOH C 19 619 100 HOH HOH . 
K 3 HOH C 20 620 101 HOH HOH . 
K 3 HOH C 21 621 107 HOH HOH . 
K 3 HOH C 22 622 111 HOH HOH . 
K 3 HOH C 23 623 116 HOH HOH . 
K 3 HOH C 24 624 119 HOH HOH . 
K 3 HOH C 25 625 121 HOH HOH . 
K 3 HOH C 26 626 122 HOH HOH . 
K 3 HOH C 27 627 123 HOH HOH . 
K 3 HOH C 28 628 130 HOH HOH . 
K 3 HOH C 29 629 137 HOH HOH . 
K 3 HOH C 30 630 139 HOH HOH . 
K 3 HOH C 31 631 145 HOH HOH . 
K 3 HOH C 32 632 146 HOH HOH . 
K 3 HOH C 33 633 163 HOH HOH . 
K 3 HOH C 34 634 167 HOH HOH . 
L 3 HOH D 1 601 7 HOH HOH . 
L 3 HOH D 2 602 9 HOH HOH . 
L 3 HOH D 3 603 14 HOH HOH . 
L 3 HOH D 4 604 22 HOH HOH . 
L 3 HOH D 5 605 23 HOH HOH . 
L 3 HOH D 6 606 38 HOH HOH . 
L 3 HOH D 7 607 40 HOH HOH . 
L 3 HOH D 8 608 42 HOH HOH . 
L 3 HOH D 9 609 46 HOH HOH . 
L 3 HOH D 10 610 53 HOH HOH . 
L 3 HOH D 11 611 54 HOH HOH . 
L 3 HOH D 12 612 57 HOH HOH . 
L 3 HOH D 13 613 72 HOH HOH . 
L 3 HOH D 14 614 73 HOH HOH . 
L 3 HOH D 15 615 77 HOH HOH . 
L 3 HOH D 16 616 79 HOH HOH . 
L 3 HOH D 17 617 83 HOH HOH . 
L 3 HOH D 18 618 84 HOH HOH . 
L 3 HOH D 19 619 86 HOH HOH . 
L 3 HOH D 20 620 95 HOH HOH . 
L 3 HOH D 21 621 108 HOH HOH . 
L 3 HOH D 22 622 109 HOH HOH . 
L 3 HOH D 23 623 114 HOH HOH . 
L 3 HOH D 24 624 115 HOH HOH . 
L 3 HOH D 25 625 124 HOH HOH . 
L 3 HOH D 26 626 126 HOH HOH . 
L 3 HOH D 27 627 127 HOH HOH . 
L 3 HOH D 28 628 128 HOH HOH . 
L 3 HOH D 29 629 136 HOH HOH . 
L 3 HOH D 30 630 138 HOH HOH . 
L 3 HOH D 31 631 140 HOH HOH . 
L 3 HOH D 32 632 148 HOH HOH . 
L 3 HOH D 33 633 149 HOH HOH . 
L 3 HOH D 34 634 154 HOH HOH . 
L 3 HOH D 35 635 155 HOH HOH . 
L 3 HOH D 36 636 156 HOH HOH . 
L 3 HOH D 37 637 172 HOH HOH . 
L 3 HOH D 38 638 173 HOH HOH . 
L 3 HOH D 39 639 175 HOH HOH . 
L 3 HOH D 40 640 177 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 UPG . . . G 2 58.549 33.95 28.324 1 19.4 ? N1 UPG 501 C 1 
HETATM 2 C C2 UPG . . . G 2 57.204 33.846 28.724 1 20.65 ? C2 UPG 501 C 1 
HETATM 3 N N3 UPG . . . G 2 56.883 33.88 30.018 1 17.91 ? N3 UPG 501 C 1 
HETATM 4 C C4 UPG . . . G 2 57.83 34.011 30.948 1 20.85 ? C4 UPG 501 C 1 
HETATM 5 C C5 UPG . . . G 2 59.17 34.113 30.583 1 22.33 ? C5 UPG 501 C 1 
HETATM 6 C C6 UPG . . . G 2 59.517 34.078 29.238 1 18.77 ? C6 UPG 501 C 1 
HETATM 7 O O2 UPG . . . G 2 56.305 33.725 27.866 1 19.9 ? O2 UPG 501 C 1 
HETATM 8 O O4 UPG . . . G 2 57.495 34.04 32.149 1 24.86 ? O4 UPG 501 C 1 
HETATM 9 C C1C UPG . . . G 2 58.865 33.9 26.9 1 22.3 ? C1C UPG 501 C 1 
HETATM 10 C C2C UPG . . . G 2 59.61 35.134 26.432 1 17.73 ? C2C UPG 501 C 1 
HETATM 11 O O2C UPG . . . G 2 58.714 36.187 26.073 1 24.66 ? O2C UPG 501 C 1 
HETATM 12 C C3C UPG . . . G 2 60.385 34.604 25.242 1 23.22 ? C3C UPG 501 C 1 
HETATM 13 C C4C UPG . . . G 2 60.645 33.15 25.578 1 18.87 ? C4C UPG 501 C 1 
HETATM 14 O O4C UPG . . . G 2 59.752 32.814 26.642 1 24.08 ? O4C UPG 501 C 1 
HETATM 15 O O3C UPG . . . G 2 59.562 34.641 24.073 1 19.18 ? O3C UPG 501 C 1 
HETATM 16 C C5C UPG . . . G 2 62.075 32.918 26.035 1 18.6 ? C5C UPG 501 C 1 
HETATM 17 O O5C UPG . . . G 2 62.503 34.014 26.845 1 15.86 ? O5C UPG 501 C 1 
HETATM 18 P PA UPG . . . G 2 63.946 33.969 27.549 1 23.08 ? PA UPG 501 C 1 
HETATM 19 O O1A UPG . . . G 2 64.008 35.135 28.503 1 33.02 ? O1A UPG 501 C 1 
HETATM 20 O O2A UPG . . . G 2 64.139 32.568 28.08 1 29.08 ? O2A UPG 501 C 1 
HETATM 21 O O3A UPG . . . G 2 64.879 34.307 26.263 1 35.11 ? O3A UPG 501 C 1 
HETATM 22 P PB UPG . . . G 2 66.064 33.406 25.623 1 24.47 ? PB UPG 501 C 1 
HETATM 23 O O1B UPG . . . G 2 65.396 32.367 24.752 1 25.06 ? O1B UPG 501 C 1 
HETATM 24 O O2B UPG . . . G 2 67.105 34.315 25.017 1 20.91 ? O2B UPG 501 C 1 
HETATM 25 O O3B UPG . . . G 2 66.782 32.695 26.882 1 39.93 ? O3B UPG 501 C 1 
HETATM 26 C C1' UPG . . . G 2 66.755 31.281 27.084 1 32.28 ? C1' UPG 501 C 1 
HETATM 27 C C2' UPG . . . G 2 67.235 30.976 28.503 1 21.4 ? C2' UPG 501 C 1 
HETATM 28 C C3' UPG . . . G 2 68.714 31.305 28.665 1 20.19 ? C3' UPG 501 C 1 
HETATM 29 C C4' UPG . . . G 2 69.501 30.666 27.531 1 20.86 ? C4' UPG 501 C 1 
HETATM 30 C C5' UPG . . . G 2 68.936 31.078 26.182 1 25.09 ? C5' UPG 501 C 1 
HETATM 31 C C6' UPG . . . G 2 69.727 30.453 25.043 1 29.49 ? C6' UPG 501 C 1 
HETATM 32 O O2' UPG . . . G 2 66.459 31.728 29.447 1 23.84 ? O2' UPG 501 C 1 
HETATM 33 O O3' UPG . . . G 2 69.192 30.776 29.904 1 23.69 ? O3' UPG 501 C 1 
HETATM 34 O O4' UPG . . . G 2 70.878 31.032 27.614 1 30.49 ? O4' UPG 501 C 1 
HETATM 35 O O5' UPG . . . G 2 67.588 30.628 26.123 1 22.78 ? O5' UPG 501 C 1 
HETATM 36 O O6' UPG . . . G 2 69.697 29.026 25.173 1 30.34 ? O6' UPG 501 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           333 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           36 
#