data_4Y7G
#
_model_server_result.job_id            bywmGFOIeqYnuGTWoyvgPA 
_model_server_result.datetime_utc      '2025-01-10 06:07:02' 
_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          4y7g 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":403}' 
#
_entry.id    4Y7G 
#
_exptl.entry_id    4Y7G 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              566.302 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE-GLUCOSE" 
_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            4Y7G 
_cell.length_a            98.18 
_cell.length_b            98.18 
_cell.length_c            127.34 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Y7G 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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' 6_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 98.18 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 OD2 ASP 140 A ASP 136 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc3 B MN MN . A MN 401 1_555 D O1A UPG . A UPG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
metalc ? metalc4 B MN MN . A MN 401 1_555 D O2B UPG . A UPG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc5 B MN MN . A MN 401 1_555 E O HOH . A HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc6 B MN MN . A MN 401 1_555 E O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
#
_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 376 n n 
N1 C6 UPG sing 377 n n 
N1 C1C UPG sing 378 n n 
C2 N3 UPG sing 379 n n 
C2 O2 UPG doub 380 n n 
N3 C4 UPG sing 381 n n 
N3 HN3 UPG sing 382 n n 
C4 C5 UPG sing 383 n n 
C4 O4 UPG doub 384 n n 
C5 C6 UPG doub 385 n n 
C5 H5 UPG sing 386 n n 
C6 H6 UPG sing 387 n n 
C1C C2C UPG sing 388 n n 
C1C O4C UPG sing 389 n n 
C1C H1C UPG sing 390 n n 
C2C O2C UPG sing 391 n n 
C2C C3C UPG sing 392 n n 
C2C H2C UPG sing 393 n n 
O2C HO2C UPG sing 394 n n 
C3C C4C UPG sing 395 n n 
C3C O3C UPG sing 396 n n 
C3C H3C UPG sing 397 n n 
C4C O4C UPG sing 398 n n 
C4C C5C UPG sing 399 n n 
C4C H4C UPG sing 400 n n 
O3C HO3C UPG sing 401 n n 
C5C O5C UPG sing 402 n n 
C5C H5C1 UPG sing 403 n n 
C5C H5C2 UPG sing 404 n n 
O5C PA UPG sing 405 n n 
PA O1A UPG doub 406 n n 
PA O2A UPG sing 407 n n 
PA O3A UPG sing 408 n n 
O2A HOA2 UPG sing 409 n n 
O3A PB UPG sing 410 n n 
PB O1B UPG doub 411 n n 
PB O2B UPG sing 412 n n 
PB O3B UPG sing 413 n n 
O2B HOB2 UPG sing 414 n n 
O3B C1' UPG sing 415 n n 
C1' C2' UPG sing 416 n n 
C1' O5' UPG sing 417 n n 
C1' H1' UPG sing 418 n n 
C2' C3' UPG sing 419 n n 
C2' O2' UPG sing 420 n n 
C2' H2' UPG sing 421 n n 
C3' C4' UPG sing 422 n n 
C3' O3' UPG sing 423 n n 
C3' H3' UPG sing 424 n n 
C4' C5' UPG sing 425 n n 
C4' O4' UPG sing 426 n n 
C4' H4' UPG sing 427 n n 
C5' C6' UPG sing 428 n n 
C5' O5' UPG sing 429 n n 
C5' H5' UPG sing 430 n n 
C6' O6' UPG sing 431 n n 
C6' "H6'1" UPG sing 432 n n 
C6' "H6'2" UPG sing 433 n n 
O2' HO2' UPG sing 434 n n 
O3' HO3' UPG sing 435 n n 
O4' HO4' UPG sing 436 n n 
O6' HO6' UPG sing 437 n n 
#
_atom_sites.entry_id                     4Y7G 
_atom_sites.fract_transf_matrix[1][1]    0.010185 
_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]    0.010185 
_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]    0.007853 
_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
B 2 MN A 1 401 1 MN MN . 
C 3 G3P A 1 402 1 G3P G3P . 
D 4 UPG A 1 403 2 UPG UPG . 
E 5 HOH A 1 501 95 HOH HOH . 
E 5 HOH A 2 502 9 HOH HOH . 
E 5 HOH A 3 503 75 HOH HOH . 
E 5 HOH A 4 504 67 HOH HOH . 
E 5 HOH A 5 505 63 HOH HOH . 
E 5 HOH A 6 506 29 HOH HOH . 
E 5 HOH A 7 507 38 HOH HOH . 
E 5 HOH A 8 508 45 HOH HOH . 
E 5 HOH A 9 509 90 HOH HOH . 
E 5 HOH A 10 510 1 HOH HOH . 
E 5 HOH A 11 511 2 HOH HOH . 
E 5 HOH A 12 512 3 HOH HOH . 
E 5 HOH A 13 513 5 HOH HOH . 
E 5 HOH A 14 514 7 HOH HOH . 
E 5 HOH A 15 515 8 HOH HOH . 
E 5 HOH A 16 516 10 HOH HOH . 
E 5 HOH A 17 517 11 HOH HOH . 
E 5 HOH A 18 518 12 HOH HOH . 
E 5 HOH A 19 519 13 HOH HOH . 
E 5 HOH A 20 520 14 HOH HOH . 
E 5 HOH A 21 521 15 HOH HOH . 
E 5 HOH A 22 522 16 HOH HOH . 
E 5 HOH A 23 523 17 HOH HOH . 
E 5 HOH A 24 524 18 HOH HOH . 
E 5 HOH A 25 525 19 HOH HOH . 
E 5 HOH A 26 526 20 HOH HOH . 
E 5 HOH A 27 527 21 HOH HOH . 
E 5 HOH A 28 528 22 HOH HOH . 
E 5 HOH A 29 529 23 HOH HOH . 
E 5 HOH A 30 530 24 HOH HOH . 
E 5 HOH A 31 531 25 HOH HOH . 
E 5 HOH A 32 532 26 HOH HOH . 
E 5 HOH A 33 533 27 HOH HOH . 
E 5 HOH A 34 534 28 HOH HOH . 
E 5 HOH A 35 535 30 HOH HOH . 
E 5 HOH A 36 536 32 HOH HOH . 
E 5 HOH A 37 537 34 HOH HOH . 
E 5 HOH A 38 538 35 HOH HOH . 
E 5 HOH A 39 539 37 HOH HOH . 
E 5 HOH A 40 540 39 HOH HOH . 
E 5 HOH A 41 541 40 HOH HOH . 
E 5 HOH A 42 542 41 HOH HOH . 
E 5 HOH A 43 543 42 HOH HOH . 
E 5 HOH A 44 544 43 HOH HOH . 
E 5 HOH A 45 545 44 HOH HOH . 
E 5 HOH A 46 546 48 HOH HOH . 
E 5 HOH A 47 547 49 HOH HOH . 
E 5 HOH A 48 548 50 HOH HOH . 
E 5 HOH A 49 549 51 HOH HOH . 
E 5 HOH A 50 550 52 HOH HOH . 
E 5 HOH A 51 551 54 HOH HOH . 
E 5 HOH A 52 552 55 HOH HOH . 
E 5 HOH A 53 553 56 HOH HOH . 
E 5 HOH A 54 554 57 HOH HOH . 
E 5 HOH A 55 555 58 HOH HOH . 
E 5 HOH A 56 556 59 HOH HOH . 
E 5 HOH A 57 557 60 HOH HOH . 
E 5 HOH A 58 558 61 HOH HOH . 
E 5 HOH A 59 559 62 HOH HOH . 
E 5 HOH A 60 560 64 HOH HOH . 
E 5 HOH A 61 561 65 HOH HOH . 
E 5 HOH A 62 562 66 HOH HOH . 
E 5 HOH A 63 563 68 HOH HOH . 
E 5 HOH A 64 564 69 HOH HOH . 
E 5 HOH A 65 565 70 HOH HOH . 
E 5 HOH A 66 566 71 HOH HOH . 
E 5 HOH A 67 567 72 HOH HOH . 
E 5 HOH A 68 568 73 HOH HOH . 
E 5 HOH A 69 569 74 HOH HOH . 
E 5 HOH A 70 570 76 HOH HOH . 
E 5 HOH A 71 571 78 HOH HOH . 
E 5 HOH A 72 572 79 HOH HOH . 
E 5 HOH A 73 573 81 HOH HOH . 
E 5 HOH A 74 574 83 HOH HOH . 
E 5 HOH A 75 575 84 HOH HOH . 
E 5 HOH A 76 576 85 HOH HOH . 
E 5 HOH A 77 577 89 HOH HOH . 
E 5 HOH A 78 578 91 HOH HOH . 
E 5 HOH A 79 579 92 HOH HOH . 
E 5 HOH A 80 580 93 HOH HOH . 
E 5 HOH A 81 581 96 HOH HOH . 
E 5 HOH A 82 582 97 HOH HOH . 
E 5 HOH A 83 583 101 HOH HOH . 
E 5 HOH A 84 584 102 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 . . . D 4 34.179 -13.009 27.114 1 64.45 ? N1 UPG 403 A 1 
HETATM 2 C C2 UPG . . . D 4 33.599 -14.116 26.478 1 64.45 ? C2 UPG 403 A 1 
HETATM 3 N N3 UPG . . . D 4 34.365 -14.955 25.764 1 64.45 ? N3 UPG 403 A 1 
HETATM 4 C C4 UPG . . . D 4 35.683 -14.78 25.637 1 64.45 ? C4 UPG 403 A 1 
HETATM 5 C C5 UPG . . . D 4 36.283 -13.694 26.262 1 64.45 ? C5 UPG 403 A 1 
HETATM 6 C C6 UPG . . . D 4 35.501 -12.808 26.992 1 64.45 ? C6 UPG 403 A 1 
HETATM 7 O O2 UPG . . . D 4 32.368 -14.31 26.578 1 64.45 ? O2 UPG 403 A 1 
HETATM 8 O O4 UPG . . . D 4 36.365 -15.591 24.965 1 64.45 ? O4 UPG 403 A 1 
HETATM 9 C C1C UPG . . . D 4 33.337 -12.094 27.893 1 64.45 ? C1C UPG 403 A 1 
HETATM 10 C C2C UPG . . . D 4 33.771 -11.97 29.365 1 64.45 ? C2C UPG 403 A 1 
HETATM 11 O O2C UPG . . . D 4 33.081 -12.863 30.245 1 64.45 ? O2C UPG 403 A 1 
HETATM 12 C C3C UPG . . . D 4 33.456 -10.535 29.699 1 64.45 ? C3C UPG 403 A 1 
HETATM 13 C C4C UPG . . . D 4 33.418 -9.82 28.362 1 64.45 ? C4C UPG 403 A 1 
HETATM 14 O O4C UPG . . . D 4 33.436 -10.801 27.328 1 64.45 ? O4C UPG 403 A 1 
HETATM 15 O O3C UPG . . . D 4 32.177 -10.428 30.302 1 64.45 ? O3C UPG 403 A 1 
HETATM 16 C C5C UPG . . . D 4 34.614 -8.903 28.183 1 64.45 ? C5C UPG 403 A 1 
HETATM 17 O O5C UPG . . . D 4 35.785 -9.69 28.346 1 64.45 ? O5C UPG 403 A 1 
HETATM 18 P PA UPG . . . D 4 36.991 -9.097 29.199 1 64.45 ? PA UPG 403 A 1 
HETATM 19 O O1A UPG . . . D 4 36.446 -8.568 30.513 1 64.45 ? O1A UPG 403 A 1 
HETATM 20 O O2A UPG . . . D 4 38.023 -10.186 29.389 1 64.45 ? O2A UPG 403 A 1 
HETATM 21 O O3A UPG . . . D 4 37.522 -7.92 28.267 1 64.45 ? O3A UPG 403 A 1 
HETATM 22 P PB UPG . . . D 4 38.235 -6.549 28.709 1 64.45 ? PB UPG 403 A 1 
HETATM 23 O O1B UPG . . . D 4 39.665 -6.723 29.15 1 64.45 ? O1B UPG 403 A 1 
HETATM 24 O O2B UPG . . . D 4 37.405 -5.732 29.671 1 64.45 ? O2B UPG 403 A 1 
HETATM 25 O O3B UPG . . . D 4 38.244 -5.838 27.264 1 64.45 ? O3B UPG 403 A 1 
HETATM 26 C C1' UPG . . . D 4 37.648 -4.577 26.957 1 64.45 ? C1' UPG 403 A 1 
HETATM 27 C C2' UPG . . . D 4 36.122 -4.638 26.985 1 64.45 ? C2' UPG 403 A 1 
HETATM 28 C C3' UPG . . . D 4 35.693 -5.861 26.185 1 64.45 ? C3' UPG 403 A 1 
HETATM 29 C C4' UPG . . . D 4 36.225 -5.688 24.772 1 64.45 ? C4' UPG 403 A 1 
HETATM 30 C C5' UPG . . . D 4 37.73 -5.43 24.757 1 64.45 ? C5' UPG 403 A 1 
HETATM 31 C C6' UPG . . . D 4 38.215 -5.149 23.342 1 64.45 ? C6' UPG 403 A 1 
HETATM 32 O O2' UPG . . . D 4 35.609 -4.666 28.328 1 64.45 ? O2' UPG 403 A 1 
HETATM 33 O O3' UPG . . . D 4 34.272 -5.962 26.17 1 64.45 ? O3' UPG 403 A 1 
HETATM 34 O O4' UPG . . . D 4 35.986 -6.844 23.975 1 64.45 ? O4' UPG 403 A 1 
HETATM 35 O O5' UPG . . . D 4 38.045 -4.326 25.626 1 64.45 ? O5' UPG 403 A 1 
HETATM 36 O O6' UPG . . . D 4 37.23 -4.38 22.65 1 64.45 ? O6' UPG 403 A 1 
#
_model_server_stats.io_time_ms              110 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           36 
#