data_5U32
#
_model_server_result.job_id            g0f4rAIeyKtjFueXjQ9mjQ 
_model_server_result.datetime_utc      '2025-01-25 11:14:02' 
_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          5u32 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":701}' 
#
_entry.id    5U32 
#
_exptl.entry_id    5U32 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_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            5U32 
_cell.length_a            49.944 
_cell.length_b            56.304 
_cell.length_c            82.393 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5U32 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 OG1 THR 27 A THR 426 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc2 B O1B GDP . A GDP 701 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc3 C MG MG . A MG 702 1_555 D O HOH . A HOH 823 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc4 C MG MG . A MG 702 1_555 D O HOH . A HOH 841 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc5 C MG MG . A MG 702 1_555 D O HOH . A HOH 843 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc6 C MG MG . A MG 702 1_555 D O HOH . A HOH 848 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
PB O1B GDP doub 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     5U32 
_atom_sites.fract_transf_matrix[1][1]    0.020022 
_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]    0.017761 
_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]    0.012137 
_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 GDP A 1 701 1 GDP GDP . 
C 3 MG A 1 702 1 MG MG . 
D 4 HOH A 1 801 558 HOH HOH . 
D 4 HOH A 2 802 628 HOH HOH . 
D 4 HOH A 3 803 595 HOH HOH . 
D 4 HOH A 4 804 573 HOH HOH . 
D 4 HOH A 5 805 619 HOH HOH . 
D 4 HOH A 6 806 615 HOH HOH . 
D 4 HOH A 7 807 611 HOH HOH . 
D 4 HOH A 8 808 604 HOH HOH . 
D 4 HOH A 9 809 547 HOH HOH . 
D 4 HOH A 10 810 544 HOH HOH . 
D 4 HOH A 11 811 612 HOH HOH . 
D 4 HOH A 12 812 542 HOH HOH . 
D 4 HOH A 13 813 621 HOH HOH . 
D 4 HOH A 14 814 556 HOH HOH . 
D 4 HOH A 15 815 3 HOH HOH . 
D 4 HOH A 16 816 567 HOH HOH . 
D 4 HOH A 17 817 555 HOH HOH . 
D 4 HOH A 18 818 571 HOH HOH . 
D 4 HOH A 19 819 626 HOH HOH . 
D 4 HOH A 20 820 533 HOH HOH . 
D 4 HOH A 21 821 545 HOH HOH . 
D 4 HOH A 22 822 550 HOH HOH . 
D 4 HOH A 23 823 625 HOH HOH . 
D 4 HOH A 24 824 566 HOH HOH . 
D 4 HOH A 25 825 537 HOH HOH . 
D 4 HOH A 26 826 565 HOH HOH . 
D 4 HOH A 27 827 620 HOH HOH . 
D 4 HOH A 28 828 5 HOH HOH . 
D 4 HOH A 29 829 574 HOH HOH . 
D 4 HOH A 30 830 586 HOH HOH . 
D 4 HOH A 31 831 585 HOH HOH . 
D 4 HOH A 32 832 572 HOH HOH . 
D 4 HOH A 33 833 6 HOH HOH . 
D 4 HOH A 34 834 543 HOH HOH . 
D 4 HOH A 35 835 548 HOH HOH . 
D 4 HOH A 36 836 549 HOH HOH . 
D 4 HOH A 37 837 584 HOH HOH . 
D 4 HOH A 38 838 2 HOH HOH . 
D 4 HOH A 39 839 557 HOH HOH . 
D 4 HOH A 40 840 1 HOH HOH . 
D 4 HOH A 41 841 605 HOH HOH . 
D 4 HOH A 42 842 536 HOH HOH . 
D 4 HOH A 43 843 560 HOH HOH . 
D 4 HOH A 44 844 587 HOH HOH . 
D 4 HOH A 45 845 538 HOH HOH . 
D 4 HOH A 46 846 570 HOH HOH . 
D 4 HOH A 47 847 581 HOH HOH . 
D 4 HOH A 48 848 624 HOH HOH . 
D 4 HOH A 49 849 541 HOH HOH . 
D 4 HOH A 50 850 582 HOH HOH . 
D 4 HOH A 51 851 540 HOH HOH . 
D 4 HOH A 52 852 600 HOH HOH . 
D 4 HOH A 53 853 535 HOH HOH . 
D 4 HOH A 54 854 596 HOH HOH . 
D 4 HOH A 55 855 617 HOH HOH . 
D 4 HOH A 56 856 568 HOH HOH . 
D 4 HOH A 57 857 551 HOH HOH . 
D 4 HOH A 58 858 563 HOH HOH . 
D 4 HOH A 59 859 564 HOH HOH . 
D 4 HOH A 60 860 590 HOH HOH . 
D 4 HOH A 61 861 606 HOH HOH . 
D 4 HOH A 62 862 554 HOH HOH . 
D 4 HOH A 63 863 552 HOH HOH . 
D 4 HOH A 64 864 578 HOH HOH . 
D 4 HOH A 65 865 583 HOH HOH . 
D 4 HOH A 66 866 576 HOH HOH . 
D 4 HOH A 67 867 569 HOH HOH . 
D 4 HOH A 68 868 546 HOH HOH . 
D 4 HOH A 69 869 559 HOH HOH . 
D 4 HOH A 70 870 561 HOH HOH . 
D 4 HOH A 71 871 601 HOH HOH . 
D 4 HOH A 72 872 562 HOH HOH . 
D 4 HOH A 73 873 4 HOH HOH . 
D 4 HOH A 74 874 534 HOH HOH . 
D 4 HOH A 75 875 614 HOH HOH . 
D 4 HOH A 76 876 618 HOH HOH . 
D 4 HOH A 77 877 593 HOH HOH . 
D 4 HOH A 78 878 589 HOH HOH . 
D 4 HOH A 79 879 591 HOH HOH . 
D 4 HOH A 80 880 622 HOH HOH . 
D 4 HOH A 81 881 532 HOH HOH . 
D 4 HOH A 82 882 603 HOH HOH . 
D 4 HOH A 83 883 607 HOH HOH . 
D 4 HOH A 84 884 539 HOH HOH . 
D 4 HOH A 85 885 609 HOH HOH . 
D 4 HOH A 86 886 553 HOH HOH . 
D 4 HOH A 87 887 613 HOH HOH . 
D 4 HOH A 88 888 627 HOH HOH . 
D 4 HOH A 89 889 598 HOH HOH . 
D 4 HOH A 90 890 594 HOH HOH . 
D 4 HOH A 91 891 577 HOH HOH . 
D 4 HOH A 92 892 608 HOH HOH . 
D 4 HOH A 93 893 630 HOH HOH . 
D 4 HOH A 94 894 599 HOH HOH . 
D 4 HOH A 95 895 575 HOH HOH . 
D 4 HOH A 96 896 602 HOH HOH . 
D 4 HOH A 97 897 592 HOH HOH . 
D 4 HOH A 98 898 579 HOH HOH . 
D 4 HOH A 99 899 588 HOH HOH . 
D 4 HOH A 100 900 610 HOH HOH . 
D 4 HOH A 101 901 633 HOH HOH . 
D 4 HOH A 102 902 580 HOH HOH . 
D 4 HOH A 103 903 597 HOH HOH . 
D 4 HOH A 104 904 629 HOH HOH . 
D 4 HOH A 105 905 632 HOH HOH . 
D 4 HOH A 106 906 616 HOH HOH . 
D 4 HOH A 107 907 631 HOH HOH . 
D 4 HOH A 108 908 623 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 P PB GDP . . . B 2 -35.809 19.398 91.998 1 34.22 ? PB GDP 701 A 1 
HETATM 2 O O1B GDP . . . B 2 -36.815 18.755 91.105 1 34.08 ? O1B GDP 701 A 1 
HETATM 3 O O2B GDP . . . B 2 -35.175 18.496 93.046 1 32.68 ? O2B GDP 701 A 1 
HETATM 4 O O3B GDP . . . B 2 -36.16 20.771 92.515 1 31.49 ? O3B GDP 701 A 1 
HETATM 5 O O3A GDP . . . B 2 -34.573 19.588 90.975 1 32.73 ? O3A GDP 701 A 1 
HETATM 6 P PA GDP . . . B 2 -34.731 19.487 89.383 1 33.14 ? PA GDP 701 A 1 
HETATM 7 O O1A GDP . . . B 2 -35.887 20.305 88.9 1 35.63 ? O1A GDP 701 A 1 
HETATM 8 O O2A GDP . . . B 2 -34.65 18.049 88.913 1 32.43 ? O2A GDP 701 A 1 
HETATM 9 O O5' GDP . . . B 2 -33.381 20.266 88.953 1 32.48 ? O5' GDP 701 A 1 
HETATM 10 C C5' GDP . . . B 2 -33.339 21.701 88.93 1 34.48 ? C5' GDP 701 A 1 
HETATM 11 C C4' GDP . . . B 2 -32.417 22.216 87.828 1 38.56 ? C4' GDP 701 A 1 
HETATM 12 O O4' GDP . . . B 2 -31.145 21.556 87.881 1 32.91 ? O4' GDP 701 A 1 
HETATM 13 C C3' GDP . . . B 2 -33.016 21.911 86.461 1 41.66 ? C3' GDP 701 A 1 
HETATM 14 O O3' GDP . . . B 2 -32.782 23.045 85.605 1 37.37 ? O3' GDP 701 A 1 
HETATM 15 C C2' GDP . . . B 2 -32.249 20.68 85.996 1 35.47 ? C2' GDP 701 A 1 
HETATM 16 O O2' GDP . . . B 2 -32.141 20.582 84.576 1 38.19 ? O2' GDP 701 A 1 
HETATM 17 C C1' GDP . . . B 2 -30.901 20.854 86.66 1 29.44 ? C1' GDP 701 A 1 
HETATM 18 N N9 GDP . . . B 2 -30.224 19.574 86.971 1 34.3 ? N9 GDP 701 A 1 
HETATM 19 C C8 GDP . . . B 2 -30.772 18.393 87.324 1 34.76 ? C8 GDP 701 A 1 
HETATM 20 N N7 GDP . . . B 2 -29.82 17.444 87.532 1 30.52 ? N7 GDP 701 A 1 
HETATM 21 C C5 GDP . . . B 2 -28.634 18.026 87.308 1 32.16 ? C5 GDP 701 A 1 
HETATM 22 C C6 GDP . . . B 2 -27.219 17.594 87.348 1 32.63 ? C6 GDP 701 A 1 
HETATM 23 O O6 GDP . . . B 2 -26.923 16.419 87.659 1 33.19 ? O6 GDP 701 A 1 
HETATM 24 N N1 GDP . . . B 2 -26.294 18.503 87.039 1 32.89 ? N1 GDP 701 A 1 
HETATM 25 C C2 GDP . . . B 2 -26.611 19.779 86.706 1 35.7 ? C2 GDP 701 A 1 
HETATM 26 N N2 GDP . . . B 2 -25.614 20.639 86.409 1 36.13 ? N2 GDP 701 A 1 
HETATM 27 N N3 GDP . . . B 2 -27.88 20.257 86.648 1 33.19 ? N3 GDP 701 A 1 
HETATM 28 C C4 GDP . . . B 2 -28.906 19.423 86.93 1 37.9 ? C4 GDP 701 A 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           28 
#