data_7ON3
#
_model_server_result.job_id            r1cLiHbfoIWI7pllV4E2Aw 
_model_server_result.datetime_utc      '2025-07-14 19:40:30' 
_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          7on3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    7ON3 
#
_exptl.entry_id    7ON3 
_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          110.979 
_cell.angle_gamma         90 
_cell.entry_id            7ON3 
_cell.length_a            71.858 
_cell.length_b            50.954 
_cell.length_c            88.488 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7ON3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_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,E 
_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 O LEU 193 A LEU 200 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? 
metalc ? metalc2 A O VAL 196 A VAL 203 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? 
metalc ? metalc3 A OD1 ASN 201 A ASN 208 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? 
metalc ? metalc4 A O LEU 202 A LEU 209 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? 
#
_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 79 n n 
PB O2B GDP sing 80 n n 
PB O3B GDP sing 81 n n 
PB O3A GDP sing 82 n n 
O2B HOB2 GDP sing 83 n n 
O3B HOB3 GDP sing 84 n n 
O3A PA GDP sing 85 n n 
PA O1A GDP doub 86 n n 
PA O2A GDP sing 87 n n 
PA O5' GDP sing 88 n n 
O2A HOA2 GDP sing 89 n n 
O5' C5' GDP sing 90 n n 
C5' C4' GDP sing 91 n n 
C5' H5' GDP sing 92 n n 
C5' "H5''" GDP sing 93 n n 
C4' O4' GDP sing 94 n n 
C4' C3' GDP sing 95 n n 
C4' H4' GDP sing 96 n n 
O4' C1' GDP sing 97 n n 
C3' O3' GDP sing 98 n n 
C3' C2' GDP sing 99 n n 
C3' H3' GDP sing 100 n n 
O3' HO3' GDP sing 101 n n 
C2' O2' GDP sing 102 n n 
C2' C1' GDP sing 103 n n 
C2' H2' GDP sing 104 n n 
O2' HO2' GDP sing 105 n n 
C1' N9 GDP sing 106 n n 
C1' H1' GDP sing 107 n n 
N9 C8 GDP sing 108 n y 
N9 C4 GDP sing 109 n y 
C8 N7 GDP doub 110 n y 
C8 H8 GDP sing 111 n n 
N7 C5 GDP sing 112 n y 
C5 C6 GDP sing 113 n n 
C5 C4 GDP doub 114 n y 
C6 O6 GDP doub 115 n n 
C6 N1 GDP sing 116 n n 
N1 C2 GDP sing 117 n n 
N1 HN1 GDP sing 118 n n 
C2 N2 GDP sing 119 n n 
C2 N3 GDP doub 120 n n 
N2 HN21 GDP sing 121 n n 
N2 HN22 GDP sing 122 n n 
N3 C4 GDP sing 123 n n 
#
_atom_sites.entry_id                     7ON3 
_atom_sites.fract_transf_matrix[1][1]    0.013916 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005336 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019626 
_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]    0.012103 
_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 1 401 1 GDP GDP . 
C 3 K A 1 402 1 K K . 
D 4 EDO A 1 403 1 EDO EDO . 
E 5 HOH A 1 501 17 HOH HOH . 
E 5 HOH A 2 502 88 HOH HOH . 
E 5 HOH A 3 503 31 HOH HOH . 
E 5 HOH A 4 504 22 HOH HOH . 
E 5 HOH A 5 505 48 HOH HOH . 
E 5 HOH A 6 506 64 HOH HOH . 
E 5 HOH A 7 507 45 HOH HOH . 
E 5 HOH A 8 508 87 HOH HOH . 
E 5 HOH A 9 509 24 HOH HOH . 
E 5 HOH A 10 510 27 HOH HOH . 
E 5 HOH A 11 511 5 HOH HOH . 
E 5 HOH A 12 512 21 HOH HOH . 
E 5 HOH A 13 513 2 HOH HOH . 
E 5 HOH A 14 514 13 HOH HOH . 
E 5 HOH A 15 515 36 HOH HOH . 
E 5 HOH A 16 516 14 HOH HOH . 
E 5 HOH A 17 517 61 HOH HOH . 
E 5 HOH A 18 518 6 HOH HOH . 
E 5 HOH A 19 519 4 HOH HOH . 
E 5 HOH A 20 520 39 HOH HOH . 
E 5 HOH A 21 521 71 HOH HOH . 
E 5 HOH A 22 522 86 HOH HOH . 
E 5 HOH A 23 523 91 HOH HOH . 
E 5 HOH A 24 524 65 HOH HOH . 
E 5 HOH A 25 525 75 HOH HOH . 
E 5 HOH A 26 526 74 HOH HOH . 
E 5 HOH A 27 527 20 HOH HOH . 
E 5 HOH A 28 528 26 HOH HOH . 
E 5 HOH A 29 529 69 HOH HOH . 
E 5 HOH A 30 530 85 HOH HOH . 
E 5 HOH A 31 531 28 HOH HOH . 
E 5 HOH A 32 532 47 HOH HOH . 
E 5 HOH A 33 533 32 HOH HOH . 
E 5 HOH A 34 534 9 HOH HOH . 
E 5 HOH A 35 535 90 HOH HOH . 
E 5 HOH A 36 536 81 HOH HOH . 
E 5 HOH A 37 537 66 HOH HOH . 
E 5 HOH A 38 538 53 HOH HOH . 
E 5 HOH A 39 539 11 HOH HOH . 
E 5 HOH A 40 540 12 HOH HOH . 
E 5 HOH A 41 541 3 HOH HOH . 
E 5 HOH A 42 542 89 HOH HOH . 
E 5 HOH A 43 543 50 HOH HOH . 
E 5 HOH A 44 544 52 HOH HOH . 
E 5 HOH A 45 545 19 HOH HOH . 
E 5 HOH A 46 546 15 HOH HOH . 
E 5 HOH A 47 547 1 HOH HOH . 
E 5 HOH A 48 548 40 HOH HOH . 
E 5 HOH A 49 549 23 HOH HOH . 
E 5 HOH A 50 550 83 HOH HOH . 
E 5 HOH A 51 551 68 HOH HOH . 
E 5 HOH A 52 552 56 HOH HOH . 
E 5 HOH A 53 553 10 HOH HOH . 
E 5 HOH A 54 554 82 HOH HOH . 
E 5 HOH A 55 555 34 HOH HOH . 
E 5 HOH A 56 556 38 HOH HOH . 
E 5 HOH A 57 557 30 HOH HOH . 
E 5 HOH A 58 558 67 HOH HOH . 
E 5 HOH A 59 559 43 HOH HOH . 
E 5 HOH A 60 560 94 HOH HOH . 
E 5 HOH A 61 561 29 HOH HOH . 
E 5 HOH A 62 562 33 HOH HOH . 
E 5 HOH A 63 563 54 HOH HOH . 
E 5 HOH A 64 564 25 HOH HOH . 
E 5 HOH A 65 565 73 HOH HOH . 
E 5 HOH A 66 566 77 HOH HOH . 
E 5 HOH A 67 567 35 HOH HOH . 
E 5 HOH A 68 568 46 HOH HOH . 
E 5 HOH A 69 569 63 HOH HOH . 
E 5 HOH A 70 570 72 HOH HOH . 
E 5 HOH A 71 571 18 HOH HOH . 
E 5 HOH A 72 572 60 HOH HOH . 
E 5 HOH A 73 573 57 HOH HOH . 
E 5 HOH A 74 574 16 HOH HOH . 
E 5 HOH A 75 575 7 HOH HOH . 
E 5 HOH A 76 576 49 HOH HOH . 
E 5 HOH A 77 577 80 HOH HOH . 
E 5 HOH A 78 578 51 HOH HOH . 
E 5 HOH A 79 579 62 HOH HOH . 
E 5 HOH A 80 580 8 HOH HOH . 
E 5 HOH A 81 581 37 HOH HOH . 
E 5 HOH A 82 582 44 HOH HOH . 
E 5 HOH A 83 583 84 HOH HOH . 
E 5 HOH A 84 584 41 HOH HOH . 
E 5 HOH A 85 585 59 HOH HOH . 
E 5 HOH A 86 586 79 HOH HOH . 
E 5 HOH A 87 587 70 HOH HOH . 
E 5 HOH A 88 588 55 HOH HOH . 
E 5 HOH A 89 589 93 HOH HOH . 
E 5 HOH A 90 590 42 HOH HOH . 
E 5 HOH A 91 591 92 HOH HOH . 
E 5 HOH A 92 592 58 HOH HOH . 
E 5 HOH A 93 593 76 HOH HOH . 
E 5 HOH A 94 594 78 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 5.449 -9.07 27.01 1 30.32 ? PB GDP 401 A 1 
HETATM 2 O O1B GDP . . . B 2 6.137 -7.744 27.229 1 32.42 ? O1B GDP 401 A 1 
HETATM 3 O O2B GDP . . . B 2 6.107 -10.133 27.857 1 35.98 ? O2B GDP 401 A 1 
HETATM 4 O O3B GDP . . . B 2 3.998 -8.955 27.407 1 33 ? O3B GDP 401 A 1 
HETATM 5 O O3A GDP . . . B 2 5.557 -9.488 25.459 1 37.43 ? O3A GDP 401 A 1 
HETATM 6 P PA GDP . . . B 2 5.221 -8.445 24.279 1 30.84 ? PA GDP 401 A 1 
HETATM 7 O O1A GDP . . . B 2 6.462 -7.687 23.87 1 29.3 ? O1A GDP 401 A 1 
HETATM 8 O O2A GDP . . . B 2 4.126 -7.487 24.685 1 32.88 ? O2A GDP 401 A 1 
HETATM 9 O O5' GDP . . . B 2 4.738 -9.411 23.085 1 28.99 ? O5' GDP 401 A 1 
HETATM 10 C C5' GDP . . . B 2 3.5 -10.109 23.205 1 31.71 ? C5' GDP 401 A 1 
HETATM 11 C C4' GDP . . . B 2 2.79 -10.166 21.859 1 34.34 ? C4' GDP 401 A 1 
HETATM 12 O O4' GDP . . . B 2 2.416 -8.844 21.474 1 34.95 ? O4' GDP 401 A 1 
HETATM 13 C C3' GDP . . . B 2 3.674 -10.714 20.75 1 33.3 ? C3' GDP 401 A 1 
HETATM 14 O O3' GDP . . . B 2 3.311 -12.067 20.458 1 34.88 ? O3' GDP 401 A 1 
HETATM 15 C C2' GDP . . . B 2 3.414 -9.822 19.55 1 31.1 ? C2' GDP 401 A 1 
HETATM 16 O O2' GDP . . . B 2 2.643 -10.535 18.576 1 30.46 ? O2' GDP 401 A 1 
HETATM 17 C C1' GDP . . . B 2 2.603 -8.647 20.072 1 29.22 ? C1' GDP 401 A 1 
HETATM 18 N N9 GDP . . . B 2 3.317 -7.362 19.868 1 33.8 ? N9 GDP 401 A 1 
HETATM 19 C C8 GDP . . . B 2 4.444 -6.976 20.497 1 32.2 ? C8 GDP 401 A 1 
HETATM 20 N N7 GDP . . . B 2 4.833 -5.738 20.092 1 32.27 ? N7 GDP 401 A 1 
HETATM 21 C C5 GDP . . . B 2 3.931 -5.307 19.191 1 35.63 ? C5 GDP 401 A 1 
HETATM 22 C C6 GDP . . . B 2 3.734 -4.088 18.371 1 35.35 ? C6 GDP 401 A 1 
HETATM 23 O O6 GDP . . . B 2 4.537 -3.132 18.432 1 36.92 ? O6 GDP 401 A 1 
HETATM 24 N N1 GDP . . . B 2 2.67 -4.044 17.561 1 34.57 ? N1 GDP 401 A 1 
HETATM 25 C C2 GDP . . . B 2 1.787 -5.057 17.47 1 34.62 ? C2 GDP 401 A 1 
HETATM 26 N N2 GDP . . . B 2 0.736 -4.929 16.624 1 29.74 ? N2 GDP 401 A 1 
HETATM 27 N N3 GDP . . . B 2 1.904 -6.201 18.191 1 32.68 ? N3 GDP 401 A 1 
HETATM 28 C C4 GDP . . . B 2 2.935 -6.38 19.049 1 35.21 ? C4 GDP 401 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#