data_7C1O
#
_model_server_result.job_id            hyE6Ul5b6p3POPec_TA45g 
_model_server_result.datetime_utc      '2025-09-01 01:04:05' 
_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          7c1o 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    7C1O 
#
_exptl.entry_id    7C1O 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_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            7C1O 
_cell.length_a            36.377 
_cell.length_b            72.86 
_cell.length_c            120.91 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7C1O 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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                      3 
_struct_asym.id                             C 
_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 OD1 ASN 20 A ASN 13 1_555 G K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? 
metalc ? metalc2 A OG SER 24 A SER 17 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc3 A O SER 39 A SER 32 1_555 G K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? 
metalc ? metalc4 A O LYS 41 A LYS 34 1_555 G K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? 
metalc ? metalc5 A OG1 THR 44 A THR 37 1_555 G K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.315 ? 
metalc ? metalc6 A OG1 THR 45 A THR 38 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc7 C O3B GDP . A GDP 402 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc8 C O1B GDP . A GDP 402 1_555 G K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.037 ? 
metalc ? metalc9 C O1A GDP . A GDP 402 1_555 G K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.074 ? 
metalc ? metalc10 F MG MG . A MG 405 1_555 H O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc11 F MG MG . A MG 405 1_555 H O HOH . A HOH 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
#
_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 74 n n 
PB O2B GDP sing 75 n n 
PB O3B GDP sing 76 n n 
PB O3A GDP sing 77 n n 
O2B HOB2 GDP sing 78 n n 
O3B HOB3 GDP sing 79 n n 
O3A PA GDP sing 80 n n 
PA O1A GDP doub 81 n n 
PA O2A GDP sing 82 n n 
PA O5' GDP sing 83 n n 
O2A HOA2 GDP sing 84 n n 
O5' C5' GDP sing 85 n n 
C5' C4' GDP sing 86 n n 
C5' H5' GDP sing 87 n n 
C5' "H5''" GDP sing 88 n n 
C4' O4' GDP sing 89 n n 
C4' C3' GDP sing 90 n n 
C4' H4' GDP sing 91 n n 
O4' C1' GDP sing 92 n n 
C3' O3' GDP sing 93 n n 
C3' C2' GDP sing 94 n n 
C3' H3' GDP sing 95 n n 
O3' HO3' GDP sing 96 n n 
C2' O2' GDP sing 97 n n 
C2' C1' GDP sing 98 n n 
C2' H2' GDP sing 99 n n 
O2' HO2' GDP sing 100 n n 
C1' N9 GDP sing 101 n n 
C1' H1' GDP sing 102 n n 
N9 C8 GDP sing 103 n y 
N9 C4 GDP sing 104 n y 
C8 N7 GDP doub 105 n y 
C8 H8 GDP sing 106 n n 
N7 C5 GDP sing 107 n y 
C5 C6 GDP sing 108 n n 
C5 C4 GDP doub 109 n y 
C6 O6 GDP doub 110 n n 
C6 N1 GDP sing 111 n n 
N1 C2 GDP sing 112 n n 
N1 HN1 GDP sing 113 n n 
C2 N2 GDP sing 114 n n 
C2 N3 GDP doub 115 n n 
N2 HN21 GDP sing 116 n n 
N2 HN22 GDP sing 117 n n 
N3 C4 GDP sing 118 n n 
#
_atom_sites.entry_id                     7C1O 
_atom_sites.fract_transf_matrix[1][1]    0.02749 
_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]    0.013725 
_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]    0.008271 
_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 ALF A 1 401 401 ALF ALF . 
C 3 GDP A 1 402 501 GDP GDP . 
D 4 PEG A 1 403 701 PEG PEG . 
E 5 TRS A 1 404 901 TRS TRS . 
F 6 MG A 1 405 1 MG MG . 
G 7 K A 1 406 1 K K . 
H 8 HOH A 1 501 59 HOH HOH . 
H 8 HOH A 2 502 64 HOH HOH . 
H 8 HOH A 3 503 27 HOH HOH . 
H 8 HOH A 4 504 15 HOH HOH . 
H 8 HOH A 5 505 65 HOH HOH . 
H 8 HOH A 6 506 10 HOH HOH . 
H 8 HOH A 7 507 45 HOH HOH . 
H 8 HOH A 8 508 60 HOH HOH . 
H 8 HOH A 9 509 98 HOH HOH . 
H 8 HOH A 10 510 46 HOH HOH . 
H 8 HOH A 11 511 77 HOH HOH . 
H 8 HOH A 12 512 36 HOH HOH . 
H 8 HOH A 13 513 79 HOH HOH . 
H 8 HOH A 14 514 56 HOH HOH . 
H 8 HOH A 15 515 63 HOH HOH . 
H 8 HOH A 16 516 58 HOH HOH . 
H 8 HOH A 17 517 23 HOH HOH . 
H 8 HOH A 18 518 93 HOH HOH . 
H 8 HOH A 19 519 24 HOH HOH . 
H 8 HOH A 20 520 8 HOH HOH . 
H 8 HOH A 21 521 75 HOH HOH . 
H 8 HOH A 22 522 26 HOH HOH . 
H 8 HOH A 23 523 41 HOH HOH . 
H 8 HOH A 24 524 62 HOH HOH . 
H 8 HOH A 25 525 34 HOH HOH . 
H 8 HOH A 26 526 54 HOH HOH . 
H 8 HOH A 27 527 73 HOH HOH . 
H 8 HOH A 28 528 35 HOH HOH . 
H 8 HOH A 29 529 50 HOH HOH . 
H 8 HOH A 30 530 7 HOH HOH . 
H 8 HOH A 31 531 12 HOH HOH . 
H 8 HOH A 32 532 74 HOH HOH . 
H 8 HOH A 33 533 68 HOH HOH . 
H 8 HOH A 34 534 30 HOH HOH . 
H 8 HOH A 35 535 5 HOH HOH . 
H 8 HOH A 36 536 16 HOH HOH . 
H 8 HOH A 37 537 53 HOH HOH . 
H 8 HOH A 38 538 39 HOH HOH . 
H 8 HOH A 39 539 22 HOH HOH . 
H 8 HOH A 40 540 95 HOH HOH . 
H 8 HOH A 41 541 19 HOH HOH . 
H 8 HOH A 42 542 13 HOH HOH . 
H 8 HOH A 43 543 72 HOH HOH . 
H 8 HOH A 44 544 11 HOH HOH . 
H 8 HOH A 45 545 2 HOH HOH . 
H 8 HOH A 46 546 6 HOH HOH . 
H 8 HOH A 47 547 69 HOH HOH . 
H 8 HOH A 48 548 9 HOH HOH . 
H 8 HOH A 49 549 86 HOH HOH . 
H 8 HOH A 50 550 44 HOH HOH . 
H 8 HOH A 51 551 1 HOH HOH . 
H 8 HOH A 52 552 94 HOH HOH . 
H 8 HOH A 53 553 78 HOH HOH . 
H 8 HOH A 54 554 47 HOH HOH . 
H 8 HOH A 55 555 66 HOH HOH . 
H 8 HOH A 56 556 48 HOH HOH . 
H 8 HOH A 57 557 29 HOH HOH . 
H 8 HOH A 58 558 38 HOH HOH . 
H 8 HOH A 59 559 3 HOH HOH . 
H 8 HOH A 60 560 14 HOH HOH . 
H 8 HOH A 61 561 32 HOH HOH . 
H 8 HOH A 62 562 96 HOH HOH . 
H 8 HOH A 63 563 43 HOH HOH . 
H 8 HOH A 64 564 25 HOH HOH . 
H 8 HOH A 65 565 21 HOH HOH . 
H 8 HOH A 66 566 82 HOH HOH . 
H 8 HOH A 67 567 89 HOH HOH . 
H 8 HOH A 68 568 40 HOH HOH . 
H 8 HOH A 69 569 91 HOH HOH . 
H 8 HOH A 70 570 28 HOH HOH . 
H 8 HOH A 71 571 85 HOH HOH . 
H 8 HOH A 72 572 88 HOH HOH . 
H 8 HOH A 73 573 52 HOH HOH . 
H 8 HOH A 74 574 90 HOH HOH . 
H 8 HOH A 75 575 84 HOH HOH . 
H 8 HOH A 76 576 18 HOH HOH . 
H 8 HOH A 77 577 31 HOH HOH . 
H 8 HOH A 78 578 87 HOH HOH . 
H 8 HOH A 79 579 61 HOH HOH . 
H 8 HOH A 80 580 33 HOH HOH . 
H 8 HOH A 81 581 42 HOH HOH . 
H 8 HOH A 82 582 67 HOH HOH . 
H 8 HOH A 83 583 92 HOH HOH . 
H 8 HOH A 84 584 76 HOH HOH . 
H 8 HOH A 85 585 81 HOH HOH . 
H 8 HOH A 86 586 4 HOH HOH . 
H 8 HOH A 87 587 49 HOH HOH . 
H 8 HOH A 88 588 83 HOH HOH . 
H 8 HOH A 89 589 17 HOH HOH . 
H 8 HOH A 90 590 70 HOH HOH . 
H 8 HOH A 91 591 97 HOH HOH . 
H 8 HOH A 92 592 80 HOH HOH . 
H 8 HOH A 93 593 71 HOH HOH . 
H 8 HOH A 94 594 55 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 . . . C 3 -11.275 0.741 -16.35 1 30.87 ? PB GDP 402 A 1 
HETATM 2 O O1B GDP . . . C 3 -11.398 1.486 -17.651 1 29.96 ? O1B GDP 402 A 1 
HETATM 3 O O2B GDP . . . C 3 -11.035 -0.753 -16.477 1 30.95 ? O2B GDP 402 A 1 
HETATM 4 O O3B GDP . . . C 3 -10.539 1.468 -15.24 1 29.23 ? O3B GDP 402 A 1 
HETATM 5 O O3A GDP . . . C 3 -12.828 0.879 -15.621 1 34.22 ? O3A GDP 402 A 1 
HETATM 6 P PA GDP . . . C 3 -13.259 1.842 -14.511 1 33.97 ? PA GDP 402 A 1 
HETATM 7 O O1A GDP . . . C 3 -13.314 3.316 -14.839 1 31.83 ? O1A GDP 402 A 1 
HETATM 8 O O2A GDP . . . C 3 -13.186 1.418 -13.088 1 33.71 ? O2A GDP 402 A 1 
HETATM 9 O O5' GDP . . . C 3 -15.057 1.573 -14.694 1 37.71 ? O5' GDP 402 A 1 
HETATM 10 C C5' GDP . . . C 3 -15.578 1.698 -15.918 1 38.34 ? C5' GDP 402 A 1 
HETATM 11 C C4' GDP . . . C 3 -17.146 1.585 -15.755 1 40.56 ? C4' GDP 402 A 1 
HETATM 12 O O4' GDP . . . C 3 -17.461 0.267 -15.315 1 38.21 ? O4' GDP 402 A 1 
HETATM 13 C C3' GDP . . . C 3 -17.691 2.559 -14.68 1 40.82 ? C3' GDP 402 A 1 
HETATM 14 O O3' GDP . . . C 3 -18.943 2.981 -15.131 1 47.76 ? O3' GDP 402 A 1 
HETATM 15 C C2' GDP . . . C 3 -17.843 1.662 -13.437 1 41.69 ? C2' GDP 402 A 1 
HETATM 16 O O2' GDP . . . C 3 -18.876 2.038 -12.581 1 41.2 ? O2' GDP 402 A 1 
HETATM 17 C C1' GDP . . . C 3 -18.243 0.326 -14.145 1 40.02 ? C1' GDP 402 A 1 
HETATM 18 N N9 GDP . . . C 3 -17.831 -0.824 -13.338 1 33.22 ? N9 GDP 402 A 1 
HETATM 19 C C8 GDP . . . C 3 -16.531 -1.166 -12.898 1 34.45 ? C8 GDP 402 A 1 
HETATM 20 N N7 GDP . . . C 3 -16.535 -2.303 -12.177 1 35.35 ? N7 GDP 402 A 1 
HETATM 21 C C5 GDP . . . C 3 -17.874 -2.704 -12.155 1 33.45 ? C5 GDP 402 A 1 
HETATM 22 C C6 GDP . . . C 3 -18.433 -3.855 -11.522 1 32.41 ? C6 GDP 402 A 1 
HETATM 23 O O6 GDP . . . C 3 -17.913 -4.743 -10.866 1 34.99 ? O6 GDP 402 A 1 
HETATM 24 N N1 GDP . . . C 3 -19.852 -3.939 -11.713 1 38.16 ? N1 GDP 402 A 1 
HETATM 25 C C2 GDP . . . C 3 -20.57 -2.979 -12.446 1 38.31 ? C2 GDP 402 A 1 
HETATM 26 N N2 GDP . . . C 3 -21.944 -3.177 -12.556 1 38.77 ? N2 GDP 402 A 1 
HETATM 27 N N3 GDP . . . C 3 -20.065 -1.889 -13.051 1 38.68 ? N3 GDP 402 A 1 
HETATM 28 C C4 GDP . . . C 3 -18.687 -1.799 -12.871 1 42.38 ? C4 GDP 402 A 1 
#
_model_server_stats.io_time_ms              204 
_model_server_stats.parse_time_ms           112 
_model_server_stats.create_model_time_ms    82 
_model_server_stats.query_time_ms           401 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#