data_7YSZ
#
_model_server_result.job_id            A_XNs1oQtNmhcZQRIymIrA 
_model_server_result.datetime_utc      '2024-12-26 17:56:34' 
_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          7ysz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":402}' 
#
_entry.id    7YSZ 
#
_exptl.entry_id    7YSZ 
_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    2 
_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            7YSZ 
_cell.length_a            106.546 
_cell.length_b            106.546 
_cell.length_c            127.603 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7YSZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    'P 4abw 2nw' 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_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,F,G 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N N 
#
_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 70 n n 
PB O2B GDP sing 71 n n 
PB O3B GDP sing 72 n n 
PB O3A GDP sing 73 n n 
O2B HOB2 GDP sing 74 n n 
O3B HOB3 GDP sing 75 n n 
O3A PA GDP sing 76 n n 
PA O1A GDP doub 77 n n 
PA O2A GDP sing 78 n n 
PA O5' GDP sing 79 n n 
O2A HOA2 GDP sing 80 n n 
O5' C5' GDP sing 81 n n 
C5' C4' GDP sing 82 n n 
C5' H5' GDP sing 83 n n 
C5' "H5''" GDP sing 84 n n 
C4' O4' GDP sing 85 n n 
C4' C3' GDP sing 86 n n 
C4' H4' GDP sing 87 n n 
O4' C1' GDP sing 88 n n 
C3' O3' GDP sing 89 n n 
C3' C2' GDP sing 90 n n 
C3' H3' GDP sing 91 n n 
O3' HO3' GDP sing 92 n n 
C2' O2' GDP sing 93 n n 
C2' C1' GDP sing 94 n n 
C2' H2' GDP sing 95 n n 
O2' HO2' GDP sing 96 n n 
C1' N9 GDP sing 97 n n 
C1' H1' GDP sing 98 n n 
N9 C8 GDP sing 99 n y 
N9 C4 GDP sing 100 n y 
C8 N7 GDP doub 101 n y 
C8 H8 GDP sing 102 n n 
N7 C5 GDP sing 103 n y 
C5 C6 GDP sing 104 n n 
C5 C4 GDP doub 105 n y 
C6 O6 GDP doub 106 n n 
C6 N1 GDP sing 107 n n 
N1 C2 GDP sing 108 n n 
N1 HN1 GDP sing 109 n n 
C2 N2 GDP sing 110 n n 
C2 N3 GDP doub 111 n n 
N2 HN21 GDP sing 112 n n 
N2 HN22 GDP sing 113 n n 
N3 C4 GDP sing 114 n n 
#
_atom_sites.entry_id                     7YSZ 
_atom_sites.fract_transf_matrix[1][1]    0.009386 
_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]    0.009386 
_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]    0.007837 
_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
C 2 GDP A 1 501 501 GDP GDP . 
D 3 TRS B 1 401 1 TRS TRS . 
E 2 GDP B 1 402 401 GDP GDP . 
F 4 HOH A 1 601 90 HOH HOH . 
F 4 HOH A 2 602 31 HOH HOH . 
F 4 HOH A 3 603 197 HOH HOH . 
F 4 HOH A 4 604 29 HOH HOH . 
F 4 HOH A 5 605 125 HOH HOH . 
F 4 HOH A 6 606 87 HOH HOH . 
F 4 HOH A 7 607 205 HOH HOH . 
F 4 HOH A 8 608 40 HOH HOH . 
F 4 HOH A 9 609 8 HOH HOH . 
F 4 HOH A 10 610 152 HOH HOH . 
F 4 HOH A 11 611 20 HOH HOH . 
F 4 HOH A 12 612 126 HOH HOH . 
F 4 HOH A 13 613 104 HOH HOH . 
F 4 HOH A 14 614 57 HOH HOH . 
F 4 HOH A 15 615 25 HOH HOH . 
F 4 HOH A 16 616 78 HOH HOH . 
F 4 HOH A 17 617 177 HOH HOH . 
F 4 HOH A 18 618 97 HOH HOH . 
F 4 HOH A 19 619 9 HOH HOH . 
F 4 HOH A 20 620 22 HOH HOH . 
F 4 HOH A 21 621 96 HOH HOH . 
F 4 HOH A 22 622 81 HOH HOH . 
F 4 HOH A 23 623 115 HOH HOH . 
F 4 HOH A 24 624 7 HOH HOH . 
F 4 HOH A 25 625 86 HOH HOH . 
F 4 HOH A 26 626 58 HOH HOH . 
F 4 HOH A 27 627 12 HOH HOH . 
F 4 HOH A 28 628 11 HOH HOH . 
F 4 HOH A 29 629 83 HOH HOH . 
F 4 HOH A 30 630 181 HOH HOH . 
F 4 HOH A 31 631 116 HOH HOH . 
F 4 HOH A 32 632 112 HOH HOH . 
F 4 HOH A 33 633 35 HOH HOH . 
F 4 HOH A 34 634 5 HOH HOH . 
F 4 HOH A 35 635 42 HOH HOH . 
F 4 HOH A 36 636 127 HOH HOH . 
F 4 HOH A 37 637 119 HOH HOH . 
F 4 HOH A 38 638 95 HOH HOH . 
F 4 HOH A 39 639 120 HOH HOH . 
F 4 HOH A 40 640 202 HOH HOH . 
F 4 HOH A 41 641 176 HOH HOH . 
F 4 HOH A 42 642 102 HOH HOH . 
F 4 HOH A 43 643 171 HOH HOH . 
F 4 HOH A 44 644 193 HOH HOH . 
F 4 HOH A 45 645 105 HOH HOH . 
F 4 HOH A 46 646 178 HOH HOH . 
F 4 HOH A 47 647 66 HOH HOH . 
F 4 HOH A 48 648 195 HOH HOH . 
F 4 HOH A 49 649 182 HOH HOH . 
F 4 HOH A 50 650 113 HOH HOH . 
F 4 HOH A 51 651 41 HOH HOH . 
F 4 HOH A 52 652 15 HOH HOH . 
F 4 HOH A 53 653 46 HOH HOH . 
F 4 HOH A 54 654 37 HOH HOH . 
F 4 HOH A 55 655 39 HOH HOH . 
F 4 HOH A 56 656 33 HOH HOH . 
F 4 HOH A 57 657 110 HOH HOH . 
F 4 HOH A 58 658 121 HOH HOH . 
F 4 HOH A 59 659 38 HOH HOH . 
F 4 HOH A 60 660 61 HOH HOH . 
F 4 HOH A 61 661 123 HOH HOH . 
F 4 HOH A 62 662 107 HOH HOH . 
F 4 HOH A 63 663 175 HOH HOH . 
F 4 HOH A 64 664 43 HOH HOH . 
F 4 HOH A 65 665 180 HOH HOH . 
F 4 HOH A 66 666 85 HOH HOH . 
F 4 HOH A 67 667 201 HOH HOH . 
F 4 HOH A 68 668 106 HOH HOH . 
F 4 HOH A 69 669 183 HOH HOH . 
F 4 HOH A 70 670 170 HOH HOH . 
F 4 HOH A 71 671 151 HOH HOH . 
F 4 HOH A 72 672 111 HOH HOH . 
F 4 HOH A 73 673 69 HOH HOH . 
F 4 HOH A 74 674 68 HOH HOH . 
F 4 HOH A 75 675 133 HOH HOH . 
F 4 HOH A 76 676 103 HOH HOH . 
F 4 HOH A 77 677 128 HOH HOH . 
F 4 HOH A 78 678 150 HOH HOH . 
F 4 HOH A 79 679 196 HOH HOH . 
F 4 HOH A 80 680 53 HOH HOH . 
F 4 HOH A 81 681 186 HOH HOH . 
F 4 HOH A 82 682 184 HOH HOH . 
G 4 HOH B 1 501 189 HOH HOH . 
G 4 HOH B 2 502 47 HOH HOH . 
G 4 HOH B 3 503 92 HOH HOH . 
G 4 HOH B 4 504 16 HOH HOH . 
G 4 HOH B 5 505 158 HOH HOH . 
G 4 HOH B 6 506 173 HOH HOH . 
G 4 HOH B 7 507 74 HOH HOH . 
G 4 HOH B 8 508 143 HOH HOH . 
G 4 HOH B 9 509 161 HOH HOH . 
G 4 HOH B 10 510 80 HOH HOH . 
G 4 HOH B 11 511 203 HOH HOH . 
G 4 HOH B 12 512 34 HOH HOH . 
G 4 HOH B 13 513 163 HOH HOH . 
G 4 HOH B 14 514 30 HOH HOH . 
G 4 HOH B 15 515 169 HOH HOH . 
G 4 HOH B 16 516 207 HOH HOH . 
G 4 HOH B 17 517 124 HOH HOH . 
G 4 HOH B 18 518 54 HOH HOH . 
G 4 HOH B 19 519 73 HOH HOH . 
G 4 HOH B 20 520 18 HOH HOH . 
G 4 HOH B 21 521 79 HOH HOH . 
G 4 HOH B 22 522 13 HOH HOH . 
G 4 HOH B 23 523 140 HOH HOH . 
G 4 HOH B 24 524 172 HOH HOH . 
G 4 HOH B 25 525 82 HOH HOH . 
G 4 HOH B 26 526 94 HOH HOH . 
G 4 HOH B 27 527 59 HOH HOH . 
G 4 HOH B 28 528 6 HOH HOH . 
G 4 HOH B 29 529 101 HOH HOH . 
G 4 HOH B 30 530 44 HOH HOH . 
G 4 HOH B 31 531 93 HOH HOH . 
G 4 HOH B 32 532 14 HOH HOH . 
G 4 HOH B 33 533 179 HOH HOH . 
G 4 HOH B 34 534 21 HOH HOH . 
G 4 HOH B 35 535 48 HOH HOH . 
G 4 HOH B 36 536 135 HOH HOH . 
G 4 HOH B 37 537 70 HOH HOH . 
G 4 HOH B 38 538 200 HOH HOH . 
G 4 HOH B 39 539 77 HOH HOH . 
G 4 HOH B 40 540 206 HOH HOH . 
G 4 HOH B 41 541 23 HOH HOH . 
G 4 HOH B 42 542 164 HOH HOH . 
G 4 HOH B 43 543 167 HOH HOH . 
G 4 HOH B 44 544 75 HOH HOH . 
G 4 HOH B 45 545 72 HOH HOH . 
G 4 HOH B 46 546 91 HOH HOH . 
G 4 HOH B 47 547 166 HOH HOH . 
G 4 HOH B 48 548 67 HOH HOH . 
G 4 HOH B 49 549 168 HOH HOH . 
G 4 HOH B 50 550 98 HOH HOH . 
G 4 HOH B 51 551 64 HOH HOH . 
G 4 HOH B 52 552 62 HOH HOH . 
G 4 HOH B 53 553 141 HOH HOH . 
G 4 HOH B 54 554 99 HOH HOH . 
G 4 HOH B 55 555 198 HOH HOH . 
G 4 HOH B 56 556 1 HOH HOH . 
G 4 HOH B 57 557 130 HOH HOH . 
G 4 HOH B 58 558 144 HOH HOH . 
G 4 HOH B 59 559 45 HOH HOH . 
G 4 HOH B 60 560 142 HOH HOH . 
G 4 HOH B 61 561 76 HOH HOH . 
G 4 HOH B 62 562 114 HOH HOH . 
G 4 HOH B 63 563 89 HOH HOH . 
G 4 HOH B 64 564 154 HOH HOH . 
G 4 HOH B 65 565 50 HOH HOH . 
G 4 HOH B 66 566 4 HOH HOH . 
G 4 HOH B 67 567 3 HOH HOH . 
G 4 HOH B 68 568 52 HOH HOH . 
G 4 HOH B 69 569 138 HOH HOH . 
G 4 HOH B 70 570 134 HOH HOH . 
G 4 HOH B 71 571 156 HOH HOH . 
G 4 HOH B 72 572 26 HOH HOH . 
G 4 HOH B 73 573 28 HOH HOH . 
G 4 HOH B 74 574 160 HOH HOH . 
G 4 HOH B 75 575 10 HOH HOH . 
G 4 HOH B 76 576 129 HOH HOH . 
G 4 HOH B 77 577 17 HOH HOH . 
G 4 HOH B 78 578 19 HOH HOH . 
G 4 HOH B 79 579 2 HOH HOH . 
G 4 HOH B 80 580 136 HOH HOH . 
G 4 HOH B 81 581 194 HOH HOH . 
G 4 HOH B 82 582 188 HOH HOH . 
G 4 HOH B 83 583 146 HOH HOH . 
G 4 HOH B 84 584 131 HOH HOH . 
G 4 HOH B 85 585 137 HOH HOH . 
G 4 HOH B 86 586 122 HOH HOH . 
G 4 HOH B 87 587 60 HOH HOH . 
G 4 HOH B 88 588 139 HOH HOH . 
G 4 HOH B 89 589 149 HOH HOH . 
G 4 HOH B 90 590 162 HOH HOH . 
G 4 HOH B 91 591 191 HOH HOH . 
G 4 HOH B 92 592 165 HOH HOH . 
G 4 HOH B 93 593 185 HOH HOH . 
G 4 HOH B 94 594 118 HOH HOH . 
G 4 HOH B 95 595 88 HOH HOH . 
G 4 HOH B 96 596 65 HOH HOH . 
G 4 HOH B 97 597 55 HOH HOH . 
G 4 HOH B 98 598 63 HOH HOH . 
G 4 HOH B 99 599 56 HOH HOH . 
G 4 HOH B 100 600 100 HOH HOH . 
G 4 HOH B 101 601 148 HOH HOH . 
G 4 HOH B 102 602 24 HOH HOH . 
G 4 HOH B 103 603 192 HOH HOH . 
G 4 HOH B 104 604 174 HOH HOH . 
G 4 HOH B 105 605 36 HOH HOH . 
G 4 HOH B 106 606 204 HOH HOH . 
G 4 HOH B 107 607 117 HOH HOH . 
G 4 HOH B 108 608 199 HOH HOH . 
G 4 HOH B 109 609 190 HOH HOH . 
G 4 HOH B 110 610 32 HOH HOH . 
G 4 HOH B 111 611 145 HOH HOH . 
G 4 HOH B 112 612 84 HOH HOH . 
G 4 HOH B 113 613 51 HOH HOH . 
G 4 HOH B 114 614 153 HOH HOH . 
G 4 HOH B 115 615 132 HOH HOH . 
G 4 HOH B 116 616 147 HOH HOH . 
G 4 HOH B 117 617 109 HOH HOH . 
G 4 HOH B 118 618 71 HOH HOH . 
G 4 HOH B 119 619 157 HOH HOH . 
G 4 HOH B 120 620 49 HOH HOH . 
G 4 HOH B 121 621 108 HOH HOH . 
G 4 HOH B 122 622 159 HOH HOH . 
G 4 HOH B 123 623 155 HOH HOH . 
G 4 HOH B 124 624 27 HOH HOH . 
G 4 HOH B 125 625 187 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 . . . E 2 25.955 -4.908 9.932 1 43.5 ? PB GDP 402 B 1 
HETATM 2 O O1B GDP . . . E 2 25.604 -3.51 9.495 1 43.89 ? O1B GDP 402 B 1 
HETATM 3 O O2B GDP . . . E 2 26.124 -5.043 11.419 1 43.93 ? O2B GDP 402 B 1 
HETATM 4 O O3B GDP . . . E 2 24.905 -5.935 9.58 1 55.23 ? O3B GDP 402 B 1 
HETATM 5 O O3A GDP . . . E 2 27.273 -5.265 9.071 1 51.24 ? O3A GDP 402 B 1 
HETATM 6 P PA GDP . . . E 2 28.701 -5.107 9.736 1 47.98 ? PA GDP 402 B 1 
HETATM 7 O O1A GDP . . . E 2 28.631 -3.85 10.611 1 47.64 ? O1A GDP 402 B 1 
HETATM 8 O O2A GDP . . . E 2 29.074 -6.283 10.624 1 49.26 ? O2A GDP 402 B 1 
HETATM 9 O O5' GDP . . . E 2 29.63 -4.917 8.459 1 39.35 ? O5' GDP 402 B 1 
HETATM 10 C C5' GDP . . . E 2 29.476 -3.745 7.639 1 35.12 ? C5' GDP 402 B 1 
HETATM 11 C C4' GDP . . . E 2 30.812 -3.449 7.011 1 33.53 ? C4' GDP 402 B 1 
HETATM 12 O O4' GDP . . . E 2 31.673 -2.845 7.977 1 33.9 ? O4' GDP 402 B 1 
HETATM 13 C C3' GDP . . . E 2 31.53 -4.711 6.584 1 31.43 ? C3' GDP 402 B 1 
HETATM 14 O O3' GDP . . . E 2 31.259 -4.997 5.208 1 36.21 ? O3' GDP 402 B 1 
HETATM 15 C C2' GDP . . . E 2 32.995 -4.352 6.738 1 40.23 ? C2' GDP 402 B 1 
HETATM 16 O O2' GDP . . . E 2 33.44 -3.737 5.541 1 35.25 ? O2' GDP 402 B 1 
HETATM 17 C C1' GDP . . . E 2 33.022 -3.244 7.763 1 33.32 ? C1' GDP 402 B 1 
HETATM 18 N N9 GDP . . . E 2 33.416 -3.752 9.074 1 35.33 ? N9 GDP 402 B 1 
HETATM 19 C C8 GDP . . . E 2 32.688 -4.553 9.878 1 33.89 ? C8 GDP 402 B 1 
HETATM 20 N N7 GDP . . . E 2 33.378 -4.787 11.036 1 38.39 ? N7 GDP 402 B 1 
HETATM 21 C C5 GDP . . . E 2 34.541 -4.102 10.994 1 31.56 ? C5 GDP 402 B 1 
HETATM 22 C C6 GDP . . . E 2 35.733 -3.903 11.855 1 33.49 ? C6 GDP 402 B 1 
HETATM 23 O O6 GDP . . . E 2 35.842 -4.439 12.973 1 32.6 ? O6 GDP 402 B 1 
HETATM 24 N N1 GDP . . . E 2 36.725 -3.152 11.376 1 32.24 ? N1 GDP 402 B 1 
HETATM 25 C C2 GDP . . . E 2 36.655 -2.557 10.178 1 35.45 ? C2 GDP 402 B 1 
HETATM 26 N N2 GDP . . . E 2 37.692 -1.787 9.748 1 34.33 ? N2 GDP 402 B 1 
HETATM 27 N N3 GDP . . . E 2 35.602 -2.715 9.327 1 34.08 ? N3 GDP 402 B 1 
HETATM 28 C C4 GDP . . . E 2 34.55 -3.436 9.683 1 33.66 ? C4 GDP 402 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           244 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#