data_4OR6
#
_model_server_result.job_id            GBU96vyYXVZdD9ordhqpuA 
_model_server_result.datetime_utc      '2024-11-05 06:56:21' 
_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          4or6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    4OR6 
#
_exptl.entry_id    4OR6 
_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            4OR6 
_cell.length_a            42.974 
_cell.length_b            90.151 
_cell.length_c            95.706 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4OR6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 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 D 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 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                     4OR6 
_atom_sites.fract_transf_matrix[1][1]    0.02327 
_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]    0.011093 
_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]    0.010449 
_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 1 GDP GDP . 
D 2 GDP B 1 501 1 GDP GDP . 
E 3 HOH A 1 601 2 HOH HOH . 
E 3 HOH A 2 602 5 HOH HOH . 
E 3 HOH A 3 603 6 HOH HOH . 
E 3 HOH A 4 604 7 HOH HOH . 
E 3 HOH A 5 605 14 HOH HOH . 
E 3 HOH A 6 606 17 HOH HOH . 
E 3 HOH A 7 607 23 HOH HOH . 
E 3 HOH A 8 608 24 HOH HOH . 
E 3 HOH A 9 609 25 HOH HOH . 
E 3 HOH A 10 610 26 HOH HOH . 
E 3 HOH A 11 611 28 HOH HOH . 
E 3 HOH A 12 612 29 HOH HOH . 
E 3 HOH A 13 613 31 HOH HOH . 
E 3 HOH A 14 614 34 HOH HOH . 
E 3 HOH A 15 615 37 HOH HOH . 
E 3 HOH A 16 616 41 HOH HOH . 
E 3 HOH A 17 617 45 HOH HOH . 
E 3 HOH A 18 618 47 HOH HOH . 
E 3 HOH A 19 619 48 HOH HOH . 
E 3 HOH A 20 620 52 HOH HOH . 
E 3 HOH A 21 621 53 HOH HOH . 
E 3 HOH A 22 622 54 HOH HOH . 
E 3 HOH A 23 623 55 HOH HOH . 
E 3 HOH A 24 624 56 HOH HOH . 
E 3 HOH A 25 625 60 HOH HOH . 
E 3 HOH A 26 626 61 HOH HOH . 
E 3 HOH A 27 627 67 HOH HOH . 
E 3 HOH A 28 628 70 HOH HOH . 
E 3 HOH A 29 629 76 HOH HOH . 
E 3 HOH A 30 630 77 HOH HOH . 
E 3 HOH A 31 631 79 HOH HOH . 
E 3 HOH A 32 632 81 HOH HOH . 
E 3 HOH A 33 633 84 HOH HOH . 
E 3 HOH A 34 634 86 HOH HOH . 
E 3 HOH A 35 635 91 HOH HOH . 
E 3 HOH A 36 636 94 HOH HOH . 
E 3 HOH A 37 637 101 HOH HOH . 
E 3 HOH A 38 638 121 HOH HOH . 
E 3 HOH A 39 639 127 HOH HOH . 
E 3 HOH A 40 640 128 HOH HOH . 
E 3 HOH A 41 641 136 HOH HOH . 
E 3 HOH A 42 642 138 HOH HOH . 
E 3 HOH A 43 643 139 HOH HOH . 
E 3 HOH A 44 644 140 HOH HOH . 
E 3 HOH A 45 645 141 HOH HOH . 
E 3 HOH A 46 646 145 HOH HOH . 
E 3 HOH A 47 647 150 HOH HOH . 
E 3 HOH A 48 648 154 HOH HOH . 
E 3 HOH A 49 649 155 HOH HOH . 
E 3 HOH A 50 650 156 HOH HOH . 
E 3 HOH A 51 651 157 HOH HOH . 
E 3 HOH A 52 652 160 HOH HOH . 
E 3 HOH A 53 653 161 HOH HOH . 
E 3 HOH A 54 654 162 HOH HOH . 
E 3 HOH A 55 655 167 HOH HOH . 
E 3 HOH A 56 656 168 HOH HOH . 
E 3 HOH A 57 657 10 HOH HOH . 
E 3 HOH A 58 658 15 HOH HOH . 
E 3 HOH A 59 659 18 HOH HOH . 
E 3 HOH A 60 660 22 HOH HOH . 
E 3 HOH A 61 661 43 HOH HOH . 
E 3 HOH A 62 662 73 HOH HOH . 
E 3 HOH A 63 663 85 HOH HOH . 
E 3 HOH A 64 664 102 HOH HOH . 
E 3 HOH A 65 665 105 HOH HOH . 
E 3 HOH A 66 666 106 HOH HOH . 
E 3 HOH A 67 667 117 HOH HOH . 
E 3 HOH A 68 668 124 HOH HOH . 
E 3 HOH A 69 669 125 HOH HOH . 
E 3 HOH A 70 670 129 HOH HOH . 
E 3 HOH A 71 671 131 HOH HOH . 
E 3 HOH A 72 672 159 HOH HOH . 
E 3 HOH A 73 673 169 HOH HOH . 
E 3 HOH A 74 674 170 HOH HOH . 
E 3 HOH A 75 675 173 HOH HOH . 
F 3 HOH B 1 601 4 HOH HOH . 
F 3 HOH B 2 602 8 HOH HOH . 
F 3 HOH B 3 603 9 HOH HOH . 
F 3 HOH B 4 604 11 HOH HOH . 
F 3 HOH B 5 605 12 HOH HOH . 
F 3 HOH B 6 606 13 HOH HOH . 
F 3 HOH B 7 607 16 HOH HOH . 
F 3 HOH B 8 608 19 HOH HOH . 
F 3 HOH B 9 609 20 HOH HOH . 
F 3 HOH B 10 610 21 HOH HOH . 
F 3 HOH B 11 611 27 HOH HOH . 
F 3 HOH B 12 612 30 HOH HOH . 
F 3 HOH B 13 613 32 HOH HOH . 
F 3 HOH B 14 614 33 HOH HOH . 
F 3 HOH B 15 615 35 HOH HOH . 
F 3 HOH B 16 616 36 HOH HOH . 
F 3 HOH B 17 617 38 HOH HOH . 
F 3 HOH B 18 618 39 HOH HOH . 
F 3 HOH B 19 619 40 HOH HOH . 
F 3 HOH B 20 620 42 HOH HOH . 
F 3 HOH B 21 621 44 HOH HOH . 
F 3 HOH B 22 622 46 HOH HOH . 
F 3 HOH B 23 623 49 HOH HOH . 
F 3 HOH B 24 624 50 HOH HOH . 
F 3 HOH B 25 625 57 HOH HOH . 
F 3 HOH B 26 626 58 HOH HOH . 
F 3 HOH B 27 627 59 HOH HOH . 
F 3 HOH B 28 628 63 HOH HOH . 
F 3 HOH B 29 629 64 HOH HOH . 
F 3 HOH B 30 630 65 HOH HOH . 
F 3 HOH B 31 631 66 HOH HOH . 
F 3 HOH B 32 632 68 HOH HOH . 
F 3 HOH B 33 633 75 HOH HOH . 
F 3 HOH B 34 634 83 HOH HOH . 
F 3 HOH B 35 635 87 HOH HOH . 
F 3 HOH B 36 636 88 HOH HOH . 
F 3 HOH B 37 637 89 HOH HOH . 
F 3 HOH B 38 638 95 HOH HOH . 
F 3 HOH B 39 639 96 HOH HOH . 
F 3 HOH B 40 640 97 HOH HOH . 
F 3 HOH B 41 641 98 HOH HOH . 
F 3 HOH B 42 642 99 HOH HOH . 
F 3 HOH B 43 643 100 HOH HOH . 
F 3 HOH B 44 644 107 HOH HOH . 
F 3 HOH B 45 645 108 HOH HOH . 
F 3 HOH B 46 646 109 HOH HOH . 
F 3 HOH B 47 647 110 HOH HOH . 
F 3 HOH B 48 648 111 HOH HOH . 
F 3 HOH B 49 649 112 HOH HOH . 
F 3 HOH B 50 650 113 HOH HOH . 
F 3 HOH B 51 651 114 HOH HOH . 
F 3 HOH B 52 652 115 HOH HOH . 
F 3 HOH B 53 653 116 HOH HOH . 
F 3 HOH B 54 654 119 HOH HOH . 
F 3 HOH B 55 655 120 HOH HOH . 
F 3 HOH B 56 656 123 HOH HOH . 
F 3 HOH B 57 657 134 HOH HOH . 
F 3 HOH B 58 658 135 HOH HOH . 
F 3 HOH B 59 659 137 HOH HOH . 
F 3 HOH B 60 660 142 HOH HOH . 
F 3 HOH B 61 661 143 HOH HOH . 
F 3 HOH B 62 662 144 HOH HOH . 
F 3 HOH B 63 663 146 HOH HOH . 
F 3 HOH B 64 664 148 HOH HOH . 
F 3 HOH B 65 665 151 HOH HOH . 
F 3 HOH B 66 666 152 HOH HOH . 
F 3 HOH B 67 667 158 HOH HOH . 
F 3 HOH B 68 668 163 HOH HOH . 
F 3 HOH B 69 669 165 HOH HOH . 
F 3 HOH B 70 670 62 HOH HOH . 
F 3 HOH B 71 671 71 HOH HOH . 
F 3 HOH B 72 672 74 HOH HOH . 
F 3 HOH B 73 673 78 HOH HOH . 
F 3 HOH B 74 674 80 HOH HOH . 
F 3 HOH B 75 675 103 HOH HOH . 
F 3 HOH B 76 676 104 HOH HOH . 
F 3 HOH B 77 677 118 HOH HOH . 
F 3 HOH B 78 678 126 HOH HOH . 
F 3 HOH B 79 679 130 HOH HOH . 
F 3 HOH B 80 680 132 HOH HOH . 
F 3 HOH B 81 681 133 HOH HOH . 
F 3 HOH B 82 682 171 HOH HOH . 
F 3 HOH B 83 683 172 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 2 -12.365 -24.584 -1.899 1 25.44 ? PB GDP 501 A 1 
HETATM 2 O O1B GDP . . . C 2 -12.542 -25.994 -1.39 1 32.94 ? O1B GDP 501 A 1 
HETATM 3 O O2B GDP . . . C 2 -13.543 -23.738 -1.478 1 35 ? O2B GDP 501 A 1 
HETATM 4 O O3B GDP . . . C 2 -12.279 -24.595 -3.407 1 17.66 ? O3B GDP 501 A 1 
HETATM 5 O O3A GDP . . . C 2 -11.017 -23.94 -1.3 1 23.21 ? O3A GDP 501 A 1 
HETATM 6 P PA GDP . . . C 2 -9.599 -24.7 -1.376 1 18.47 ? PA GDP 501 A 1 
HETATM 7 O O1A GDP . . . C 2 -9.741 -26.179 -1.104 1 18.48 ? O1A GDP 501 A 1 
HETATM 8 O O2A GDP . . . C 2 -8.614 -24.069 -0.422 1 19.47 ? O2A GDP 501 A 1 
HETATM 9 O O5' GDP . . . C 2 -9.139 -24.443 -2.893 1 23.91 ? O5' GDP 501 A 1 
HETATM 10 C C5' GDP . . . C 2 -8.741 -23.139 -3.296 1 19.3 ? C5' GDP 501 A 1 
HETATM 11 C C4' GDP . . . C 2 -7.643 -23.251 -4.338 1 17.69 ? C4' GDP 501 A 1 
HETATM 12 O O4' GDP . . . C 2 -7.769 -22.17 -5.259 1 21.89 ? O4' GDP 501 A 1 
HETATM 13 C C3' GDP . . . C 2 -6.282 -23.12 -3.68 1 22.89 ? C3' GDP 501 A 1 
HETATM 14 O O3' GDP . . . C 2 -5.441 -24.178 -4.14 1 17.57 ? O3' GDP 501 A 1 
HETATM 15 C C2' GDP . . . C 2 -5.722 -21.798 -4.157 1 21.4 ? C2' GDP 501 A 1 
HETATM 16 O O2' GDP . . . C 2 -4.329 -21.929 -4.445 1 30.23 ? O2' GDP 501 A 1 
HETATM 17 C C1' GDP . . . C 2 -6.521 -21.495 -5.412 1 18.82 ? C1' GDP 501 A 1 
HETATM 18 N N9 GDP . . . C 2 -6.781 -20.045 -5.559 1 17.28 ? N9 GDP 501 A 1 
HETATM 19 C C8 GDP . . . C 2 -7.036 -19.163 -4.575 1 18.96 ? C8 GDP 501 A 1 
HETATM 20 N N7 GDP . . . C 2 -7.244 -17.92 -5.084 1 16.99 ? N7 GDP 501 A 1 
HETATM 21 C C5 GDP . . . C 2 -7.135 -18.007 -6.424 1 15.46 ? C5 GDP 501 A 1 
HETATM 22 C C6 GDP . . . C 2 -7.24 -17.081 -7.575 1 17.31 ? C6 GDP 501 A 1 
HETATM 23 O O6 GDP . . . C 2 -7.492 -15.869 -7.403 1 22.62 ? O6 GDP 501 A 1 
HETATM 24 N N1 GDP . . . C 2 -7.057 -17.582 -8.804 1 20.86 ? N1 GDP 501 A 1 
HETATM 25 C C2 GDP . . . C 2 -6.785 -18.883 -9.021 1 16.61 ? C2 GDP 501 A 1 
HETATM 26 N N2 GDP . . . C 2 -6.614 -19.315 -10.294 1 15.6 ? N2 GDP 501 A 1 
HETATM 27 N N3 GDP . . . C 2 -6.674 -19.786 -8.016 1 11.99 ? N3 GDP 501 A 1 
HETATM 28 C C4 GDP . . . C 2 -6.836 -19.412 -6.727 1 18.58 ? C4 GDP 501 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#