data_6I0M
#
_model_server_result.job_id            G9l_sZ8wI8vxTv1JeYHg_A 
_model_server_result.datetime_utc      '2024-11-26 20:28:12' 
_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          6i0m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":602}' 
#
_entry.id    6I0M 
#
_exptl.entry_id    6I0M 
_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    6 
_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            6I0M 
_cell.length_a            134.729 
_cell.length_b            134.729 
_cell.length_c            324.081 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6I0M 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_795 -x+2,-y+4,z -1 0 0 0 -1 0 0 0 1 269.458 538.916 0 
3 'crystal symmetry operation' 3_865 -y+3,x+1,z 0 -1 0 1 0 0 0 0 1 404.187 134.729 0 
4 'crystal symmetry operation' 4_485 y-1,-x+3,z 0 1 0 -1 0 0 0 0 1 -134.729 404.187 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 E N N 
? 3 F N N 
? 3 O N N 
? 3 P N N 
? 3 Q 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 123 n n 
PB O2B GDP sing 124 n n 
PB O3B GDP sing 125 n n 
PB O3A GDP sing 126 n n 
O2B HOB2 GDP sing 127 n n 
O3B HOB3 GDP sing 128 n n 
O3A PA GDP sing 129 n n 
PA O1A GDP doub 130 n n 
PA O2A GDP sing 131 n n 
PA O5' GDP sing 132 n n 
O2A HOA2 GDP sing 133 n n 
O5' C5' GDP sing 134 n n 
C5' C4' GDP sing 135 n n 
C5' H5' GDP sing 136 n n 
C5' "H5''" GDP sing 137 n n 
C4' O4' GDP sing 138 n n 
C4' C3' GDP sing 139 n n 
C4' H4' GDP sing 140 n n 
O4' C1' GDP sing 141 n n 
C3' O3' GDP sing 142 n n 
C3' C2' GDP sing 143 n n 
C3' H3' GDP sing 144 n n 
O3' HO3' GDP sing 145 n n 
C2' O2' GDP sing 146 n n 
C2' C1' GDP sing 147 n n 
C2' H2' GDP sing 148 n n 
O2' HO2' GDP sing 149 n n 
C1' N9 GDP sing 150 n n 
C1' H1' GDP sing 151 n n 
N9 C8 GDP sing 152 n y 
N9 C4 GDP sing 153 n y 
C8 N7 GDP doub 154 n y 
C8 H8 GDP sing 155 n n 
N7 C5 GDP sing 156 n y 
C5 C6 GDP sing 157 n n 
C5 C4 GDP doub 158 n y 
C6 O6 GDP doub 159 n n 
C6 N1 GDP sing 160 n n 
N1 C2 GDP sing 161 n n 
N1 HN1 GDP sing 162 n n 
C2 N2 GDP sing 163 n n 
C2 N3 GDP doub 164 n n 
N2 HN21 GDP sing 165 n n 
N2 HN22 GDP sing 166 n n 
N3 C4 GDP sing 167 n n 
#
_atom_sites.entry_id                     6I0M 
_atom_sites.fract_transf_matrix[1][1]    0.007422 
_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]    0.007422 
_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]    0.003086 
_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 5GP A 1 601 600 5GP 5GP . 
D 3 GDP A 1 602 601 GDP GDP . 
E 3 GDP A 1 603 602 GDP GDP . 
F 3 GDP A 1 604 603 GDP GDP . 
G 4 SO4 A 1 605 1 SO4 SO4 . 
H 4 SO4 A 1 606 3 SO4 SO4 . 
I 4 SO4 A 1 607 4 SO4 SO4 . 
J 4 SO4 A 1 608 5 SO4 SO4 . 
K 4 SO4 A 1 609 6 SO4 SO4 . 
L 4 SO4 A 1 610 7 SO4 SO4 . 
M 4 SO4 A 1 611 10 SO4 SO4 . 
N 2 5GP B 1 601 600 5GP 5GP . 
O 3 GDP B 1 602 601 GDP GDP . 
P 3 GDP B 1 603 602 GDP GDP . 
Q 3 GDP B 1 604 603 GDP GDP . 
R 4 SO4 B 1 605 2 SO4 SO4 . 
S 4 SO4 B 1 606 8 SO4 SO4 . 
T 4 SO4 B 1 607 9 SO4 SO4 . 
U 5 HOH A 1 701 41 HOH HOH . 
U 5 HOH A 2 702 46 HOH HOH . 
U 5 HOH A 3 703 2 HOH HOH . 
U 5 HOH A 4 704 17 HOH HOH . 
U 5 HOH A 5 705 74 HOH HOH . 
U 5 HOH A 6 706 13 HOH HOH . 
U 5 HOH A 7 707 48 HOH HOH . 
U 5 HOH A 8 708 4 HOH HOH . 
U 5 HOH A 9 709 28 HOH HOH . 
U 5 HOH A 10 710 79 HOH HOH . 
U 5 HOH A 11 711 12 HOH HOH . 
U 5 HOH A 12 712 3 HOH HOH . 
U 5 HOH A 13 713 16 HOH HOH . 
U 5 HOH A 14 714 30 HOH HOH . 
U 5 HOH A 15 715 39 HOH HOH . 
U 5 HOH A 16 716 38 HOH HOH . 
U 5 HOH A 17 717 14 HOH HOH . 
U 5 HOH A 18 718 75 HOH HOH . 
U 5 HOH A 19 719 44 HOH HOH . 
U 5 HOH A 20 720 37 HOH HOH . 
U 5 HOH A 21 721 26 HOH HOH . 
U 5 HOH A 22 722 90 HOH HOH . 
U 5 HOH A 23 723 9 HOH HOH . 
U 5 HOH A 24 724 18 HOH HOH . 
U 5 HOH A 25 725 92 HOH HOH . 
U 5 HOH A 26 726 96 HOH HOH . 
U 5 HOH A 27 727 47 HOH HOH . 
U 5 HOH A 28 728 97 HOH HOH . 
U 5 HOH A 29 729 78 HOH HOH . 
U 5 HOH A 30 730 29 HOH HOH . 
U 5 HOH A 31 731 21 HOH HOH . 
U 5 HOH A 32 732 25 HOH HOH . 
U 5 HOH A 33 733 32 HOH HOH . 
U 5 HOH A 34 734 76 HOH HOH . 
U 5 HOH A 35 735 91 HOH HOH . 
U 5 HOH A 36 736 35 HOH HOH . 
U 5 HOH A 37 737 83 HOH HOH . 
U 5 HOH A 38 738 15 HOH HOH . 
U 5 HOH A 39 739 20 HOH HOH . 
U 5 HOH A 40 740 22 HOH HOH . 
U 5 HOH A 41 741 100 HOH HOH . 
U 5 HOH A 42 742 111 HOH HOH . 
U 5 HOH A 43 743 40 HOH HOH . 
U 5 HOH A 44 744 33 HOH HOH . 
U 5 HOH A 45 745 36 HOH HOH . 
U 5 HOH A 46 746 27 HOH HOH . 
U 5 HOH A 47 747 19 HOH HOH . 
U 5 HOH A 48 748 94 HOH HOH . 
U 5 HOH A 49 749 77 HOH HOH . 
U 5 HOH A 50 750 43 HOH HOH . 
U 5 HOH A 51 751 95 HOH HOH . 
U 5 HOH A 52 752 98 HOH HOH . 
U 5 HOH A 53 753 93 HOH HOH . 
V 5 HOH B 1 701 8 HOH HOH . 
V 5 HOH B 2 702 89 HOH HOH . 
V 5 HOH B 3 703 10 HOH HOH . 
V 5 HOH B 4 704 88 HOH HOH . 
V 5 HOH B 5 705 81 HOH HOH . 
V 5 HOH B 6 706 87 HOH HOH . 
V 5 HOH B 7 707 106 HOH HOH . 
V 5 HOH B 8 708 67 HOH HOH . 
V 5 HOH B 9 709 86 HOH HOH . 
V 5 HOH B 10 710 24 HOH HOH . 
V 5 HOH B 11 711 105 HOH HOH . 
V 5 HOH B 12 712 64 HOH HOH . 
V 5 HOH B 13 713 65 HOH HOH . 
V 5 HOH B 14 714 53 HOH HOH . 
V 5 HOH B 15 715 54 HOH HOH . 
V 5 HOH B 16 716 112 HOH HOH . 
V 5 HOH B 17 717 68 HOH HOH . 
V 5 HOH B 18 718 108 HOH HOH . 
V 5 HOH B 19 719 107 HOH HOH . 
V 5 HOH B 20 720 110 HOH HOH . 
V 5 HOH B 21 721 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 . . . O 3 179.953 308.379 370.647 0.74 96.88 ? PB GDP 602 B 1 
HETATM 2 O O1B GDP . . . O 3 179.846 307.592 369.371 0.74 98.61 ? O1B GDP 602 B 1 
HETATM 3 O O2B GDP . . . O 3 180.872 307.771 371.67 0.74 98.82 ? O2B GDP 602 B 1 
HETATM 4 O O3B GDP . . . O 3 178.642 308.863 371.209 0.74 94.34 ? O3B GDP 602 B 1 
HETATM 5 O O3A GDP . . . O 3 180.712 309.719 370.205 0.74 93.41 ? O3A GDP 602 B 1 
HETATM 6 P PA GDP . . . O 3 182.25 309.663 369.758 0.74 92.19 ? PA GDP 602 B 1 
HETATM 7 O O1A GDP . . . O 3 182.339 310.155 368.341 0.74 92.28 ? O1A GDP 602 B 1 
HETATM 8 O O2A GDP . . . O 3 182.828 308.326 370.129 0.74 91.51 ? O2A GDP 602 B 1 
HETATM 9 O O5' GDP . . . O 3 182.895 310.78 370.707 0.74 92.36 ? O5' GDP 602 B 1 
HETATM 10 C C5' GDP . . . O 3 183.986 310.468 371.565 0.74 91.76 ? C5' GDP 602 B 1 
HETATM 11 C C4' GDP . . . O 3 184.448 311.765 372.201 0.74 90.06 ? C4' GDP 602 B 1 
HETATM 12 O O4' GDP . . . O 3 185.019 312.583 371.188 0.74 89.83 ? O4' GDP 602 B 1 
HETATM 13 C C3' GDP . . . O 3 183.276 312.522 372.794 0.74 88.46 ? C3' GDP 602 B 1 
HETATM 14 O O3' GDP . . . O 3 183.635 313.015 374.087 0.74 89.48 ? O3' GDP 602 B 1 
HETATM 15 C C2' GDP . . . O 3 182.985 313.649 371.822 0.74 86.19 ? C2' GDP 602 B 1 
HETATM 16 O O2' GDP . . . O 3 182.678 314.876 372.489 0.74 82.53 ? O2' GDP 602 B 1 
HETATM 17 C C1' GDP . . . O 3 184.25 313.766 370.983 0.74 88.77 ? C1' GDP 602 B 1 
HETATM 18 N N9 GDP . . . O 3 183.987 313.907 369.529 0.74 91.11 ? N9 GDP 602 B 1 
HETATM 19 C C8 GDP . . . O 3 182.826 313.691 368.883 0.74 91.46 ? C8 GDP 602 B 1 
HETATM 20 N N7 GDP . . . O 3 182.965 313.924 367.553 0.74 91.23 ? N7 GDP 602 B 1 
HETATM 21 C C5 GDP . . . O 3 184.235 314.296 367.336 0.74 91.63 ? C5 GDP 602 B 1 
HETATM 22 C C6 GDP . . . O 3 185.047 314.688 366.165 0.74 94.31 ? C6 GDP 602 B 1 
HETATM 23 O O6 GDP . . . O 3 184.551 314.722 365.021 0.74 95.54 ? O6 GDP 602 B 1 
HETATM 24 N N1 GDP . . . O 3 186.33 315.003 366.366 0.74 94.22 ? N1 GDP 602 B 1 
HETATM 25 C C2 GDP . . . O 3 186.886 314.972 367.589 0.74 92.89 ? C2 GDP 602 B 1 
HETATM 26 N N2 GDP . . . O 3 188.19 315.303 367.711 0.74 93.92 ? N2 GDP 602 B 1 
HETATM 27 N N3 GDP . . . O 3 186.204 314.624 368.705 0.74 91.45 ? N3 GDP 602 B 1 
HETATM 28 C C4 GDP . . . O 3 184.9 314.287 368.64 0.74 91.18 ? C4 GDP 602 B 1 
HETATM 29 H H5' GDP . . . O 3 184.799 310.018 370.993 0.74 110.56 ? H5' GDP 602 B 1 
HETATM 30 H "H5''" GDP . . . O 3 183.669 309.763 372.336 0.74 110.56 ? "H5''" GDP 602 B 1 
HETATM 31 H H4' GDP . . . O 3 185.184 311.549 372.988 0.74 108.53 ? H4' GDP 602 B 1 
HETATM 32 H H3' GDP . . . O 3 182.403 311.856 372.859 0.74 106.6 ? H3' GDP 602 B 1 
HETATM 33 H H2' GDP . . . O 3 182.14 313.346 371.19 0.74 103.88 ? H2' GDP 602 B 1 
HETATM 34 H HO2' GDP . . . O 3 181.905 314.75 373.056 0.74 99.48 ? HO2' GDP 602 B 1 
HETATM 35 H H1' GDP . . . O 3 184.819 314.637 371.337 0.74 106.98 ? H1' GDP 602 B 1 
HETATM 36 H H8 GDP . . . O 3 181.906 313.374 369.359 0.74 110.2 ? H8 GDP 602 B 1 
HETATM 37 H HN1 GDP . . . O 3 186.916 315.279 365.552 0.74 113.51 ? HN1 GDP 602 B 1 
HETATM 38 H HN21 GDP . . . O 3 188.723 315.567 366.895 0.74 113.15 ? HN21 GDP 602 B 1 
HETATM 39 H HN22 GDP . . . O 3 188.631 315.289 368.619 0.74 113.15 ? HN22 GDP 602 B 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#