data_2F3R
#
_model_server_result.job_id            p2JPvXwQ7TJumSNcKy9-pA 
_model_server_result.datetime_utc      '2024-11-18 21:44:04' 
_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          2f3r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    2F3R 
#
_exptl.entry_id    2F3R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              932.366 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE" 
_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         120 
_cell.entry_id            2F3R 
_cell.length_a            67.527 
_cell.length_b            67.527 
_cell.length_c            149.703 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2F3R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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           'C20 H29 N10 O23 P5' 
_chem_comp.formula_weight    932.366 
_chem_comp.id                G5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
PE O1E G5P sing 70 n n 
PE O2E G5P doub 71 n n 
PE O3D G5P sing 72 n n 
PE O5F G5P sing 73 n n 
O1E H1E G5P sing 74 n n 
PD O1D G5P sing 75 n n 
PD O2D G5P doub 76 n n 
PD O3D G5P sing 77 n n 
PD O3G G5P sing 78 n n 
O1D H1D G5P sing 79 n n 
PG O1G G5P sing 80 n n 
PG O2G G5P doub 81 n n 
PG O3G G5P sing 82 n n 
PG O3B G5P sing 83 n n 
O1G H1G G5P sing 84 n n 
PB O1B G5P sing 85 n n 
PB O2B G5P doub 86 n n 
PB O3B G5P sing 87 n n 
PB O3A G5P sing 88 n n 
O1B H1B G5P sing 89 n n 
O3A PA G5P sing 90 n n 
PA O1A G5P sing 91 n n 
PA O2A G5P doub 92 n n 
PA O5' G5P sing 93 n n 
O1A H1A G5P sing 94 n n 
O5' C5' G5P sing 95 n n 
C5' C4' G5P sing 96 n n 
C5' "H5'1" G5P sing 97 n n 
C5' "H5'2" G5P sing 98 n n 
C4' O4' G5P sing 99 n n 
C4' C3' G5P sing 100 n n 
C4' H4' G5P sing 101 n n 
O4' C1' G5P sing 102 n n 
C3' O3' G5P sing 103 n n 
C3' C2' G5P sing 104 n n 
C3' H7 G5P sing 105 n n 
O3' H9 G5P sing 106 n n 
C2' O2' G5P sing 107 n n 
C2' C1' G5P sing 108 n n 
C2' H10 G5P sing 109 n n 
O2' H11 G5P sing 110 n n 
C1' N9 G5P sing 111 n n 
C1' H1' G5P sing 112 n n 
N9 C8 G5P sing 113 n y 
N9 C4 G5P sing 114 n y 
C8 N7 G5P doub 115 n y 
C8 H8 G5P sing 116 n n 
N7 C5 G5P sing 117 n y 
C5 C6 G5P sing 118 n y 
C5 C4 G5P doub 119 n y 
C6 O6 G5P doub 120 n n 
C6 N1 G5P sing 121 n y 
N1 C2 G5P sing 122 n y 
N1 HN1 G5P sing 123 n n 
C2 N2 G5P sing 124 n n 
C2 N3 G5P doub 125 n y 
N2 HN21 G5P sing 126 n n 
N2 HN22 G5P sing 127 n n 
N3 C4 G5P sing 128 n y 
O5F C5F G5P sing 129 n n 
C5F C4F G5P sing 130 n n 
C5F H11X G5P sing 131 n n 
C5F H12 G5P sing 132 n n 
C4F O4F G5P sing 133 n n 
C4F C3F G5P sing 134 n n 
C4F H1 G5P sing 135 n n 
O4F C1F G5P sing 136 n n 
C1F C2F G5P sing 137 n n 
C1F N9A G5P sing 138 n n 
C1F H2 G5P sing 139 n n 
C2F O2F G5P sing 140 n n 
C2F C3F G5P sing 141 n n 
C2F H2' G5P sing 142 n n 
O2F H3 G5P sing 143 n n 
C3F O3F G5P sing 144 n n 
C3F H3' G5P sing 145 n n 
O3F H4 G5P sing 146 n n 
N9A C4A G5P sing 147 n y 
N9A C8A G5P sing 148 n y 
C4A N3A G5P sing 149 n y 
C4A C5A G5P doub 150 n y 
N3A C2A G5P doub 151 n y 
C2A N1A G5P sing 152 n y 
C2A H6 G5P sing 153 n n 
N1A C6A G5P doub 154 n y 
C6A N6A G5P sing 155 n n 
C6A C5A G5P sing 156 n y 
N6A HN61 G5P sing 157 n n 
N6A HN62 G5P sing 158 n n 
C5A N7A G5P sing 159 n y 
N7A C8A G5P doub 160 n y 
C8A H5 G5P sing 161 n n 
#
_atom_sites.entry_id                     2F3R 
_atom_sites.fract_transf_matrix[1][1]    0.014809 
_atom_sites.fract_transf_matrix[1][2]    0.00855 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.0171 
_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]    0.00668 
_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 G5P A 1 601 601 G5P G5P . 
D 2 G5P B 1 602 602 G5P G5P . 
E 3 HOH A 1 602 2 HOH HOH . 
E 3 HOH A 2 603 3 HOH HOH . 
E 3 HOH A 3 604 6 HOH HOH . 
E 3 HOH A 4 605 7 HOH HOH . 
E 3 HOH A 5 606 11 HOH HOH . 
E 3 HOH A 6 607 17 HOH HOH . 
E 3 HOH A 7 608 18 HOH HOH . 
E 3 HOH A 8 609 21 HOH HOH . 
E 3 HOH A 9 610 22 HOH HOH . 
E 3 HOH A 10 611 25 HOH HOH . 
E 3 HOH A 11 612 26 HOH HOH . 
F 3 HOH B 1 603 1 HOH HOH . 
F 3 HOH B 2 604 4 HOH HOH . 
F 3 HOH B 3 605 5 HOH HOH . 
F 3 HOH B 4 606 8 HOH HOH . 
F 3 HOH B 5 607 9 HOH HOH . 
F 3 HOH B 6 608 10 HOH HOH . 
F 3 HOH B 7 609 12 HOH HOH . 
F 3 HOH B 8 610 13 HOH HOH . 
F 3 HOH B 9 611 14 HOH HOH . 
F 3 HOH B 10 612 15 HOH HOH . 
F 3 HOH B 11 613 16 HOH HOH . 
F 3 HOH B 12 614 19 HOH HOH . 
F 3 HOH B 13 615 20 HOH HOH . 
F 3 HOH B 14 616 23 HOH HOH . 
F 3 HOH B 15 617 24 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 PE G5P . . . D 2 4.317 15.076 36.871 1 69.94 ? PE G5P 602 B 1 
HETATM 2 O O1E G5P . . . D 2 4.268 15.036 35.385 1 70.05 ? O1E G5P 602 B 1 
HETATM 3 O O2E G5P . . . D 2 4.416 13.816 37.609 1 71.16 ? O2E G5P 602 B 1 
HETATM 4 P PD G5P . . . D 2 6.733 16.983 36.792 1 70.06 ? PD G5P 602 B 1 
HETATM 5 O O1D G5P . . . D 2 7.82 16.278 36.048 1 71.32 ? O1D G5P 602 B 1 
HETATM 6 O O2D G5P . . . D 2 5.88 17.773 35.811 1 72.45 ? O2D G5P 602 B 1 
HETATM 7 O O3D G5P . . . D 2 5.668 15.907 37.378 1 71.92 ? O3D G5P 602 B 1 
HETATM 8 P PG G5P . . . D 2 7.405 18.145 39.319 1 75.82 ? PG G5P 602 B 1 
HETATM 9 O O1G G5P . . . D 2 6.145 18.788 39.835 1 74.36 ? O1G G5P 602 B 1 
HETATM 10 O O2G G5P . . . D 2 8.528 19.015 39.932 1 73.23 ? O2G G5P 602 B 1 
HETATM 11 O O3G G5P . . . D 2 7.415 18.012 37.825 1 72.61 ? O3G G5P 602 B 1 
HETATM 12 P PB G5P . . . D 2 8.817 16.033 40.73 1 73.86 ? PB G5P 602 B 1 
HETATM 13 O O1B G5P . . . D 2 10.03 15.837 39.853 1 70.56 ? O1B G5P 602 B 1 
HETATM 14 O O2B G5P . . . D 2 8.452 14.803 41.572 1 72.61 ? O2B G5P 602 B 1 
HETATM 15 O O3B G5P . . . D 2 7.616 16.687 40.014 1 73.77 ? O3B G5P 602 B 1 
HETATM 16 O O3A G5P . . . D 2 9.263 17.192 41.861 1 67.82 ? O3A G5P 602 B 1 
HETATM 17 P PA G5P . . . D 2 10.187 17.102 43.147 1 63.37 ? PA G5P 602 B 1 
HETATM 18 O O1A G5P . . . D 2 10.658 15.716 43.382 1 59.89 ? O1A G5P 602 B 1 
HETATM 19 O O2A G5P . . . D 2 9.613 17.865 44.333 1 63.72 ? O2A G5P 602 B 1 
HETATM 20 O O5' G5P . . . D 2 11.446 17.995 42.658 1 58.11 ? O5' G5P 602 B 1 
HETATM 21 C C5' G5P . . . D 2 12.181 17.52 41.559 1 50.93 ? C5' G5P 602 B 1 
HETATM 22 C C4' G5P . . . D 2 13.135 18.548 41.036 1 45.19 ? C4' G5P 602 B 1 
HETATM 23 O O4' G5P . . . D 2 14.407 18.172 41.679 1 41.51 ? O4' G5P 602 B 1 
HETATM 24 C C3' G5P . . . D 2 13.298 18.392 39.51 1 43.69 ? C3' G5P 602 B 1 
HETATM 25 O O3' G5P . . . D 2 13.648 19.734 38.984 1 43.31 ? O3' G5P 602 B 1 
HETATM 26 C C2' G5P . . . D 2 14.457 17.429 39.398 1 41.95 ? C2' G5P 602 B 1 
HETATM 27 O O2' G5P . . . D 2 15.078 17.53 38.158 1 45.82 ? O2' G5P 602 B 1 
HETATM 28 C C1' G5P . . . D 2 15.306 17.758 40.689 1 39.09 ? C1' G5P 602 B 1 
HETATM 29 N N9 G5P . . . D 2 16.055 16.47 41.226 1 35.68 ? N9 G5P 602 B 1 
HETATM 30 C C8 G5P . . . D 2 15.461 15.325 41.709 1 30.9 ? C8 G5P 602 B 1 
HETATM 31 N N7 G5P . . . D 2 16.396 14.435 42.076 1 30.02 ? N7 G5P 602 B 1 
HETATM 32 C C5 G5P . . . D 2 17.634 15.053 41.812 1 30.69 ? C5 G5P 602 B 1 
HETATM 33 C C6 G5P . . . D 2 18.993 14.593 42.002 1 30.95 ? C6 G5P 602 B 1 
HETATM 34 O O6 G5P . . . D 2 19.358 13.487 42.467 1 27.4 ? O6 G5P 602 B 1 
HETATM 35 N N1 G5P . . . D 2 19.957 15.539 41.603 1 30.12 ? N1 G5P 602 B 1 
HETATM 36 C C2 G5P . . . D 2 19.639 16.772 41.088 1 29.24 ? C2 G5P 602 B 1 
HETATM 37 N N2 G5P . . . D 2 20.643 17.582 40.754 1 32 ? N2 G5P 602 B 1 
HETATM 38 N N3 G5P . . . D 2 18.374 17.202 40.909 1 31.63 ? N3 G5P 602 B 1 
HETATM 39 C C4 G5P . . . D 2 17.434 16.299 41.291 1 31.95 ? C4 G5P 602 B 1 
HETATM 40 O O5F G5P . . . D 2 3.234 15.983 37.497 1 72.06 ? O5F G5P 602 B 1 
HETATM 41 C C5F G5P . . . D 2 1.872 16.122 37.028 1 74.52 ? C5F G5P 602 B 1 
HETATM 42 C C4F G5P . . . D 2 1.578 17.564 36.74 1 76.21 ? C4F G5P 602 B 1 
HETATM 43 O O4F G5P . . . D 2 0.184 17.777 36.753 1 77.07 ? O4F G5P 602 B 1 
HETATM 44 C C1F G5P . . . D 2 -0.214 18.87 37.628 1 77 ? C1F G5P 602 B 1 
HETATM 45 C C2F G5P . . . D 2 0.952 19.047 38.6 1 77.07 ? C2F G5P 602 B 1 
HETATM 46 O O2F G5P . . . D 2 0.921 20.417 39.016 1 75.89 ? O2F G5P 602 B 1 
HETATM 47 C C3F G5P . . . D 2 2.209 18.632 37.759 1 76.74 ? C3F G5P 602 B 1 
HETATM 48 O O3F G5P . . . D 2 2.726 19.687 36.894 1 77.33 ? O3F G5P 602 B 1 
HETATM 49 N N9A G5P . . . D 2 -1.494 18.581 38.362 1 77.44 ? N9A G5P 602 B 1 
HETATM 50 C C4A G5P . . . D 2 -2.749 19.082 38.001 1 77.42 ? C4A G5P 602 B 1 
HETATM 51 N N3A G5P . . . D 2 -3.025 19.928 36.917 1 78.07 ? N3A G5P 602 B 1 
HETATM 52 C C2A G5P . . . D 2 -4.345 20.254 36.818 1 77.61 ? C2A G5P 602 B 1 
HETATM 53 N N1A G5P . . . D 2 -5.348 19.828 37.667 1 77.07 ? N1A G5P 602 B 1 
HETATM 54 C C6A G5P . . . D 2 -5.064 19 38.731 1 76.97 ? C6A G5P 602 B 1 
HETATM 55 N N6A G5P . . . D 2 -6.116 18.66 39.474 1 77.68 ? N6A G5P 602 B 1 
HETATM 56 C C5A G5P . . . D 2 -3.676 18.585 38.928 1 76.88 ? C5A G5P 602 B 1 
HETATM 57 N N7A G5P . . . D 2 -3.01 17.785 39.848 1 76.89 ? N7A G5P 602 B 1 
HETATM 58 C C8A G5P . . . D 2 -1.737 17.803 39.485 1 77.52 ? C8A G5P 602 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           58 
#