data_4JK1
#
_model_server_result.job_id            sZ3X1u-d1vxq5Puek-u8eA 
_model_server_result.datetime_utc      '2025-03-09 01:54:24' 
_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          4jk1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":1503}' 
#
_entry.id    4JK1 
#
_exptl.entry_id    4JK1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              603.16 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5',3'-TETRAPHOSPHATE" 
_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            4JK1 
_cell.length_a            184.567 
_cell.length_b            203.817 
_cell.length_c            307.674 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4JK1 
_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 hexameric 6 author_and_software_defined_assembly 1 
PISA hexameric 6 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,B,C,D,E,F,M,N,O 1 1 
G,H,I,J,K,L,P,Q 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      7 
_struct_asym.id                             O 
_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 D SG CYS 70 D CYS 70 1_555 M ZN ZN . D ZN 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc2 D SG CYS 72 D CYS 72 1_555 M ZN ZN . D ZN 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc3 D SG CYS 85 D CYS 85 1_555 M ZN ZN . D ZN 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
metalc ? metalc4 D SG CYS 88 D CYS 88 1_555 M ZN ZN . D ZN 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
metalc ? metalc5 D SG CYS 888 D CYS 888 1_555 N ZN ZN . D ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc6 D SG CYS 898 D CYS 898 1_555 N ZN ZN . D ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc7 J SG CYS 72 I CYS 72 1_555 P ZN ZN . I ZN 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc8 J SG CYS 85 I CYS 85 1_555 P ZN ZN . I ZN 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc9 J SG CYS 88 I CYS 88 1_555 P ZN ZN . I ZN 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc10 J SG CYS 814 I CYS 814 1_555 Q ZN ZN . I ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? 
metalc ? metalc11 J SG CYS 888 I CYS 888 1_555 Q ZN ZN . I ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc12 J SG CYS 895 I CYS 895 1_555 Q ZN ZN . I ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc13 J SG CYS 898 I CYS 898 1_555 Q ZN ZN . I ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
#
_chem_comp.formula           'C10 H17 N5 O17 P4' 
_chem_comp.formula_weight    603.16 
_chem_comp.id                G4P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "GUANOSINE-5',3'-TETRAPHOSPHATE" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     'guanosine tetraphosphate;ppGpp' 
#
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 G4P doub 83 n n 
PB O2B G4P sing 84 n n 
PB O3B G4P sing 85 n n 
PB O3A G4P sing 86 n n 
O2B HOB2 G4P sing 87 n n 
O3B HOB3 G4P sing 88 n n 
O3A PA G4P sing 89 n n 
PA O1A G4P doub 90 n n 
PA O2A G4P sing 91 n n 
PA O5' G4P sing 92 n n 
O2A HOA2 G4P sing 93 n n 
O5' C5' G4P sing 94 n n 
C5' C4' G4P sing 95 n n 
C5' H5' G4P sing 96 n n 
C5' "H5''" G4P sing 97 n n 
C4' O4' G4P sing 98 n n 
C4' C3' G4P sing 99 n n 
C4' H4' G4P sing 100 n n 
O4' C1' G4P sing 101 n n 
C3' O3' G4P sing 102 n n 
C3' C2' G4P sing 103 n n 
C3' H3' G4P sing 104 n n 
O3' PC G4P sing 105 n n 
C2' O2' G4P sing 106 n n 
C2' C1' G4P sing 107 n n 
C2' H2' G4P sing 108 n n 
O2' HO2' G4P sing 109 n n 
C1' N9 G4P sing 110 n n 
C1' H1' G4P sing 111 n n 
N9 C8 G4P sing 112 n y 
N9 C4 G4P sing 113 n y 
C8 N7 G4P doub 114 n y 
C8 H8 G4P sing 115 n n 
N7 C5 G4P sing 116 n y 
C5 C6 G4P sing 117 n n 
C5 C4 G4P doub 118 n y 
C6 O6 G4P doub 119 n n 
C6 N1 G4P sing 120 n n 
N1 C2 G4P sing 121 n n 
N1 HN1 G4P sing 122 n n 
C2 N2 G4P sing 123 n n 
C2 N3 G4P doub 124 n n 
N2 HN21 G4P sing 125 n n 
N2 HN22 G4P sing 126 n n 
N3 C4 G4P sing 127 n n 
PC O1C G4P doub 128 n n 
PC O2C G4P sing 129 n n 
PC O3C G4P sing 130 n n 
O2C H2C G4P sing 131 n n 
O3C PD G4P sing 132 n n 
PD O1D G4P doub 133 n n 
PD O2D G4P sing 134 n n 
PD O3D G4P sing 135 n n 
O2D H2D G4P sing 136 n n 
O3D H3D G4P sing 137 n n 
#
_atom_sites.entry_id                     4JK1 
_atom_sites.fract_transf_matrix[1][1]    0.005418 
_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]    0.004906 
_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]    0.00325 
_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
M 6 ZN D 1 1501 1501 ZN ZN . 
N 6 ZN D 1 1502 1502 ZN ZN . 
O 7 G4P D 1 1503 1 G4P G4P . 
P 6 ZN I 1 1501 1501 ZN ZN . 
Q 6 ZN I 1 1502 1502 ZN ZN . 
#
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 G4P . . . O 7 -63.998 12.51 -11.117 1 85.22 ? PB G4P 1503 D 1 
HETATM 2 O O1B G4P . . . O 7 -64.326 13.534 -10.073 1 52.7 ? O1B G4P 1503 D 1 
HETATM 3 O O2B G4P . . . O 7 -62.682 12.867 -11.748 1 55.68 ? O2B G4P 1503 D 1 
HETATM 4 O O3B G4P . . . O 7 -63.868 11.16 -10.459 1 71.88 ? O3B G4P 1503 D 1 
HETATM 5 O O3A G4P . . . O 7 -65.121 12.471 -12.215 1 118.23 ? O3A G4P 1503 D 1 
HETATM 6 P PA G4P . . . O 7 -66.656 12.643 -11.828 1 93.59 ? PA G4P 1503 D 1 
HETATM 7 O O1A G4P . . . O 7 -66.843 13.894 -10.983 1 57.58 ? O1A G4P 1503 D 1 
HETATM 8 O O2A G4P . . . O 7 -67.51 12.789 -13.081 1 47.91 ? O2A G4P 1503 D 1 
HETATM 9 O O5' G4P . . . O 7 -67.131 11.374 -10.992 1 66.96 ? O5' G4P 1503 D 1 
HETATM 10 C C5' G4P . . . O 7 -68.094 10.51 -11.514 1 52.07 ? C5' G4P 1503 D 1 
HETATM 11 C C4' G4P . . . O 7 -67.866 9.12 -11.043 1 57.32 ? C4' G4P 1503 D 1 
HETATM 12 O O4' G4P . . . O 7 -66.619 9.012 -10.29 1 62 ? O4' G4P 1503 D 1 
HETATM 13 C C3' G4P . . . O 7 -68.921 8.611 -10.157 1 57.94 ? C3' G4P 1503 D 1 
HETATM 14 O O3' G4P . . . O 7 -69.367 7.318 -10.59 1 64.37 ? O3' G4P 1503 D 1 
HETATM 15 C C2' G4P . . . O 7 -68.245 8.499 -8.884 1 57.29 ? C2' G4P 1503 D 1 
HETATM 16 O O2' G4P . . . O 7 -68.896 7.587 -8.042 1 59.01 ? O2' G4P 1503 D 1 
HETATM 17 C C1' G4P . . . O 7 -66.933 8.031 -9.299 1 56.3 ? C1' G4P 1503 D 1 
HETATM 18 N N9 G4P . . . O 7 -66.019 7.996 -8.228 1 44.93 ? N9 G4P 1503 D 1 
HETATM 19 C C8 G4P . . . O 7 -64.873 8.803 -8.028 1 44.65 ? C8 G4P 1503 D 1 
HETATM 20 N N7 G4P . . . O 7 -64.298 8.39 -6.838 1 50.55 ? N7 G4P 1503 D 1 
HETATM 21 C C5 G4P . . . O 7 -65.015 7.436 -6.366 1 45.6 ? C5 G4P 1503 D 1 
HETATM 22 C C6 G4P . . . O 7 -64.797 6.744 -5.201 1 44.97 ? C6 G4P 1503 D 1 
HETATM 23 O O6 G4P . . . O 7 -63.853 7.006 -4.499 1 45.6 ? O6 G4P 1503 D 1 
HETATM 24 N N1 G4P . . . O 7 -65.63 5.795 -4.863 1 38.48 ? N1 G4P 1503 D 1 
HETATM 25 C C2 G4P . . . O 7 -66.674 5.504 -5.642 1 32.99 ? C2 G4P 1503 D 1 
HETATM 26 N N2 G4P . . . O 7 -67.548 4.465 -5.232 1 31.98 ? N2 G4P 1503 D 1 
HETATM 27 N N3 G4P . . . O 7 -66.941 6.174 -6.835 1 32.5 ? N3 G4P 1503 D 1 
HETATM 28 C C4 G4P . . . O 7 -66.037 7.169 -7.148 1 41.21 ? C4 G4P 1503 D 1 
HETATM 29 P PC G4P . . . O 7 -70.593 6.463 -10.074 1 101.2 ? PC G4P 1503 D 1 
HETATM 30 O O1C G4P . . . O 7 -70.764 6.535 -8.584 1 72.11 ? O1C G4P 1503 D 1 
HETATM 31 O O2C G4P . . . O 7 -70.339 5.032 -10.442 1 97.85 ? O2C G4P 1503 D 1 
HETATM 32 O O3C G4P . . . O 7 -71.935 6.881 -10.752 1 70.49 ? O3C G4P 1503 D 1 
HETATM 33 P PD G4P . . . O 7 -73.258 6.204 -10.212 1 52.67 ? PD G4P 1503 D 1 
HETATM 34 O O1D G4P . . . O 7 -74.347 6.257 -11.264 1 52.02 ? O1D G4P 1503 D 1 
HETATM 35 O O2D G4P . . . O 7 -73.707 6.947 -8.97 1 62.81 ? O2D G4P 1503 D 1 
HETATM 36 O O3D G4P . . . O 7 -72.994 4.758 -9.849 1 40.35 ? O3D G4P 1503 D 1 
HETATM 37 H H5' G4P . . . O 7 -68.977 10.812 -11.222 1 62.48 ? H5' G4P 1503 D 1 
HETATM 38 H "H5''" G4P . . . O 7 -68.047 10.539 -12.492 1 62.48 ? "H5''" G4P 1503 D 1 
HETATM 39 H H4' G4P . . . O 7 -67.809 8.535 -11.822 1 68.78 ? H4' G4P 1503 D 1 
HETATM 40 H H3' G4P . . . O 7 -69.664 9.238 -10.104 1 69.53 ? H3' G4P 1503 D 1 
HETATM 41 H H2' G4P . . . O 7 -68.177 9.37 -8.457 1 68.75 ? H2' G4P 1503 D 1 
HETATM 42 H HO2' G4P . . . O 7 -68.952 7.932 -7.212 1 70.82 ? HO2' G4P 1503 D 1 
HETATM 43 H H1' G4P . . . O 7 -67.005 7.145 -9.712 1 67.56 ? H1' G4P 1503 D 1 
HETATM 44 H H8 G4P . . . O 7 -64.555 9.503 -8.606 1 53.57 ? H8 G4P 1503 D 1 
HETATM 45 H HN1 G4P . . . O 7 -65.495 5.329 -4.094 1 46.18 ? HN1 G4P 1503 D 1 
HETATM 46 H HN21 G4P . . . O 7 -67.388 4.017 -4.457 1 38.38 ? HN21 G4P 1503 D 1 
HETATM 47 H HN22 G4P . . . O 7 -68.272 4.246 -5.747 1 38.38 ? HN22 G4P 1503 D 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    95 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           47 
#