data_4JKR
#
_model_server_result.job_id            qZ2ODiovGBvF4dFEtg7KvQ 
_model_server_result.datetime_utc      '2024-12-21 16:52:41' 
_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          4jkr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":101}' 
#
_entry.id    4JKR 
#
_exptl.entry_id    4JKR 
_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    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            4JKR 
_cell.length_a            187.575 
_cell.length_b            206.164 
_cell.length_c            311.062 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4JKR 
_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,P,Q,R,S,T,U 1 1 
G,H,I,J,K,L,V,W,X,Y,Z 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
? 7 P N N 
? 7 Z N 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 C O VAL 24 C VAL 24 1_555 O SR SR . C SR 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? 
metalc ? metalc2 D SG CYS 70 D CYS 70 1_555 Q ZN ZN . D ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc3 D SG CYS 72 D CYS 72 1_555 Q ZN ZN . D ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc4 D SG CYS 88 D CYS 88 1_555 Q ZN ZN . D ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? 
metalc ? metalc5 D SG CYS 814 D CYS 814 1_555 R ZN ZN . D ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
metalc ? metalc6 D SG CYS 898 D CYS 898 1_555 R ZN ZN . D ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc7 J SG CYS 70 J CYS 70 1_555 W ZN ZN . J ZN 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc8 J SG CYS 72 J CYS 72 1_555 W ZN ZN . J ZN 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc9 J OD1 ASP 460 J ASP 460 1_555 Y SR SR . J SR 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? 
metalc ? metalc10 J SG CYS 814 J CYS 814 1_555 X ZN ZN . J ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc11 J SG CYS 888 J CYS 888 1_555 X ZN ZN . J ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc12 J SG CYS 895 J CYS 895 1_555 X ZN ZN . J ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? 
metalc ? metalc13 J SG CYS 898 J CYS 898 1_555 X ZN ZN . J ZN 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? 
#
_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                     4JKR 
_atom_sites.fract_transf_matrix[1][1]    0.005331 
_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]    0.004851 
_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]    0.003215 
_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 SR A 1 401 3012 SR SR . 
N 6 SR C 1 1401 3004 SR SR . 
O 6 SR C 1 1402 3010 SR SR . 
P 7 G4P D 1 2001 2001 G4P G4P . 
Q 8 ZN D 1 2002 3001 ZN ZN . 
R 8 ZN D 1 2003 3002 ZN ZN . 
S 6 SR D 1 2004 3003 SR SR . 
T 6 SR E 1 101 3011 SR SR . 
U 6 SR F 1 701 3009 SR SR . 
V 6 SR I 1 1401 3008 SR SR . 
W 8 ZN J 1 1501 3005 ZN ZN . 
X 8 ZN J 1 1502 3006 ZN ZN . 
Y 6 SR J 1 1503 3007 SR SR . 
Z 7 G4P K 1 101 2002 G4P G4P . 
#
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 . . . Z 7 -63.018 120.97 13.705 1 256.08 ? PB G4P 101 K 1 
HETATM 2 O O1B G4P . . . Z 7 -63.453 121.801 12.476 1 215.11 ? O1B G4P 101 K 1 
HETATM 3 O O2B G4P . . . Z 7 -63.193 119.51 13.464 1 262.06 ? O2B G4P 101 K 1 
HETATM 4 O O3B G4P . . . Z 7 -61.669 121.361 14.337 1 264.94 ? O3B G4P 101 K 1 
HETATM 5 O O3A G4P . . . Z 7 -64.077 121.338 14.942 1 234.19 ? O3A G4P 101 K 1 
HETATM 6 P PA G4P . . . Z 7 -64.04 122.78 15.634 1 225.42 ? PA G4P 101 K 1 
HETATM 7 O O1A G4P . . . Z 7 -63.479 122.574 16.991 1 158.93 ? O1A G4P 101 K 1 
HETATM 8 O O2A G4P . . . Z 7 -63.416 123.802 14.736 1 248.48 ? O2A G4P 101 K 1 
HETATM 9 O O5' G4P . . . Z 7 -65.622 123.141 15.771 1 257.16 ? O5' G4P 101 K 1 
HETATM 10 C C5' G4P . . . Z 7 -66.43 123.387 14.608 1 280.88 ? C5' G4P 101 K 1 
HETATM 11 C C4' G4P . . . Z 7 -67.872 123.621 14.983 1 285.09 ? C4' G4P 101 K 1 
HETATM 12 O O4' G4P . . . Z 7 -68.329 122.641 15.923 1 283.81 ? O4' G4P 101 K 1 
HETATM 13 C C3' G4P . . . Z 7 -68.082 125.014 15.603 1 285.04 ? C3' G4P 101 K 1 
HETATM 14 O O3' G4P . . . Z 7 -69.011 125.74 14.774 1 296.33 ? O3' G4P 101 K 1 
HETATM 15 C C2' G4P . . . Z 7 -68.652 124.776 17.012 1 250.12 ? C2' G4P 101 K 1 
HETATM 16 O O2' G4P . . . Z 7 -69.804 125.582 17.222 1 268.12 ? O2' G4P 101 K 1 
HETATM 17 C C1' G4P . . . Z 7 -69.085 123.295 16.974 1 272.86 ? C1' G4P 101 K 1 
HETATM 18 N N9 G4P . . . Z 7 -68.836 122.645 18.294 1 216.64 ? N9 G4P 101 K 1 
HETATM 19 C C8 G4P . . . Z 7 -67.692 122.11 18.711 1 215.48 ? C8 G4P 101 K 1 
HETATM 20 N N7 G4P . . . Z 7 -67.837 121.55 19.945 1 248.07 ? N7 G4P 101 K 1 
HETATM 21 C C5 G4P . . . Z 7 -69.114 121.74 20.329 1 241.41 ? C5 G4P 101 K 1 
HETATM 22 C C6 G4P . . . Z 7 -69.941 121.397 21.515 1 237.1 ? C6 G4P 101 K 1 
HETATM 23 O O6 G4P . . . Z 7 -69.459 120.801 22.499 1 258.57 ? O6 G4P 101 K 1 
HETATM 24 N N1 G4P . . . Z 7 -71.222 121.768 21.525 1 202.04 ? N1 G4P 101 K 1 
HETATM 25 C C2 G4P . . . Z 7 -71.79 122.433 20.484 1 249.18 ? C2 G4P 101 K 1 
HETATM 26 N N2 G4P . . . Z 7 -73.108 122.747 20.567 1 250.71 ? N2 G4P 101 K 1 
HETATM 27 N N3 G4P . . . Z 7 -71.097 122.764 19.362 1 254.56 ? N3 G4P 101 K 1 
HETATM 28 C C4 G4P . . . Z 7 -69.775 122.46 19.234 1 235.7 ? C4 G4P 101 K 1 
HETATM 29 P PC G4P . . . Z 7 -68.805 127.306 14.464 1 298.77 ? PC G4P 101 K 1 
HETATM 30 O O1C G4P . . . Z 7 -68.656 128.033 15.752 1 222.56 ? O1C G4P 101 K 1 
HETATM 31 O O2C G4P . . . Z 7 -69.919 127.753 13.551 1 269.05 ? O2C G4P 101 K 1 
HETATM 32 O O3C G4P . . . Z 7 -67.387 127.343 13.654 1 306.67 ? O3C G4P 101 K 1 
HETATM 33 P PD G4P . . . Z 7 -67.354 127.014 12.055 1 307.94 ? PD G4P 101 K 1 
HETATM 34 O O1D G4P . . . Z 7 -68.226 125.776 11.881 1 275.57 ? O1D G4P 101 K 1 
HETATM 35 O O2D G4P . . . Z 7 -65.894 126.764 11.782 1 293.44 ? O2D G4P 101 K 1 
HETATM 36 O O3D G4P . . . Z 7 -67.91 128.265 11.407 1 299.19 ? O3D G4P 101 K 1 
#
_model_server_stats.io_time_ms              121 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    529 
_model_server_stats.query_time_ms           347 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           36 
#