data_4JKR
#
_model_server_result.job_id            gbAODZXpQNRR_j5vdGeSUw 
_model_server_result.datetime_utc      '2024-12-21 17:24:57' 
_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":"P","auth_seq_id":2001}' 
#
_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 . . . P 7 -28.923 97.579 -6.567 1 194.54 ? PB G4P 2001 D 1 
HETATM 2 O O1B G4P . . . P 7 -29.775 96.619 -7.435 1 185.23 ? O1B G4P 2001 D 1 
HETATM 3 O O2B G4P . . . P 7 -29.111 99.013 -6.779 1 178 ? O2B G4P 2001 D 1 
HETATM 4 O O3B G4P . . . P 7 -28.989 97.304 -5.093 1 175.84 ? O3B G4P 2001 D 1 
HETATM 5 O O3A G4P . . . P 7 -27.301 97.235 -6.974 1 194.19 ? O3A G4P 2001 D 1 
HETATM 6 P PA G4P . . . P 7 -26.693 95.78 -6.492 1 172.72 ? PA G4P 2001 D 1 
HETATM 7 O O1A G4P . . . P 7 -25.728 96.078 -5.417 1 125.44 ? O1A G4P 2001 D 1 
HETATM 8 O O2A G4P . . . P 7 -27.728 94.783 -6.207 1 158.94 ? O2A G4P 2001 D 1 
HETATM 9 O O5' G4P . . . P 7 -25.88 95.311 -7.813 1 175.11 ? O5' G4P 2001 D 1 
HETATM 10 C C5' G4P . . . P 7 -26.569 94.986 -9.03 1 238.59 ? C5' G4P 2001 D 1 
HETATM 11 C C4' G4P . . . P 7 -25.585 94.749 -10.163 1 247.5 ? C4' G4P 2001 D 1 
HETATM 12 O O4' G4P . . . P 7 -24.594 95.795 -10.223 1 244.08 ? O4' G4P 2001 D 1 
HETATM 13 C C3' G4P . . . P 7 -24.862 93.394 -10.027 1 221.91 ? C3' G4P 2001 D 1 
HETATM 14 O O3' G4P . . . P 7 -25.241 92.585 -11.18 1 266.82 ? O3' G4P 2001 D 1 
HETATM 15 C C2' G4P . . . P 7 -23.353 93.719 -10.022 1 175.51 ? C2' G4P 2001 D 1 
HETATM 16 O O2' G4P . . . P 7 -22.688 92.942 -11.052 1 179.62 ? O2' G4P 2001 D 1 
HETATM 17 C C1' G4P . . . P 7 -23.301 95.19 -10.47 1 193.99 ? C1' G4P 2001 D 1 
HETATM 18 N N9 G4P . . . P 7 -22.218 95.887 -9.715 1 188.72 ? N9 G4P 2001 D 1 
HETATM 19 C C8 G4P . . . P 7 -22.348 96.511 -8.549 1 212.76 ? C8 G4P 2001 D 1 
HETATM 20 N N7 G4P . . . P 7 -21.16 97.076 -8.181 1 240.55 ? N7 G4P 2001 D 1 
HETATM 21 C C5 G4P . . . P 7 -20.25 96.836 -9.158 1 210.06 ? C5 G4P 2001 D 1 
HETATM 22 C C6 G4P . . . P 7 -18.841 97.18 -9.426 1 170.23 ? C6 G4P 2001 D 1 
HETATM 23 O O6 G4P . . . P 7 -18.171 97.823 -8.599 1 164.11 ? O6 G4P 2001 D 1 
HETATM 24 N N1 G4P . . . P 7 -18.282 96.769 -10.556 1 179.37 ? N1 G4P 2001 D 1 
HETATM 25 C C2 G4P . . . P 7 -18.976 96.041 -11.484 1 211.21 ? C2 G4P 2001 D 1 
HETATM 26 N N2 G4P . . . P 7 -18.341 95.631 -12.615 1 211.82 ? N2 G4P 2001 D 1 
HETATM 27 N N3 G4P . . . P 7 -20.283 95.677 -11.3 1 205.96 ? N3 G4P 2001 D 1 
HETATM 28 C C4 G4P . . . P 7 -20.962 96.049 -10.182 1 210.66 ? C4 G4P 2001 D 1 
HETATM 29 P PC G4P . . . P 7 -25.426 90.982 -11.059 1 213.04 ? PC G4P 2001 D 1 
HETATM 30 O O1C G4P . . . P 7 -24.238 90.392 -10.345 1 170.35 ? O1C G4P 2001 D 1 
HETATM 31 O O2C G4P . . . P 7 -25.783 90.416 -12.372 1 172.41 ? O2C G4P 2001 D 1 
HETATM 32 O O3C G4P . . . P 7 -26.741 90.872 -10.04 1 225.54 ? O3C G4P 2001 D 1 
HETATM 33 P PD G4P . . . P 7 -28.232 90.943 -10.634 1 187.08 ? PD G4P 2001 D 1 
HETATM 34 O O1D G4P . . . P 7 -28.19 92.143 -11.634 1 174.16 ? O1D G4P 2001 D 1 
HETATM 35 O O2D G4P . . . P 7 -29.026 91.15 -9.349 1 198.7 ? O2D G4P 2001 D 1 
HETATM 36 O O3D G4P . . . P 7 -28.416 89.548 -11.236 1 156.18 ? O3D G4P 2001 D 1 
#
_model_server_stats.io_time_ms              94 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    321 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           36 
#