data_6UT4
#
_model_server_result.job_id            tk-ESewe3_UFVBkORkb8Hg 
_model_server_result.datetime_utc      '2024-10-19 12:35:44' 
_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          6ut4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":701}' 
#
_entry.id    6UT4 
#
_exptl.entry_id    6UT4 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_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            6UT4 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6UT4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_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,W 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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
? 2 G N N 
? 2 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 Q 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 A OG1 THR 37 A THR 222 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc2 A OD1 ASP 171 A ASP 356 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? 
metalc ? metalc3 A OD2 ASP 171 A ASP 356 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? 
metalc ? metalc4 G O2G GSP . A GSP 701 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? 
metalc ? metalc5 G O2B GSP . A GSP 701 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc6 B OG1 THR 37 B THR 222 1_555 J MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc7 B OD1 ASP 171 B ASP 356 1_555 J MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? 
metalc ? metalc8 I O2G GSP . B GSP 701 1_555 J MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc9 I O2B GSP . B GSP 701 1_555 J MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc10 J MG MG . B MG 702 1_555 S O HOH . B HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc11 J MG MG . B MG 702 1_555 T O HOH . C HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc12 C OG1 THR 37 C THR 222 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc13 C OD1 ASP 171 C ASP 356 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? 
metalc ? metalc14 K O2G GSP . C GSP 701 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc15 K O2B GSP . C GSP 701 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc16 L MG MG . C MG 702 1_555 T O HOH . C HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc17 L MG MG . C MG 702 1_555 U O HOH . D HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc18 D OG1 THR 37 D THR 222 1_555 N MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc19 D OD2 ASP 171 D ASP 356 1_555 N MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? 
metalc ? metalc20 M O2G GSP . D GSP 701 1_555 N MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc21 M O2B GSP . D GSP 701 1_555 N MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc22 N MG MG . D MG 702 1_555 U O HOH . D HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc23 N MG MG . D MG 702 1_555 U O HOH . D HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc24 E OG1 THR 37 E THR 222 1_555 P MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc25 E OD2 ASP 171 E ASP 356 1_555 P MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? 
metalc ? metalc26 O O2G GSP . E GSP 701 1_555 P MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc27 O O2B GSP . E GSP 701 1_555 P MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? 
metalc ? metalc28 P MG MG . E MG 702 1_555 V O HOH . E HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc29 P MG MG . E MG 702 1_555 W O HOH . F HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc30 F OG1 THR 37 F THR 222 1_555 R MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc31 F OD1 ASP 171 F ASP 356 1_555 R MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc32 Q O2G GSP . F GSP 701 1_555 R MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc33 Q O2B GSP . F GSP 701 1_555 R MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3 S' 
_chem_comp.formula_weight    539.246 
_chem_comp.id                GSP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_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
PG O3B GSP sing 116 n n 
PG S1G GSP doub 117 n n 
PG O2G GSP sing 118 n n 
PG O3G GSP sing 119 n n 
O3B PB GSP sing 120 n n 
O2G HOG2 GSP sing 121 n n 
O3G HOG3 GSP sing 122 n n 
PB O1B GSP doub 123 n n 
PB O2B GSP sing 124 n n 
PB O3A GSP sing 125 n n 
O2B HOB2 GSP sing 126 n n 
PA O1A GSP doub 127 n n 
PA O2A GSP sing 128 n n 
PA O3A GSP sing 129 n n 
PA O5' GSP sing 130 n n 
O2A HOA2 GSP sing 131 n n 
O5' C5' GSP sing 132 n n 
C5' C4' GSP sing 133 n n 
C5' "H5'1" GSP sing 134 n n 
C5' "H5'2" GSP sing 135 n n 
C4' O4' GSP sing 136 n n 
C4' C3' GSP sing 137 n n 
C4' H4' GSP sing 138 n n 
O4' C1' GSP sing 139 n n 
C3' O3' GSP sing 140 n n 
C3' C2' GSP sing 141 n n 
C3' H3' GSP sing 142 n n 
O3' HO3' GSP sing 143 n n 
C2' O2' GSP sing 144 n n 
C2' C1' GSP sing 145 n n 
C2' H2' GSP sing 146 n n 
O2' HO2' GSP sing 147 n n 
C1' N9 GSP sing 148 n n 
C1' H1' GSP sing 149 n n 
N9 C8 GSP sing 150 n y 
N9 C4 GSP sing 151 n y 
C8 N7 GSP doub 152 n y 
C8 H8 GSP sing 153 n n 
N7 C5 GSP sing 154 n y 
C5 C6 GSP sing 155 n n 
C5 C4 GSP doub 156 n y 
C6 O6 GSP doub 157 n n 
C6 N1 GSP sing 158 n n 
N1 C2 GSP sing 159 n n 
N1 HN1 GSP sing 160 n n 
C2 N2 GSP sing 161 n n 
C2 N3 GSP doub 162 n n 
N2 HN21 GSP sing 163 n n 
N2 HN22 GSP sing 164 n n 
N3 C4 GSP sing 165 n n 
#
_atom_sites.entry_id                     6UT4 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
G 2 GSP A 1 701 701 GSP GSP . 
H 3 MG A 1 702 801 MG MG . 
I 2 GSP B 1 701 701 GSP GSP . 
J 3 MG B 1 702 801 MG MG . 
K 2 GSP C 1 701 701 GSP GSP . 
L 3 MG C 1 702 801 MG MG . 
M 2 GSP D 1 701 701 GSP GSP . 
N 3 MG D 1 702 801 MG MG . 
O 2 GSP E 1 701 701 GSP GSP . 
P 3 MG E 1 702 801 MG MG . 
Q 2 GSP F 1 701 701 GSP GSP . 
R 3 MG F 1 702 801 MG MG . 
S 4 HOH B 1 901 901 HOH HOH . 
S 4 HOH B 2 902 902 HOH HOH . 
T 4 HOH C 1 801 902 HOH HOH . 
T 4 HOH C 2 802 903 HOH HOH . 
T 4 HOH C 3 803 901 HOH HOH . 
U 4 HOH D 1 801 903 HOH HOH . 
U 4 HOH D 2 802 902 HOH HOH . 
U 4 HOH D 3 803 903 HOH HOH . 
U 4 HOH D 4 804 901 HOH HOH . 
V 4 HOH E 1 801 902 HOH HOH . 
V 4 HOH E 2 802 901 HOH HOH . 
W 4 HOH F 1 801 903 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 PG GSP . . . G 2 170.259 186.35 157.943 1 49.99 ? PG GSP 701 A 1 
HETATM 2 O O3B GSP . . . G 2 170.812 187.835 157.683 1 49.99 ? O3B GSP 701 A 1 
HETATM 3 S S1G GSP . . . G 2 171.258 185.22 157.161 1 49.99 ? S1G GSP 701 A 1 
HETATM 4 O O2G GSP . . . G 2 170.26 186.078 159.458 1 49.99 ? O2G GSP 701 A 1 
HETATM 5 O O3G GSP . . . G 2 168.823 186.24 157.401 1 49.99 ? O3G GSP 701 A 1 
HETATM 6 P PB GSP . . . G 2 169.989 189.073 158.289 1 49.99 ? PB GSP 701 A 1 
HETATM 7 O O1B GSP . . . G 2 168.701 189.186 157.578 1 49.99 ? O1B GSP 701 A 1 
HETATM 8 O O2B GSP . . . G 2 169.767 188.876 159.736 1 49.99 ? O2B GSP 701 A 1 
HETATM 9 P PA GSP . . . G 2 171.36 191.358 159.183 1 49.99 ? PA GSP 701 A 1 
HETATM 10 O O1A GSP . . . G 2 170.179 192.105 159.663 1 49.99 ? O1A GSP 701 A 1 
HETATM 11 O O2A GSP . . . G 2 172.024 190.639 160.291 1 49.99 ? O2A GSP 701 A 1 
HETATM 12 O O3A GSP . . . G 2 170.914 190.359 158.002 1 49.99 ? O3A GSP 701 A 1 
HETATM 13 O O5' GSP . . . G 2 172.384 192.379 158.475 1 49.99 ? O5' GSP 701 A 1 
HETATM 14 C C5' GSP . . . G 2 173.765 192.099 158.452 1 49.99 ? C5' GSP 701 A 1 
HETATM 15 C C4' GSP . . . G 2 174.556 193.255 159.055 1 49.99 ? C4' GSP 701 A 1 
HETATM 16 O O4' GSP . . . G 2 174.513 194.374 158.191 1 49.99 ? O4' GSP 701 A 1 
HETATM 17 C C3' GSP . . . G 2 173.994 193.688 160.398 1 49.99 ? C3' GSP 701 A 1 
HETATM 18 O O3' GSP . . . G 2 175.013 193.664 161.367 1 49.99 ? O3' GSP 701 A 1 
HETATM 19 C C2' GSP . . . G 2 173.519 195.108 160.196 1 49.99 ? C2' GSP 701 A 1 
HETATM 20 O O2' GSP . . . G 2 174.027 195.924 161.223 1 49.99 ? O2' GSP 701 A 1 
HETATM 21 C C1' GSP . . . G 2 174.101 195.543 158.865 1 49.99 ? C1' GSP 701 A 1 
HETATM 22 N N9 GSP . . . G 2 173.093 196.255 158.06 1 49.99 ? N9 GSP 701 A 1 
HETATM 23 C C8 GSP . . . G 2 172.159 195.681 157.241 1 49.99 ? C8 GSP 701 A 1 
HETATM 24 N N7 GSP . . . G 2 171.417 196.661 156.679 1 49.99 ? N7 GSP 701 A 1 
HETATM 25 C C5 GSP . . . G 2 171.862 197.852 157.132 1 49.99 ? C5 GSP 701 A 1 
HETATM 26 C C6 GSP . . . G 2 171.461 199.156 156.881 1 49.99 ? C6 GSP 701 A 1 
HETATM 27 O O6 GSP . . . G 2 170.529 199.377 156.111 1 49.99 ? O6 GSP 701 A 1 
HETATM 28 N N1 GSP . . . G 2 172.114 200.201 157.499 1 49.99 ? N1 GSP 701 A 1 
HETATM 29 C C2 GSP . . . G 2 173.159 199.943 158.362 1 49.99 ? C2 GSP 701 A 1 
HETATM 30 N N2 GSP . . . G 2 173.79 200.949 158.959 1 49.99 ? N2 GSP 701 A 1 
HETATM 31 N N3 GSP . . . G 2 173.552 198.643 158.607 1 49.99 ? N3 GSP 701 A 1 
HETATM 32 C C4 GSP . . . G 2 172.915 197.613 158.002 1 49.99 ? C4 GSP 701 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           348 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#