data_6UT5
#
_model_server_result.job_id            LQQRtqFQPIknnsGnfx0gnw 
_model_server_result.datetime_utc      '2024-10-19 16:31:21' 
_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          6ut5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":701}' 
#
_entry.id    6UT5 
#
_exptl.entry_id    6UT5 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_entity.pdbx_number_of_molecules    5 
_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            6UT5 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6UT5 
_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    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_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,X,Y 
_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
? 3 H N N 
? 3 J N N 
? 3 L N N 
? 3 N N N 
? 3 P 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 222 A THR 222 1_555 I MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc2 A OD1 ASP 356 A ASP 356 1_555 I MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? 
metalc ? metalc3 H O3G GSP . A GSP 701 1_555 I MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? 
metalc ? metalc4 H O2B GSP . A GSP 701 1_555 I MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? 
metalc ? metalc5 I MG MG . A MG 702 1_555 T O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc6 I MG MG . A MG 702 1_555 T O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc7 B OG1 THR 222 B THR 222 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc8 B OD1 ASP 356 B ASP 356 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? 
metalc ? metalc9 J O2G GSP . B GSP 701 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc10 J O1B GSP . B GSP 701 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? 
metalc ? metalc11 K MG MG . B MG 702 1_555 U O HOH . B HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc12 K MG MG . B MG 702 1_555 U O HOH . B HOH 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc13 C OG1 THR 222 C THR 222 1_555 M MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc14 C OD2 ASP 356 C ASP 356 1_555 M MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? 
metalc ? metalc15 L O2G GSP . C GSP 701 1_555 M MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc16 L O2B GSP . C GSP 701 1_555 M MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? 
metalc ? metalc17 M MG MG . C MG 702 1_555 V O HOH . C HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc18 M MG MG . C MG 702 1_555 V O HOH . C HOH 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc19 D OG1 THR 222 D THR 222 1_555 O MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc20 N O2G GSP . D GSP 701 1_555 O MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc21 N O1B GSP . D GSP 701 1_555 O MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc22 O MG MG . D MG 702 1_555 W O HOH . D HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc23 O MG MG . D MG 702 1_555 W O HOH . D HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? 
metalc ? metalc24 O MG MG . D MG 702 1_555 W O HOH . D HOH 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc25 E OG1 THR 222 E THR 222 1_555 Q MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc26 P O3G GSP . E GSP 701 1_555 Q MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc27 P O1B GSP . E GSP 701 1_555 Q MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc28 Q MG MG . E MG 702 1_555 X O HOH . E HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc29 Q MG MG . E MG 702 1_555 X O HOH . E HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc30 Q MG MG . E MG 702 1_555 X O HOH . E HOH 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc31 F OG1 THR 222 F THR 222 1_555 S MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc32 R O1B GDP . F GDP 701 1_555 S MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc33 S MG MG . F MG 702 1_555 Y O HOH . F HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc34 S MG MG . F MG 702 1_555 Y O HOH . F HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
#
_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 174 n n 
PG S1G GSP doub 175 n n 
PG O2G GSP sing 176 n n 
PG O3G GSP sing 177 n n 
O3B PB GSP sing 178 n n 
O2G HOG2 GSP sing 179 n n 
O3G HOG3 GSP sing 180 n n 
PB O1B GSP doub 181 n n 
PB O2B GSP sing 182 n n 
PB O3A GSP sing 183 n n 
O2B HOB2 GSP sing 184 n n 
PA O1A GSP doub 185 n n 
PA O2A GSP sing 186 n n 
PA O3A GSP sing 187 n n 
PA O5' GSP sing 188 n n 
O2A HOA2 GSP sing 189 n n 
O5' C5' GSP sing 190 n n 
C5' C4' GSP sing 191 n n 
C5' "H5'1" GSP sing 192 n n 
C5' "H5'2" GSP sing 193 n n 
C4' O4' GSP sing 194 n n 
C4' C3' GSP sing 195 n n 
C4' H4' GSP sing 196 n n 
O4' C1' GSP sing 197 n n 
C3' O3' GSP sing 198 n n 
C3' C2' GSP sing 199 n n 
C3' H3' GSP sing 200 n n 
O3' HO3' GSP sing 201 n n 
C2' O2' GSP sing 202 n n 
C2' C1' GSP sing 203 n n 
C2' H2' GSP sing 204 n n 
O2' HO2' GSP sing 205 n n 
C1' N9 GSP sing 206 n n 
C1' H1' GSP sing 207 n n 
N9 C8 GSP sing 208 n y 
N9 C4 GSP sing 209 n y 
C8 N7 GSP doub 210 n y 
C8 H8 GSP sing 211 n n 
N7 C5 GSP sing 212 n y 
C5 C6 GSP sing 213 n n 
C5 C4 GSP doub 214 n y 
C6 O6 GSP doub 215 n n 
C6 N1 GSP sing 216 n n 
N1 C2 GSP sing 217 n n 
N1 HN1 GSP sing 218 n n 
C2 N2 GSP sing 219 n n 
C2 N3 GSP doub 220 n n 
N2 HN21 GSP sing 221 n n 
N2 HN22 GSP sing 222 n n 
N3 C4 GSP sing 223 n n 
#
_atom_sites.entry_id                     6UT5 
_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
H 3 GSP A 1 701 701 GSP GSP . 
I 4 MG A 1 702 801 MG MG . 
J 3 GSP B 1 701 701 GSP GSP . 
K 4 MG B 1 702 801 MG MG . 
L 3 GSP C 1 701 701 GSP GSP . 
M 4 MG C 1 702 801 MG MG . 
N 3 GSP D 1 701 701 GSP GSP . 
O 4 MG D 1 702 801 MG MG . 
P 3 GSP E 1 701 701 GSP GSP . 
Q 4 MG E 1 702 801 MG MG . 
R 5 GDP F 1 701 701 GDP GDP . 
S 4 MG F 1 702 801 MG MG . 
T 6 HOH A 1 801 902 HOH HOH . 
T 6 HOH A 2 802 901 HOH HOH . 
T 6 HOH A 3 803 903 HOH HOH . 
U 6 HOH B 1 801 902 HOH HOH . 
U 6 HOH B 2 802 904 HOH HOH . 
U 6 HOH B 3 803 903 HOH HOH . 
U 6 HOH B 4 804 901 HOH HOH . 
V 6 HOH C 1 901 901 HOH HOH . 
V 6 HOH C 2 902 903 HOH HOH . 
V 6 HOH C 3 903 905 HOH HOH . 
V 6 HOH C 4 904 904 HOH HOH . 
V 6 HOH C 5 905 902 HOH HOH . 
W 6 HOH D 1 801 904 HOH HOH . 
W 6 HOH D 2 802 907 HOH HOH . 
W 6 HOH D 3 803 905 HOH HOH . 
W 6 HOH D 4 804 903 HOH HOH . 
W 6 HOH D 5 805 901 HOH HOH . 
W 6 HOH D 6 806 906 HOH HOH . 
W 6 HOH D 7 807 902 HOH HOH . 
X 6 HOH E 1 801 903 HOH HOH . 
X 6 HOH E 2 802 904 HOH HOH . 
X 6 HOH E 3 803 901 HOH HOH . 
X 6 HOH E 4 804 902 HOH HOH . 
X 6 HOH E 5 805 906 HOH HOH . 
X 6 HOH E 6 806 905 HOH HOH . 
Y 6 HOH F 1 801 903 HOH HOH . 
Y 6 HOH F 2 802 901 HOH HOH . 
Y 6 HOH F 3 803 902 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 . . . L 3 174.787 192.077 210.704 1 27.84 ? PG GSP 701 C 1 
HETATM 2 O O3B GSP . . . L 3 173.695 191.749 211.833 1 27.84 ? O3B GSP 701 C 1 
HETATM 3 S S1G GSP . . . L 3 175.905 190.812 210.663 1 27.84 ? S1G GSP 701 C 1 
HETATM 4 O O2G GSP . . . L 3 174.079 192.148 209.344 1 27.84 ? O2G GSP 701 C 1 
HETATM 5 O O3G GSP . . . L 3 175.525 193.392 211.008 1 27.84 ? O3G GSP 701 C 1 
HETATM 6 P PB GSP . . . L 3 172.291 192.517 211.871 1 27.84 ? PB GSP 701 C 1 
HETATM 7 O O1B GSP . . . L 3 172.302 193.533 212.935 1 27.84 ? O1B GSP 701 C 1 
HETATM 8 O O2B GSP . . . L 3 171.97 193.084 210.549 1 27.84 ? O2B GSP 701 C 1 
HETATM 9 P PA GSP . . . L 3 170.001 190.959 211.407 1 27.84 ? PA GSP 701 C 1 
HETATM 10 O O1A GSP . . . L 3 169.096 192.102 211.202 1 27.84 ? O1A GSP 701 C 1 
HETATM 11 O O2A GSP . . . L 3 170.402 190.348 210.128 1 27.84 ? O2A GSP 701 C 1 
HETATM 12 O O3A GSP . . . L 3 171.259 191.378 212.302 1 27.84 ? O3A GSP 701 C 1 
HETATM 13 O O5' GSP . . . L 3 169.311 189.895 212.379 1 27.84 ? O5' GSP 701 C 1 
HETATM 14 C C5' GSP . . . L 3 169.663 188.54 212.306 1 27.84 ? C5' GSP 701 C 1 
HETATM 15 C C4' GSP . . . L 3 168.389 187.734 212.456 1 27.84 ? C4' GSP 701 C 1 
HETATM 16 O O4' GSP . . . L 3 167.992 187.749 213.81 1 27.84 ? O4' GSP 701 C 1 
HETATM 17 C C3' GSP . . . L 3 167.265 188.363 211.652 1 27.84 ? C3' GSP 701 C 1 
HETATM 18 O O3' GSP . . . L 3 166.97 187.586 210.525 1 27.84 ? O3' GSP 701 C 1 
HETATM 19 C C2' GSP . . . L 3 166.072 188.383 212.57 1 27.84 ? C2' GSP 701 C 1 
HETATM 20 O O2' GSP . . . L 3 165.145 187.408 212.159 1 27.84 ? O2' GSP 701 C 1 
HETATM 21 C C1' GSP . . . L 3 166.611 188.006 213.93 1 27.84 ? C1' GSP 701 C 1 
HETATM 22 N N9 GSP . . . L 3 166.374 189.13 214.846 1 27.84 ? N9 GSP 701 C 1 
HETATM 23 C C8 GSP . . . L 3 167.279 190.089 215.192 1 27.84 ? C8 GSP 701 C 1 
HETATM 24 N N7 GSP . . . L 3 166.677 190.956 216.03 1 27.84 ? N7 GSP 701 C 1 
HETATM 25 C C5 GSP . . . L 3 165.403 190.566 216.22 1 27.84 ? C5 GSP 701 C 1 
HETATM 26 C C6 GSP . . . L 3 164.369 191.091 216.977 1 27.84 ? C6 GSP 701 C 1 
HETATM 27 O O6 GSP . . . L 3 164.547 192.108 217.637 1 27.84 ? O6 GSP 701 C 1 
HETATM 28 N N1 GSP . . . L 3 163.14 190.47 216.974 1 27.84 ? N1 GSP 701 C 1 
HETATM 29 C C2 GSP . . . L 3 162.954 189.332 216.222 1 27.84 ? C2 GSP 701 C 1 
HETATM 30 N N2 GSP . . . L 3 161.773 188.726 216.214 1 27.84 ? N2 GSP 701 C 1 
HETATM 31 N N3 GSP . . . L 3 163.989 188.816 215.476 1 27.84 ? N3 GSP 701 C 1 
HETATM 32 C C4 GSP . . . L 3 165.195 189.424 215.474 1 27.84 ? C4 GSP 701 C 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    79 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           32 
#