data_4D0L
#
_model_server_result.job_id            wRSj8zORL4tnOMw4-guX-w 
_model_server_result.datetime_utc      '2024-11-08 22:29:25' 
_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          4d0l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":2000}' 
#
_entry.id    4D0L 
#
_exptl.entry_id    4D0L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            4D0L 
_cell.length_a            102.795 
_cell.length_b            146.925 
_cell.length_c            188.335 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D0L 
_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 dimeric 2 software_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G,H,I,P,Q 1 1 
C,D,J,K,L,R 2 1 
E,F,M,N,O,S,T 3 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
? 4 H N N 
? 4 K N N 
? 4 N 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
covale ? covale1 C NZ LYS 331 C LYS 549 1_555 J OAM 093 . C 093 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? 
metalc ? metalc1 H O3G GSP . B GSP 2000 1_555 I MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? 
metalc ? metalc2 H O2B GSP . B GSP 2000 1_555 I MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc3 D OG SER 28 D SER 25 1_555 L MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
metalc ? metalc4 K O3G GSP . D GSP 2000 1_555 L MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? 
metalc ? metalc5 K O2B GSP . D GSP 2000 1_555 L MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc6 F OG SER 28 F SER 25 1_555 O MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? 
metalc ? metalc7 F OG1 THR 46 F THR 43 1_555 O MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? 
metalc ? metalc8 N O3G GSP . F GSP 2000 1_555 O MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc9 N O2B GSP . F GSP 2000 1_555 O MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
#
_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 170 n n 
PG S1G GSP doub 171 n n 
PG O2G GSP sing 172 n n 
PG O3G GSP sing 173 n n 
O3B PB GSP sing 174 n n 
O2G HOG2 GSP sing 175 n n 
O3G HOG3 GSP sing 176 n n 
PB O1B GSP doub 177 n n 
PB O2B GSP sing 178 n n 
PB O3A GSP sing 179 n n 
O2B HOB2 GSP sing 180 n n 
PA O1A GSP doub 181 n n 
PA O2A GSP sing 182 n n 
PA O3A GSP sing 183 n n 
PA O5' GSP sing 184 n n 
O2A HOA2 GSP sing 185 n n 
O5' C5' GSP sing 186 n n 
C5' C4' GSP sing 187 n n 
C5' "H5'1" GSP sing 188 n n 
C5' "H5'2" GSP sing 189 n n 
C4' O4' GSP sing 190 n n 
C4' C3' GSP sing 191 n n 
C4' H4' GSP sing 192 n n 
O4' C1' GSP sing 193 n n 
C3' O3' GSP sing 194 n n 
C3' C2' GSP sing 195 n n 
C3' H3' GSP sing 196 n n 
O3' HO3' GSP sing 197 n n 
C2' O2' GSP sing 198 n n 
C2' C1' GSP sing 199 n n 
C2' H2' GSP sing 200 n n 
O2' HO2' GSP sing 201 n n 
C1' N9 GSP sing 202 n n 
C1' H1' GSP sing 203 n n 
N9 C8 GSP sing 204 n y 
N9 C4 GSP sing 205 n y 
C8 N7 GSP doub 206 n y 
C8 H8 GSP sing 207 n n 
N7 C5 GSP sing 208 n y 
C5 C6 GSP sing 209 n n 
C5 C4 GSP doub 210 n y 
C6 O6 GSP doub 211 n n 
C6 N1 GSP sing 212 n n 
N1 C2 GSP sing 213 n n 
N1 HN1 GSP sing 214 n n 
C2 N2 GSP sing 215 n n 
C2 N3 GSP doub 216 n n 
N2 HN21 GSP sing 217 n n 
N2 HN22 GSP sing 218 n n 
N3 C4 GSP sing 219 n n 
#
_atom_sites.entry_id                     4D0L 
_atom_sites.fract_transf_matrix[1][1]    0.009728 
_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]    0.006806 
_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]    0.00531 
_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 3 093 A 1 2002 2002 093 093 . 
H 4 GSP B 1 2000 2000 GSP GSP . 
I 5 MG B 1 2001 2001 MG MG . 
J 3 093 C 1 2002 2002 093 093 . 
K 4 GSP D 1 2000 2000 GSP GSP . 
L 5 MG D 1 2001 2001 MG MG . 
M 3 093 E 1 2002 2002 093 093 . 
N 4 GSP F 1 2000 2000 GSP GSP . 
O 5 MG F 1 2001 2001 MG MG . 
P 6 HOH A 1 3001 3001 HOH HOH . 
P 6 HOH A 2 3002 3002 HOH HOH . 
P 6 HOH A 3 3003 3003 HOH HOH . 
P 6 HOH A 4 3004 3004 HOH HOH . 
P 6 HOH A 5 3005 3005 HOH HOH . 
P 6 HOH A 6 3006 3006 HOH HOH . 
P 6 HOH A 7 3007 3007 HOH HOH . 
P 6 HOH A 8 3008 3008 HOH HOH . 
Q 6 HOH B 1 3001 3001 HOH HOH . 
Q 6 HOH B 2 3002 3002 HOH HOH . 
R 6 HOH C 1 3001 3001 HOH HOH . 
S 6 HOH E 1 3001 3001 HOH HOH . 
S 6 HOH E 2 3002 3002 HOH HOH . 
S 6 HOH E 3 3003 3003 HOH HOH . 
S 6 HOH E 4 3004 3004 HOH HOH . 
T 6 HOH F 1 3001 3001 HOH HOH . 
T 6 HOH F 2 3002 3002 HOH HOH . 
T 6 HOH F 3 3003 3003 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 . . . K 4 -23.936 323.34 32.384 1 60.98 ? PG GSP 2000 D 1 
HETATM 2 O O3B GSP . . . K 4 -24.187 321.845 32.942 1 52.48 ? O3B GSP 2000 D 1 
HETATM 3 S S1G GSP . . . K 4 -23.866 324.767 33.706 1 58.91 ? S1G GSP 2000 D 1 
HETATM 4 O O2G GSP . . . K 4 -25.134 323.845 31.461 1 60.71 ? O2G GSP 2000 D 1 
HETATM 5 O O3G GSP . . . K 4 -22.55 323.301 31.531 1 70.55 ? O3G GSP 2000 D 1 
HETATM 6 P PB GSP . . . K 4 -23.829 320.547 32.063 1 47.31 ? PB GSP 2000 D 1 
HETATM 7 O O1B GSP . . . K 4 -25.068 319.972 31.446 1 46.3 ? O1B GSP 2000 D 1 
HETATM 8 O O2B GSP . . . K 4 -22.669 320.905 31.156 1 50.83 ? O2B GSP 2000 D 1 
HETATM 9 P PA GSP . . . K 4 -21.692 319.291 33.307 1 50.33 ? PA GSP 2000 D 1 
HETATM 10 O O1A GSP . . . K 4 -21.234 318.449 32.126 1 51.53 ? O1A GSP 2000 D 1 
HETATM 11 O O2A GSP . . . K 4 -20.988 320.558 33.658 1 50.52 ? O2A GSP 2000 D 1 
HETATM 12 O O3A GSP . . . K 4 -23.285 319.54 33.168 1 46.98 ? O3A GSP 2000 D 1 
HETATM 13 O O5' GSP . . . K 4 -21.589 318.364 34.611 1 48.71 ? O5' GSP 2000 D 1 
HETATM 14 C C5' GSP . . . K 4 -22.083 318.792 35.862 1 46.39 ? C5' GSP 2000 D 1 
HETATM 15 C C4' GSP . . . K 4 -21.321 318.037 36.944 1 50.02 ? C4' GSP 2000 D 1 
HETATM 16 O O4' GSP . . . K 4 -21.859 316.739 37.201 1 51 ? O4' GSP 2000 D 1 
HETATM 17 C C3' GSP . . . K 4 -19.857 317.829 36.608 1 52.94 ? C3' GSP 2000 D 1 
HETATM 18 O O3' GSP . . . K 4 -19.058 318.371 37.675 1 55.76 ? O3' GSP 2000 D 1 
HETATM 19 C C2' GSP . . . K 4 -19.619 316.349 36.537 1 53.39 ? C2' GSP 2000 D 1 
HETATM 20 O O2' GSP . . . K 4 -18.579 316.077 37.447 1 60.36 ? O2' GSP 2000 D 1 
HETATM 21 C C1' GSP . . . K 4 -20.891 315.707 37.031 1 53.51 ? C1' GSP 2000 D 1 
HETATM 22 N N9 GSP . . . K 4 -21.365 314.736 36.043 1 55.15 ? N9 GSP 2000 D 1 
HETATM 23 C C8 GSP . . . K 4 -21.667 315.009 34.765 1 57.8 ? C8 GSP 2000 D 1 
HETATM 24 N N7 GSP . . . K 4 -22.102 313.886 34.132 1 57.86 ? N7 GSP 2000 D 1 
HETATM 25 C C5 GSP . . . K 4 -22.069 312.88 35.011 1 59.19 ? C5 GSP 2000 D 1 
HETATM 26 C C6 GSP . . . K 4 -22.38 311.436 34.985 1 63.92 ? C6 GSP 2000 D 1 
HETATM 27 O O6 GSP . . . K 4 -22.78 310.867 33.95 1 72.86 ? O6 GSP 2000 D 1 
HETATM 28 N N1 GSP . . . K 4 -22.212 310.745 36.119 1 65.54 ? N1 GSP 2000 D 1 
HETATM 29 C C2 GSP . . . K 4 -21.783 311.331 37.269 1 63.45 ? C2 GSP 2000 D 1 
HETATM 30 N N2 GSP . . . K 4 -21.637 310.593 38.398 1 61.29 ? N2 GSP 2000 D 1 
HETATM 31 N N3 GSP . . . K 4 -21.478 312.653 37.355 1 57.75 ? N3 GSP 2000 D 1 
HETATM 32 C C4 GSP . . . K 4 -21.591 313.452 36.277 1 56.54 ? C4 GSP 2000 D 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           32 
#