data_4D0M
#
_model_server_result.job_id            IiFQya5liTdEHRf9nEysJg 
_model_server_result.datetime_utc      '2024-11-22 16:37:02' 
_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          4d0m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"XA","auth_seq_id":2000}' 
#
_entry.id    4D0M 
#
_exptl.entry_id    4D0M 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_entity.pdbx_number_of_molecules    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.33 
_cell.angle_gamma         90 
_cell.entry_id            4D0M 
_cell.length_a            199.504 
_cell.length_b            134.465 
_cell.length_c            294.328 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D0M 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 dodecameric 12 author_and_software_defined_assembly 1 
PISA dodecameric 12 author_and_software_defined_assembly 2 
PISA dodecameric 12 author_and_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,C,D,E,F,O,P,S,T,U,V,KA,LA,MA,NA,OA,PA,ZA,AB,BB,FB,GB,HB 1 1 
G,H,I,J,K,L,M,N,Q,R,EA,FA,QA,RA,SA,TA,UA,VA,WA,XA,YA,CB,DB,EB 2 1 
W,X,Y,Z,AA,BA,CA,DA,GA,HA,IA,JA,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB 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
? 5 LA N N 
? 5 OA N N 
? 5 RA N N 
? 5 UA N N 
? 5 XA N N 
? 5 AB N N 
? 5 DB N N 
? 5 GB N N 
? 5 JB N N 
? 5 MB N N 
? 5 PB N N 
? 5 SB 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 B OG SER 28 B SER 25 1_555 MA MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.759 ? 
metalc ? metalc2 LA O3G GSP . B GSP 2000 1_555 MA MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.761 ? 
metalc ? metalc3 LA O2B GSP . B GSP 2000 1_555 MA MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc4 OA O3G GSP . D GSP 2000 1_555 PA MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? 
metalc ? metalc5 OA O2B GSP . D GSP 2000 1_555 PA MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc6 H OG1 THR 46 H THR 43 1_555 SA MG MG . H MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? 
metalc ? metalc7 RA O3G GSP . H GSP 2000 1_555 SA MG MG . H MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? 
metalc ? metalc8 RA O2B GSP . H GSP 2000 1_555 SA MG MG . H MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc9 UA O3G GSP . J GSP 2000 1_555 VA MG MG . J MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
metalc ? metalc10 UA O2B GSP . J GSP 2000 1_555 VA MG MG . J MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc11 XA O3G GSP . N GSP 2000 1_555 YA MG MG . N MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.858 ? 
metalc ? metalc12 XA O2B GSP . N GSP 2000 1_555 YA MG MG . N MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc13 AB O3G GSP . P GSP 2000 1_555 BB MG MG . P MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? 
metalc ? metalc14 AB O2B GSP . P GSP 2000 1_555 BB MG MG . P MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc15 DB O3G GSP . R GSP 2000 1_555 EB MG MG . R MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? 
metalc ? metalc16 DB O2B GSP . R GSP 2000 1_555 EB MG MG . R MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc17 T OG1 THR 46 T THR 43 1_555 HB MG MG . T MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.808 ? 
metalc ? metalc18 GB O3G GSP . T GSP 2000 1_555 HB MG MG . T MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
metalc ? metalc19 GB O2B GSP . T GSP 2000 1_555 HB MG MG . T MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc20 JB O3G GSP . X GSP 2000 1_555 KB MG MG . X MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? 
metalc ? metalc21 JB O2B GSP . X GSP 2000 1_555 KB MG MG . X MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc22 MB O3G GSP . Z GSP 2000 1_555 NB MG MG . Z MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
metalc ? metalc23 MB O2B GSP . Z GSP 2000 1_555 NB MG MG . Z MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc24 PB O3G GSP . d GSP 2000 1_555 QB MG MG . d MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc25 PB O2B GSP . d GSP 2000 1_555 QB MG MG . d MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc26 SB O3G GSP . h GSP 2000 1_555 TB MG MG . h MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? 
metalc ? metalc27 SB O2B GSP . h GSP 2000 1_555 TB MG MG . h MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
#
_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                     4D0M 
_atom_sites.fract_transf_matrix[1][1]    0.005012 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000029 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007437 
_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]    0.003398 
_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
KA 4 093 A 1 2002 2002 093 093 . 
LA 5 GSP B 1 2000 2000 GSP GSP . 
MA 6 MG B 1 2001 2001 MG MG . 
NA 4 093 C 1 2002 2002 093 093 . 
OA 5 GSP D 1 2000 2000 GSP GSP . 
PA 6 MG D 1 2001 2001 MG MG . 
QA 4 093 G 1 2002 2002 093 093 . 
RA 5 GSP H 1 2000 2000 GSP GSP . 
SA 6 MG H 1 2001 2001 MG MG . 
TA 4 093 I 1 2002 2002 093 093 . 
UA 5 GSP J 1 2000 2000 GSP GSP . 
VA 6 MG J 1 2001 2001 MG MG . 
WA 4 093 M 1 2002 2002 093 093 . 
XA 5 GSP N 1 2000 2000 GSP GSP . 
YA 6 MG N 1 2001 2001 MG MG . 
ZA 4 093 O 1 2002 2002 093 093 . 
AB 5 GSP P 1 2000 2000 GSP GSP . 
BB 6 MG P 1 2001 2001 MG MG . 
CB 4 093 Q 1 2002 2002 093 093 . 
DB 5 GSP R 1 2000 2000 GSP GSP . 
EB 6 MG R 1 2001 2001 MG MG . 
FB 4 093 S 1 2002 2002 093 093 . 
GB 5 GSP T 1 2000 2000 GSP GSP . 
HB 6 MG T 1 2001 2001 MG MG . 
IB 4 093 W 1 2002 2002 093 093 . 
JB 5 GSP X 1 2000 2000 GSP GSP . 
KB 6 MG X 1 2001 2001 MG MG . 
LB 4 093 Y 1 2002 2002 093 093 . 
MB 5 GSP Z 1 2000 2000 GSP GSP . 
NB 6 MG Z 1 2001 2001 MG MG . 
OB 4 093 c 1 2002 2002 093 093 . 
PB 5 GSP d 1 2000 2000 GSP GSP . 
QB 6 MG d 1 2001 2001 MG MG . 
RB 4 093 g 1 2002 2002 093 093 . 
SB 5 GSP h 1 2000 2000 GSP GSP . 
TB 6 MG h 1 2001 2001 MG MG . 
#
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 . . . XA 5 17.603 276.72 31.653 1 255.57 ? PG GSP 2000 N 1 
HETATM 2 O O3B GSP . . . XA 5 16.356 277.323 30.847 1 192.89 ? O3B GSP 2000 N 1 
HETATM 3 S S1G GSP . . . XA 5 18.737 275.885 30.306 1 301.01 ? S1G GSP 2000 N 1 
HETATM 4 O O2G GSP . . . XA 5 17.147 275.769 32.912 1 239.57 ? O2G GSP 2000 N 1 
HETATM 5 O O3G GSP . . . XA 5 18.453 277.981 32.189 1 280.4 ? O3G GSP 2000 N 1 
HETATM 6 P PB GSP . . . XA 5 15.596 278.51 31.6 1 143.59 ? PB GSP 2000 N 1 
HETATM 7 O O1B GSP . . . XA 5 14.469 277.833 32.36 1 145.56 ? O1B GSP 2000 N 1 
HETATM 8 O O2B GSP . . . XA 5 16.66 279.38 32.257 1 169.59 ? O2B GSP 2000 N 1 
HETATM 9 P PA GSP . . . XA 5 15.781 280.182 29.412 1 106.41 ? PA GSP 2000 N 1 
HETATM 10 O O1A GSP . . . XA 5 16.001 281.618 29.789 1 97.25 ? O1A GSP 2000 N 1 
HETATM 11 O O2A GSP . . . XA 5 16.971 279.317 29.068 1 98.2 ? O2A GSP 2000 N 1 
HETATM 12 O O3A GSP . . . XA 5 14.898 279.422 30.501 1 123.88 ? O3A GSP 2000 N 1 
HETATM 13 O O5' GSP . . . XA 5 14.663 280.266 28.242 1 151.46 ? O5' GSP 2000 N 1 
HETATM 14 C C5' GSP . . . XA 5 14.687 279.341 27.165 1 197.18 ? C5' GSP 2000 N 1 
HETATM 15 C C4' GSP . . . XA 5 14.041 279.913 25.894 1 193.96 ? C4' GSP 2000 N 1 
HETATM 16 O O4' GSP . . . XA 5 12.661 280.28 26.064 1 178.17 ? O4' GSP 2000 N 1 
HETATM 17 C C3' GSP . . . XA 5 14.773 281.15 25.378 1 197.59 ? C3' GSP 2000 N 1 
HETATM 18 O O3' GSP . . . XA 5 14.878 281.128 23.952 1 220.85 ? O3' GSP 2000 N 1 
HETATM 19 C C2' GSP . . . XA 5 13.878 282.303 25.699 1 181.12 ? C2' GSP 2000 N 1 
HETATM 20 O O2' GSP . . . XA 5 14.063 283.333 24.727 1 179.7 ? O2' GSP 2000 N 1 
HETATM 21 C C1' GSP . . . XA 5 12.525 281.626 25.614 1 164.67 ? C1' GSP 2000 N 1 
HETATM 22 N N9 GSP . . . XA 5 11.59 282.268 26.513 1 143.05 ? N9 GSP 2000 N 1 
HETATM 23 C C8 GSP . . . XA 5 11.759 282.446 27.832 1 142.36 ? C8 GSP 2000 N 1 
HETATM 24 N N7 GSP . . . XA 5 10.675 283.074 28.326 1 153.41 ? N7 GSP 2000 N 1 
HETATM 25 C C5 GSP . . . XA 5 9.818 283.285 27.311 1 144.57 ? C5 GSP 2000 N 1 
HETATM 26 C C6 GSP . . . XA 5 8.484 283.901 27.154 1 147.87 ? C6 GSP 2000 N 1 
HETATM 27 O O6 GSP . . . XA 5 7.865 284.379 28.132 1 163.28 ? O6 GSP 2000 N 1 
HETATM 28 N N1 GSP . . . XA 5 7.95 283.912 25.931 1 139.6 ? N1 GSP 2000 N 1 
HETATM 29 C C2 GSP . . . XA 5 8.593 283.392 24.868 1 132.58 ? C2 GSP 2000 N 1 
HETATM 30 N N2 GSP . . . XA 5 7.973 283.454 23.673 1 136.34 ? N2 GSP 2000 N 1 
HETATM 31 N N3 GSP . . . XA 5 9.82 282.816 24.928 1 123.08 ? N3 GSP 2000 N 1 
HETATM 32 C C4 GSP . . . XA 5 10.441 282.743 26.111 1 131.26 ? C4 GSP 2000 N 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    73 
_model_server_stats.query_time_ms           248 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           32 
#