data_4LWZ
#
_model_server_result.job_id            i6vXAiKhhrt2sjBAmDsMwA 
_model_server_result.datetime_utc      '2024-11-22 12:42:10' 
_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          4lwz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":201}' 
#
_entry.id    4LWZ 
#
_exptl.entry_id    4LWZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_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            4LWZ 
_cell.length_a            67.68 
_cell.length_b            143.14 
_cell.length_c            162.64 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4LWZ 
_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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_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,E,F,I,J 1 1 
C,D,G,H,K,L 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
? 3 E N N 
? 3 G 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 OG SER 25 A SER 25 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? 
metalc ? metalc2 A OG1 THR 43 A THR 43 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc3 E O1B GDP . A GDP 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc4 F MG MG . A MG 202 1_555 I O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc5 F MG MG . A MG 202 1_555 I O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc6 F MG MG . A MG 202 1_555 I O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc7 C OG SER 25 C SER 25 1_555 H MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? 
metalc ? metalc8 C OG1 THR 43 C THR 43 1_555 H MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
metalc ? metalc9 G O1B GDP . C GDP 201 1_555 H MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc10 H MG MG . C MG 202 1_555 K O HOH . C HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc11 H MG MG . C MG 202 1_555 K O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
PB O1B GDP doub 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     4LWZ 
_atom_sites.fract_transf_matrix[1][1]    0.014775 
_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]    0.006986 
_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]    0.006149 
_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
E 3 GDP A 1 201 1 GDP GDP . 
F 4 MG A 1 202 2 MG MG . 
G 3 GDP C 1 201 1 GDP GDP . 
H 4 MG C 1 202 2 MG MG . 
I 5 HOH A 1 301 1 HOH HOH . 
I 5 HOH A 2 302 2 HOH HOH . 
I 5 HOH A 3 303 4 HOH HOH . 
I 5 HOH A 4 304 5 HOH HOH . 
I 5 HOH A 5 305 7 HOH HOH . 
I 5 HOH A 6 306 8 HOH HOH . 
I 5 HOH A 7 307 10 HOH HOH . 
I 5 HOH A 8 308 12 HOH HOH . 
I 5 HOH A 9 309 33 HOH HOH . 
I 5 HOH A 10 310 34 HOH HOH . 
I 5 HOH A 11 311 35 HOH HOH . 
I 5 HOH A 12 312 37 HOH HOH . 
I 5 HOH A 13 313 39 HOH HOH . 
I 5 HOH A 14 314 55 HOH HOH . 
I 5 HOH A 15 315 57 HOH HOH . 
I 5 HOH A 16 316 59 HOH HOH . 
I 5 HOH A 17 317 60 HOH HOH . 
I 5 HOH A 18 318 62 HOH HOH . 
I 5 HOH A 19 319 68 HOH HOH . 
I 5 HOH A 20 320 84 HOH HOH . 
I 5 HOH A 21 321 123 HOH HOH . 
I 5 HOH A 22 322 130 HOH HOH . 
I 5 HOH A 23 323 149 HOH HOH . 
I 5 HOH A 24 324 157 HOH HOH . 
I 5 HOH A 25 325 160 HOH HOH . 
I 5 HOH A 26 326 166 HOH HOH . 
I 5 HOH A 27 327 172 HOH HOH . 
I 5 HOH A 28 328 186 HOH HOH . 
I 5 HOH A 29 329 190 HOH HOH . 
I 5 HOH A 30 330 191 HOH HOH . 
I 5 HOH A 31 331 194 HOH HOH . 
I 5 HOH A 32 332 198 HOH HOH . 
I 5 HOH A 33 333 214 HOH HOH . 
J 5 HOH B 1 1901 3 HOH HOH . 
J 5 HOH B 2 1902 6 HOH HOH . 
J 5 HOH B 3 1903 9 HOH HOH . 
J 5 HOH B 4 1904 11 HOH HOH . 
J 5 HOH B 5 1905 15 HOH HOH . 
J 5 HOH B 6 1906 16 HOH HOH . 
J 5 HOH B 7 1907 20 HOH HOH . 
J 5 HOH B 8 1908 22 HOH HOH . 
J 5 HOH B 9 1909 29 HOH HOH . 
J 5 HOH B 10 1910 40 HOH HOH . 
J 5 HOH B 11 1911 41 HOH HOH . 
J 5 HOH B 12 1912 42 HOH HOH . 
J 5 HOH B 13 1913 47 HOH HOH . 
J 5 HOH B 14 1914 53 HOH HOH . 
J 5 HOH B 15 1915 66 HOH HOH . 
J 5 HOH B 16 1916 71 HOH HOH . 
J 5 HOH B 17 1917 74 HOH HOH . 
J 5 HOH B 18 1918 75 HOH HOH . 
J 5 HOH B 19 1919 83 HOH HOH . 
J 5 HOH B 20 1920 87 HOH HOH . 
J 5 HOH B 21 1921 88 HOH HOH . 
J 5 HOH B 22 1922 90 HOH HOH . 
J 5 HOH B 23 1923 91 HOH HOH . 
J 5 HOH B 24 1924 99 HOH HOH . 
J 5 HOH B 25 1925 100 HOH HOH . 
J 5 HOH B 26 1926 107 HOH HOH . 
J 5 HOH B 27 1927 117 HOH HOH . 
J 5 HOH B 28 1928 120 HOH HOH . 
J 5 HOH B 29 1929 121 HOH HOH . 
J 5 HOH B 30 1930 128 HOH HOH . 
J 5 HOH B 31 1931 134 HOH HOH . 
J 5 HOH B 32 1932 144 HOH HOH . 
J 5 HOH B 33 1933 147 HOH HOH . 
J 5 HOH B 34 1934 152 HOH HOH . 
J 5 HOH B 35 1935 153 HOH HOH . 
J 5 HOH B 36 1936 162 HOH HOH . 
J 5 HOH B 37 1937 167 HOH HOH . 
J 5 HOH B 38 1938 173 HOH HOH . 
J 5 HOH B 39 1939 177 HOH HOH . 
J 5 HOH B 40 1940 178 HOH HOH . 
J 5 HOH B 41 1941 179 HOH HOH . 
J 5 HOH B 42 1942 181 HOH HOH . 
J 5 HOH B 43 1943 183 HOH HOH . 
J 5 HOH B 44 1944 185 HOH HOH . 
J 5 HOH B 45 1945 189 HOH HOH . 
J 5 HOH B 46 1946 195 HOH HOH . 
J 5 HOH B 47 1947 196 HOH HOH . 
J 5 HOH B 48 1948 199 HOH HOH . 
J 5 HOH B 49 1949 213 HOH HOH . 
K 5 HOH C 1 301 14 HOH HOH . 
K 5 HOH C 2 302 24 HOH HOH . 
K 5 HOH C 3 303 31 HOH HOH . 
K 5 HOH C 4 304 73 HOH HOH . 
K 5 HOH C 5 305 77 HOH HOH . 
K 5 HOH C 6 306 92 HOH HOH . 
K 5 HOH C 7 307 94 HOH HOH . 
K 5 HOH C 8 308 105 HOH HOH . 
K 5 HOH C 9 309 106 HOH HOH . 
K 5 HOH C 10 310 124 HOH HOH . 
K 5 HOH C 11 311 126 HOH HOH . 
K 5 HOH C 12 312 143 HOH HOH . 
K 5 HOH C 13 313 156 HOH HOH . 
K 5 HOH C 14 314 176 HOH HOH . 
K 5 HOH C 15 315 184 HOH HOH . 
K 5 HOH C 16 316 192 HOH HOH . 
K 5 HOH C 17 317 201 HOH HOH . 
L 5 HOH D 1 1901 26 HOH HOH . 
L 5 HOH D 2 1902 38 HOH HOH . 
L 5 HOH D 3 1903 44 HOH HOH . 
L 5 HOH D 4 1904 46 HOH HOH . 
L 5 HOH D 5 1905 48 HOH HOH . 
L 5 HOH D 6 1906 51 HOH HOH . 
L 5 HOH D 7 1907 52 HOH HOH . 
L 5 HOH D 8 1908 54 HOH HOH . 
L 5 HOH D 9 1909 63 HOH HOH . 
L 5 HOH D 10 1910 67 HOH HOH . 
L 5 HOH D 11 1911 79 HOH HOH . 
L 5 HOH D 12 1912 80 HOH HOH . 
L 5 HOH D 13 1913 93 HOH HOH . 
L 5 HOH D 14 1914 95 HOH HOH . 
L 5 HOH D 15 1915 101 HOH HOH . 
L 5 HOH D 16 1916 115 HOH HOH . 
L 5 HOH D 17 1917 118 HOH HOH . 
L 5 HOH D 18 1918 135 HOH HOH . 
L 5 HOH D 19 1919 136 HOH HOH . 
L 5 HOH D 20 1920 139 HOH HOH . 
L 5 HOH D 21 1921 140 HOH HOH . 
L 5 HOH D 22 1922 145 HOH HOH . 
L 5 HOH D 23 1923 146 HOH HOH . 
L 5 HOH D 24 1924 182 HOH HOH . 
L 5 HOH D 25 1925 188 HOH HOH . 
L 5 HOH D 26 1926 216 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 PB GDP . . . G 3 35.116 -8.715 -0.071 1 81.73 ? PB GDP 201 C 1 
HETATM 2 O O1B GDP . . . G 3 35.454 -10.116 0.394 1 82.93 ? O1B GDP 201 C 1 
HETATM 3 O O2B GDP . . . G 3 33.781 -8.718 -0.785 1 69.74 ? O2B GDP 201 C 1 
HETATM 4 O O3B GDP . . . G 3 36.241 -8.212 -0.945 1 81.16 ? O3B GDP 201 C 1 
HETATM 5 O O3A GDP . . . G 3 34.965 -7.691 1.148 1 84.69 ? O3A GDP 201 C 1 
HETATM 6 P PA GDP . . . G 3 36.097 -7.524 2.274 1 73.6 ? PA GDP 201 C 1 
HETATM 7 O O1A GDP . . . G 3 35.743 -8.412 3.437 1 73.66 ? O1A GDP 201 C 1 
HETATM 8 O O2A GDP . . . G 3 37.489 -7.807 1.756 1 73.08 ? O2A GDP 201 C 1 
HETATM 9 O O5' GDP . . . G 3 36.001 -5.972 2.664 1 75.69 ? O5' GDP 201 C 1 
HETATM 10 C C5' GDP . . . G 3 36.678 -4.998 1.856 1 66.15 ? C5' GDP 201 C 1 
HETATM 11 C C4' GDP . . . G 3 36.686 -3.686 2.609 1 73.52 ? C4' GDP 201 C 1 
HETATM 12 O O4' GDP . . . G 3 35.338 -3.289 2.893 1 70.11 ? O4' GDP 201 C 1 
HETATM 13 C C3' GDP . . . G 3 37.399 -3.865 3.947 1 76.71 ? C3' GDP 201 C 1 
HETATM 14 O O3' GDP . . . G 3 38.291 -2.789 4.233 1 86.77 ? O3' GDP 201 C 1 
HETATM 15 C C2' GDP . . . G 3 36.324 -3.814 4.99 1 61.83 ? C2' GDP 201 C 1 
HETATM 16 O O2' GDP . . . G 3 36.767 -3.145 6.169 1 96.86 ? O2' GDP 201 C 1 
HETATM 17 C C1' GDP . . . G 3 35.232 -3.034 4.306 1 61.74 ? C1' GDP 201 C 1 
HETATM 18 N N9 GDP . . . G 3 33.952 -3.505 4.852 1 70.42 ? N9 GDP 201 C 1 
HETATM 19 C C8 GDP . . . G 3 33.497 -4.778 4.873 1 78.42 ? C8 GDP 201 C 1 
HETATM 20 N N7 GDP . . . G 3 32.269 -4.829 5.448 1 73.14 ? N7 GDP 201 C 1 
HETATM 21 C C5 GDP . . . G 3 31.945 -3.563 5.793 1 59.01 ? C5 GDP 201 C 1 
HETATM 22 C C6 GDP . . . G 3 30.809 -2.884 6.442 1 57.27 ? C6 GDP 201 C 1 
HETATM 23 O O6 GDP . . . G 3 29.811 -3.522 6.82 1 69.57 ? O6 GDP 201 C 1 
HETATM 24 N N1 GDP . . . G 3 30.879 -1.562 6.617 1 63.4 ? N1 GDP 201 C 1 
HETATM 25 C C2 GDP . . . G 3 31.933 -0.836 6.232 1 56.71 ? C2 GDP 201 C 1 
HETATM 26 N N2 GDP . . . G 3 31.914 0.499 6.433 1 65.8 ? N2 GDP 201 C 1 
HETATM 27 N N3 GDP . . . G 3 33.01 -1.388 5.639 1 67 ? N3 GDP 201 C 1 
HETATM 28 C C4 GDP . . . G 3 33.064 -2.71 5.409 1 58.74 ? C4 GDP 201 C 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           445 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#