data_3WV9
#
_model_server_result.job_id            GWwpnKjuJzb-QD7BsszOEQ 
_model_server_result.datetime_utc      '2024-11-07 01:36:39' 
_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          3wv9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    3WV9 
#
_exptl.entry_id    3WV9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              542.393 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine" 
_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         120 
_cell.entry_id            3WV9 
_cell.length_a            85 
_cell.length_b            85 
_cell.length_c            120.78 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3WV9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        143 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
PISA trimeric 3 software_defined_assembly 5 
PISA trimeric 3 software_defined_assembly 6 
PISA trimeric 3 software_defined_assembly 7 
PISA trimeric 3 software_defined_assembly 8 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,H,I,U 1 1 
B,J,K,L,V 2 1 
C,M,N,O,P,Q,R,W 3 1 
D,S,T,X 4 1 
A,E,F,G,H,I,U 5 1,2,3 
B,J,K,L,V 6 1,2,3 
C,M,N,O,P,Q,R,W 7 1,4,5 
D,S,T,X 8 1,6,7 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 85 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 42.5 73.612159 0 
4 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
5 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
6 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 42.5 -73.612159 0 
7 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 85 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 K N N 
? 3 N N N 
#
_chem_comp.formula           'C19 H23 N6 O11 P' 
_chem_comp.formula_weight    542.393 
_chem_comp.id                FEG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine" 
_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
N1 C2 FEG doub 132 n y 
N1 C6 FEG sing 133 n y 
C2 O2 FEG sing 134 n n 
C2 C3 FEG sing 135 n y 
C3 C3M FEG sing 136 n n 
C3 C4 FEG doub 137 n y 
C3M H3M FEG sing 138 n n 
C3M H3MA FEG sing 139 n n 
C3M H3MB FEG sing 140 n n 
C4 C5 FEG sing 141 n y 
C4 O3P FEG sing 142 n n 
C5 C5M FEG sing 143 n n 
C5 C6 FEG doub 144 n y 
C5M H5M FEG sing 145 n n 
C5M H5MA FEG sing 146 n n 
C5M H5MB FEG sing 147 n n 
C6 C7 FEG sing 148 n n 
C7 C8 FEG sing 149 n n 
C7 H7 FEG sing 150 n n 
C7 H7A FEG sing 151 n n 
C8 O28 FEG doub 152 n n 
C8 O18 FEG sing 153 n n 
O18 H20 FEG sing 154 n n 
O3P P1 FEG sing 155 n n 
P1 O1P FEG doub 156 n n 
P1 O2P FEG sing 157 n n 
P1 O5S FEG sing 158 n n 
O2P H24 FEG sing 159 n n 
O5S C5S FEG sing 160 n n 
C5S C4S FEG sing 161 n n 
C5S H5S FEG sing 162 n n 
C5S H5SA FEG sing 163 n n 
C4S C3S FEG sing 164 n n 
C4S O4S FEG sing 165 n n 
C4S H4S FEG sing 166 n n 
C3S O3S FEG sing 167 n n 
C3S C2S FEG sing 168 n n 
C3S H3S FEG sing 169 n n 
O3S HO3S FEG sing 170 n n 
C2S O2S FEG sing 171 n n 
C2S C1S FEG sing 172 n n 
C2S H2S FEG sing 173 n n 
O2S HO2S FEG sing 174 n n 
C1S O4S FEG sing 175 n n 
C1S N9A FEG sing 176 n n 
C1S H23 FEG sing 177 n n 
N9A C8A FEG sing 178 n y 
N9A C4A FEG sing 179 n y 
C8A N7A FEG doub 180 n y 
C8A H8A FEG sing 181 n n 
N7A C5A FEG sing 182 n y 
C5A C4A FEG doub 183 n y 
C5A C6A FEG sing 184 n n 
C4A N3A FEG sing 185 n n 
C6A O6A FEG doub 186 n n 
C6A N1A FEG sing 187 n n 
N1A C2A FEG sing 188 n n 
N1A HN1A FEG sing 189 n n 
C2A N3A FEG doub 190 n n 
C2A N2A FEG sing 191 n n 
N2A HN2A FEG sing 192 n n 
N2A HN2B FEG sing 193 n n 
O2 H25 FEG sing 194 n n 
#
_atom_sites.entry_id                     3WV9 
_atom_sites.fract_transf_matrix[1][1]    0.011765 
_atom_sites.fract_transf_matrix[1][2]    0.006792 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013585 
_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]    0.00828 
_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 2 ATP A 1 301 301 ATP ATP . 
F 3 FEG A 1 302 302 FEG FEG . 
G 4 SO4 A 1 303 303 SO4 SO4 . 
H 4 SO4 A 1 304 305 SO4 SO4 . 
I 4 SO4 A 1 305 306 SO4 SO4 . 
J 2 ATP B 1 301 301 ATP ATP . 
K 3 FEG B 1 302 302 FEG FEG . 
L 4 SO4 B 1 303 303 SO4 SO4 . 
M 2 ATP C 1 302 301 ATP ATP . 
N 3 FEG C 1 303 302 FEG FEG . 
O 4 SO4 C 1 304 303 SO4 SO4 . 
P 4 SO4 C 1 301 304 SO4 SO4 . 
Q 4 SO4 C 1 305 304 SO4 SO4 . 
R 4 SO4 C 1 306 305 SO4 SO4 . 
S 2 ATP D 1 301 301 ATP ATP . 
T 4 SO4 D 1 302 302 SO4 SO4 . 
U 5 HOH A 1 401 401 HOH HOH . 
U 5 HOH A 2 402 402 HOH HOH . 
U 5 HOH A 3 403 403 HOH HOH . 
V 5 HOH B 1 401 401 HOH HOH . 
V 5 HOH B 2 402 402 HOH HOH . 
V 5 HOH B 3 403 403 HOH HOH . 
V 5 HOH B 4 404 404 HOH HOH . 
V 5 HOH B 5 405 405 HOH HOH . 
W 5 HOH C 1 401 401 HOH HOH . 
W 5 HOH C 2 402 402 HOH HOH . 
W 5 HOH C 3 403 403 HOH HOH . 
X 5 HOH D 1 401 401 HOH HOH . 
X 5 HOH D 2 402 402 HOH HOH . 
X 5 HOH D 3 403 403 HOH HOH . 
X 5 HOH D 4 404 404 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 N N1 FEG . . . F 3 46.073 5.787 -42.334 1 51.43 ? N1 FEG 302 A 1 
HETATM 2 C C2 FEG . . . F 3 46.752 4.691 -42.728 1 51.91 ? C2 FEG 302 A 1 
HETATM 3 O O2 FEG . . . F 3 48.026 4.456 -42.277 1 50.13 ? O2 FEG 302 A 1 
HETATM 4 C C3 FEG . . . F 3 46.087 3.754 -43.64 1 52.4 ? C3 FEG 302 A 1 
HETATM 5 C C3M FEG . . . F 3 46.763 2.534 -44.131 1 64.92 ? C3M FEG 302 A 1 
HETATM 6 C C4 FEG . . . F 3 44.727 4.008 -44.074 1 57.65 ? C4 FEG 302 A 1 
HETATM 7 C C5 FEG . . . F 3 44.048 5.187 -43.578 1 53.93 ? C5 FEG 302 A 1 
HETATM 8 C C5M FEG . . . F 3 42.656 5.487 -44.025 1 59.56 ? C5M FEG 302 A 1 
HETATM 9 C C6 FEG . . . F 3 44.798 6.055 -42.676 1 48.76 ? C6 FEG 302 A 1 
HETATM 10 C C7 FEG . . . F 3 44.103 7.286 -42.184 1 54.06 ? C7 FEG 302 A 1 
HETATM 11 C C8 FEG . . . F 3 43.953 7.338 -40.689 1 48.86 ? C8 FEG 302 A 1 
HETATM 12 O O28 FEG . . . F 3 42.828 7.457 -40.169 1 47.68 ? O28 FEG 302 A 1 
HETATM 13 O O18 FEG . . . F 3 44.988 7.314 -40.007 1 52.28 ? O18 FEG 302 A 1 
HETATM 14 O O3P FEG . . . F 3 44.099 3.163 -44.914 1 63.97 ? O3P FEG 302 A 1 
HETATM 15 P P1 FEG . . . F 3 44.226 3.261 -46.527 1 64.22 ? P1 FEG 302 A 1 
HETATM 16 O O1P FEG . . . F 3 43.085 4.044 -47.099 1 59.09 ? O1P FEG 302 A 1 
HETATM 17 O O2P FEG . . . F 3 45.571 3.808 -46.882 1 53.33 ? O2P FEG 302 A 1 
HETATM 18 O O5S FEG . . . F 3 44.022 1.711 -46.988 1 67.27 ? O5S FEG 302 A 1 
HETATM 19 C C5S FEG . . . F 3 43.893 0.634 -46.044 1 72.32 ? C5S FEG 302 A 1 
HETATM 20 C C4S FEG . . . F 3 43.821 -0.729 -46.685 1 73.3 ? C4S FEG 302 A 1 
HETATM 21 C C3S FEG . . . F 3 44.726 -1.635 -45.897 1 67.85 ? C3S FEG 302 A 1 
HETATM 22 O O3S FEG . . . F 3 43.908 -2.633 -45.324 1 66.42 ? O3S FEG 302 A 1 
HETATM 23 C C2S FEG . . . F 3 45.591 -2.276 -46.955 1 67.02 ? C2S FEG 302 A 1 
HETATM 24 O O2S FEG . . . F 3 45.425 -3.689 -46.975 1 73.52 ? O2S FEG 302 A 1 
HETATM 25 C C1S FEG . . . F 3 45.158 -1.774 -48.308 1 66.44 ? C1S FEG 302 A 1 
HETATM 26 O O4S FEG . . . F 3 44.289 -0.7 -48.025 1 74.09 ? O4S FEG 302 A 1 
HETATM 27 N N9A FEG . . . F 3 46.309 -1.234 -49.034 1 68.51 ? N9A FEG 302 A 1 
HETATM 28 C C8A FEG . . . F 3 46.451 0.02 -49.516 1 59.86 ? C8A FEG 302 A 1 
HETATM 29 N N7A FEG . . . F 3 47.648 0.143 -50.067 1 56.64 ? N7A FEG 302 A 1 
HETATM 30 C C5A FEG . . . F 3 48.263 -1.025 -49.98 1 68.31 ? C5A FEG 302 A 1 
HETATM 31 C C4A FEG . . . F 3 47.398 -1.962 -49.292 1 70.51 ? C4A FEG 302 A 1 
HETATM 32 C C6A FEG . . . F 3 49.58 -1.496 -50.426 1 73.87 ? C6A FEG 302 A 1 
HETATM 33 O O6A FEG . . . F 3 50.245 -0.618 -51.003 1 69.03 ? O6A FEG 302 A 1 
HETATM 34 N N1A FEG . . . F 3 49.98 -2.764 -50.179 1 69.16 ? N1A FEG 302 A 1 
HETATM 35 C C2A FEG . . . F 3 49.156 -3.627 -49.526 1 72.54 ? C2A FEG 302 A 1 
HETATM 36 N N3A FEG . . . F 3 47.892 -3.241 -49.088 1 77.8 ? N3A FEG 302 A 1 
HETATM 37 N N2A FEG . . . F 3 49.607 -4.895 -49.31 1 79.21 ? N2A FEG 302 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           341 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           37 
#