data_3WB2
#
_model_server_result.job_id            k7ZN9PmM7dHEKghfLFtMDA 
_model_server_result.datetime_utc      '2024-11-05 01:15:01' 
_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          3wb2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":204}' 
#
_entry.id    3WB2 
#
_exptl.entry_id    3WB2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            3WB2 
_cell.length_a            115.01 
_cell.length_b            97.37 
_cell.length_c            63.54 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3WB2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_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 
_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    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             H 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OE1 GLU 160 A GLU 160 1_555 I MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc2 A OE2 GLU 160 A GLU 160 1_555 I MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? 
metalc ? metalc3 G MG MG . A MG 203 1_555 H O3B GDP . A GDP 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc4 G MG MG . A MG 203 1_555 H O1A GDP . A GDP 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc5 G MG MG . A MG 203 1_555 L O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc6 G MG MG . A MG 203 1_555 L O HOH . A HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc7 G MG MG . A MG 203 1_555 L O HOH . A HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? 
metalc ? metalc8 G MG MG . A MG 203 1_555 L O HOH . A HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
metalc ? metalc9 I MG MG . A MG 205 1_555 L O HOH . A HOH 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? 
metalc ? metalc10 I MG MG . A MG 205 1_555 L O HOH . A HOH 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
#
_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                     3WB2 
_atom_sites.fract_transf_matrix[1][1]    0.008695 
_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]    0.01027 
_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]    0.015738 
_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 YGP A 1 201 1 YGP GPY . 
F 2 YGP A 1 202 2 YGP GPY . 
G 3 MG A 1 203 1 MG MG . 
H 4 GDP A 1 204 1 GDP GDP . 
I 3 MG A 1 205 1 MG MG . 
J 2 YGP C 1 201 3 YGP GPY . 
K 2 YGP C 1 202 4 YGP GPY . 
L 5 HOH A 1 301 7 HOH HOH . 
L 5 HOH A 2 302 12 HOH HOH . 
L 5 HOH A 3 303 13 HOH HOH . 
L 5 HOH A 4 304 14 HOH HOH . 
L 5 HOH A 5 305 23 HOH HOH . 
L 5 HOH A 6 306 24 HOH HOH . 
L 5 HOH A 7 307 25 HOH HOH . 
L 5 HOH A 8 308 27 HOH HOH . 
L 5 HOH A 9 309 28 HOH HOH . 
L 5 HOH A 10 310 30 HOH HOH . 
L 5 HOH A 11 311 38 HOH HOH . 
L 5 HOH A 12 312 41 HOH HOH . 
L 5 HOH A 13 313 42 HOH HOH . 
L 5 HOH A 14 314 50 HOH HOH . 
L 5 HOH A 15 315 56 HOH HOH . 
L 5 HOH A 16 316 62 HOH HOH . 
L 5 HOH A 17 317 74 HOH HOH . 
L 5 HOH A 18 318 76 HOH HOH . 
L 5 HOH A 19 319 79 HOH HOH . 
L 5 HOH A 20 320 84 HOH HOH . 
L 5 HOH A 21 321 85 HOH HOH . 
L 5 HOH A 22 322 88 HOH HOH . 
L 5 HOH A 23 323 90 HOH HOH . 
L 5 HOH A 24 324 91 HOH HOH . 
L 5 HOH A 25 325 101 HOH HOH . 
L 5 HOH A 26 326 102 HOH HOH . 
L 5 HOH A 27 327 103 HOH HOH . 
L 5 HOH A 28 328 104 HOH HOH . 
L 5 HOH A 29 329 105 HOH HOH . 
L 5 HOH A 30 330 106 HOH HOH . 
L 5 HOH A 31 331 115 HOH HOH . 
L 5 HOH A 32 332 116 HOH HOH . 
L 5 HOH A 33 333 117 HOH HOH . 
L 5 HOH A 34 334 118 HOH HOH . 
L 5 HOH A 35 335 119 HOH HOH . 
L 5 HOH A 36 336 120 HOH HOH . 
L 5 HOH A 37 337 121 HOH HOH . 
L 5 HOH A 38 338 122 HOH HOH . 
L 5 HOH A 39 339 123 HOH HOH . 
L 5 HOH A 40 340 124 HOH HOH . 
L 5 HOH A 41 341 135 HOH HOH . 
L 5 HOH A 42 342 136 HOH HOH . 
M 5 HOH B 1 201 1 HOH HOH . 
M 5 HOH B 2 202 2 HOH HOH . 
M 5 HOH B 3 203 3 HOH HOH . 
M 5 HOH B 4 204 6 HOH HOH . 
M 5 HOH B 5 205 8 HOH HOH . 
M 5 HOH B 6 206 10 HOH HOH . 
M 5 HOH B 7 207 11 HOH HOH . 
M 5 HOH B 8 208 15 HOH HOH . 
M 5 HOH B 9 209 18 HOH HOH . 
M 5 HOH B 10 210 20 HOH HOH . 
M 5 HOH B 11 211 21 HOH HOH . 
M 5 HOH B 12 212 26 HOH HOH . 
M 5 HOH B 13 213 29 HOH HOH . 
M 5 HOH B 14 214 33 HOH HOH . 
M 5 HOH B 15 215 34 HOH HOH . 
M 5 HOH B 16 216 35 HOH HOH . 
M 5 HOH B 17 217 36 HOH HOH . 
M 5 HOH B 18 218 39 HOH HOH . 
M 5 HOH B 19 219 44 HOH HOH . 
M 5 HOH B 20 220 49 HOH HOH . 
M 5 HOH B 21 221 54 HOH HOH . 
M 5 HOH B 22 222 55 HOH HOH . 
M 5 HOH B 23 223 58 HOH HOH . 
M 5 HOH B 24 224 60 HOH HOH . 
M 5 HOH B 25 225 64 HOH HOH . 
M 5 HOH B 26 226 72 HOH HOH . 
M 5 HOH B 27 227 73 HOH HOH . 
M 5 HOH B 28 228 75 HOH HOH . 
M 5 HOH B 29 229 77 HOH HOH . 
M 5 HOH B 30 230 80 HOH HOH . 
M 5 HOH B 31 231 81 HOH HOH . 
M 5 HOH B 32 232 82 HOH HOH . 
M 5 HOH B 33 233 92 HOH HOH . 
M 5 HOH B 34 234 93 HOH HOH . 
M 5 HOH B 35 235 95 HOH HOH . 
M 5 HOH B 36 236 107 HOH HOH . 
M 5 HOH B 37 237 108 HOH HOH . 
M 5 HOH B 38 238 114 HOH HOH . 
M 5 HOH B 39 239 125 HOH HOH . 
M 5 HOH B 40 240 126 HOH HOH . 
M 5 HOH B 41 241 127 HOH HOH . 
M 5 HOH B 42 242 128 HOH HOH . 
M 5 HOH B 43 243 133 HOH HOH . 
N 5 HOH C 1 301 4 HOH HOH . 
N 5 HOH C 2 302 5 HOH HOH . 
N 5 HOH C 3 303 16 HOH HOH . 
N 5 HOH C 4 304 22 HOH HOH . 
N 5 HOH C 5 305 31 HOH HOH . 
N 5 HOH C 6 306 32 HOH HOH . 
N 5 HOH C 7 307 37 HOH HOH . 
N 5 HOH C 8 308 45 HOH HOH . 
N 5 HOH C 9 309 46 HOH HOH . 
N 5 HOH C 10 310 47 HOH HOH . 
N 5 HOH C 11 311 52 HOH HOH . 
N 5 HOH C 12 312 53 HOH HOH . 
N 5 HOH C 13 313 66 HOH HOH . 
N 5 HOH C 14 314 68 HOH HOH . 
N 5 HOH C 15 315 70 HOH HOH . 
N 5 HOH C 16 316 78 HOH HOH . 
N 5 HOH C 17 317 83 HOH HOH . 
N 5 HOH C 18 318 87 HOH HOH . 
N 5 HOH C 19 319 89 HOH HOH . 
N 5 HOH C 20 320 97 HOH HOH . 
N 5 HOH C 21 321 109 HOH HOH . 
N 5 HOH C 22 322 110 HOH HOH . 
N 5 HOH C 23 323 111 HOH HOH . 
N 5 HOH C 24 324 112 HOH HOH . 
N 5 HOH C 25 325 129 HOH HOH . 
N 5 HOH C 26 326 130 HOH HOH . 
N 5 HOH C 27 327 131 HOH HOH . 
N 5 HOH C 28 328 134 HOH HOH . 
O 5 HOH D 1 201 9 HOH HOH . 
O 5 HOH D 2 202 17 HOH HOH . 
O 5 HOH D 3 203 19 HOH HOH . 
O 5 HOH D 4 204 40 HOH HOH . 
O 5 HOH D 5 205 48 HOH HOH . 
O 5 HOH D 6 206 51 HOH HOH . 
O 5 HOH D 7 207 57 HOH HOH . 
O 5 HOH D 8 208 59 HOH HOH . 
O 5 HOH D 9 209 61 HOH HOH . 
O 5 HOH D 10 210 63 HOH HOH . 
O 5 HOH D 11 211 65 HOH HOH . 
O 5 HOH D 12 212 67 HOH HOH . 
O 5 HOH D 13 213 69 HOH HOH . 
O 5 HOH D 14 214 71 HOH HOH . 
O 5 HOH D 15 215 86 HOH HOH . 
O 5 HOH D 16 216 94 HOH HOH . 
O 5 HOH D 17 217 96 HOH HOH . 
O 5 HOH D 18 218 98 HOH HOH . 
O 5 HOH D 19 219 99 HOH HOH . 
O 5 HOH D 20 220 100 HOH HOH . 
O 5 HOH D 21 221 113 HOH HOH . 
O 5 HOH D 22 222 132 HOH HOH . 
O 5 HOH D 23 223 137 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 . . . H 4 24.437 -14.238 6.101 1 45.36 ? PB GDP 204 A 1 
HETATM 2 O O1B GDP . . . H 4 25.528 -13.536 5.294 1 39.29 ? O1B GDP 204 A 1 
HETATM 3 O O2B GDP . . . H 4 24.872 -15.437 6.927 1 36.37 ? O2B GDP 204 A 1 
HETATM 4 O O3B GDP . . . H 4 23.144 -14.484 5.309 1 45.04 ? O3B GDP 204 A 1 
HETATM 5 O O3A GDP . . . H 4 24.137 -13.132 7.258 1 42.6 ? O3A GDP 204 A 1 
HETATM 6 P PA GDP . . . H 4 22.721 -12.798 7.99 1 41.29 ? PA GDP 204 A 1 
HETATM 7 O O1A GDP . . . H 4 21.621 -12.647 6.956 1 39.49 ? O1A GDP 204 A 1 
HETATM 8 O O2A GDP . . . H 4 22.519 -13.648 9.251 1 42.6 ? O2A GDP 204 A 1 
HETATM 9 O O5' GDP . . . H 4 23.093 -11.315 8.492 1 44.45 ? O5' GDP 204 A 1 
HETATM 10 C C5' GDP . . . H 4 23.065 -10.213 7.563 1 47 ? C5' GDP 204 A 1 
HETATM 11 C C4' GDP . . . H 4 23.007 -8.838 8.238 1 48.22 ? C4' GDP 204 A 1 
HETATM 12 O O4' GDP . . . H 4 21.63 -8.494 8.492 1 43.3 ? O4' GDP 204 A 1 
HETATM 13 C C3' GDP . . . H 4 23.738 -8.702 9.599 1 49.23 ? C3' GDP 204 A 1 
HETATM 14 O O3' GDP . . . H 4 25.181 -8.594 9.571 1 44.71 ? O3' GDP 204 A 1 
HETATM 15 C C2' GDP . . . H 4 22.999 -7.527 10.21 1 46.76 ? C2' GDP 204 A 1 
HETATM 16 O O2' GDP . . . H 4 23.517 -6.287 9.735 1 50.71 ? O2' GDP 204 A 1 
HETATM 17 C C1' GDP . . . H 4 21.569 -7.668 9.663 1 52.81 ? C1' GDP 204 A 1 
HETATM 18 N N9 GDP . . . H 4 20.82 -8.317 10.761 1 57.68 ? N9 GDP 204 A 1 
HETATM 19 C C8 GDP . . . H 4 20.598 -9.647 10.917 1 61.74 ? C8 GDP 204 A 1 
HETATM 20 N N7 GDP . . . H 4 19.928 -9.915 12.067 1 62.55 ? N7 GDP 204 A 1 
HETATM 21 C C5 GDP . . . H 4 19.731 -8.714 12.683 1 70.76 ? C5 GDP 204 A 1 
HETATM 22 C C6 GDP . . . H 4 19.074 -8.232 13.94 1 70.85 ? C6 GDP 204 A 1 
HETATM 23 O O6 GDP . . . H 4 18.521 -9.027 14.736 1 63.78 ? O6 GDP 204 A 1 
HETATM 24 N N1 GDP . . . H 4 19.082 -6.907 14.189 1 76.08 ? N1 GDP 204 A 1 
HETATM 25 C C2 GDP . . . H 4 19.653 -6.001 13.36 1 72.02 ? C2 GDP 204 A 1 
HETATM 26 N N2 GDP . . . H 4 19.597 -4.694 13.721 1 68.37 ? N2 GDP 204 A 1 
HETATM 27 N N3 GDP . . . H 4 20.271 -6.358 12.194 1 64.44 ? N3 GDP 204 A 1 
HETATM 28 C C4 GDP . . . H 4 20.328 -7.666 11.815 1 64.19 ? C4 GDP 204 A 1 
#
_model_server_stats.io_time_ms              32 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           370 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#