data_3WB2 # _model_server_result.job_id 5kJiFOIoQ9nPQnc1D1TKIw _model_server_result.datetime_utc '2024-11-05 01:19:21' _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":"K","auth_seq_id":202}' # _entry.id 3WB2 # _exptl.entry_id 3WB2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.357 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine" _entity.pdbx_number_of_molecules 4 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 J N N ? 2 K 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 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 'C17 H21 N6 O9 P' _chem_comp.formula_weight 484.357 _chem_comp.id YGP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-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 CAB CAV YGP sing 393 n n OAD CAX YGP doub 394 n n CAV CAX YGP sing 395 n n CAV CAW YGP doub 396 n n CAX NAO YGP sing 397 n n OAF PBG YGP doub 398 n n OAR CAW YGP sing 399 n n OAR PBG YGP sing 400 n n CAW CAK YGP sing 401 n n C5' C4' YGP sing 402 n n C5' O5' YGP sing 403 n n PBG O5' YGP sing 404 n n PBG OAI YGP sing 405 n n NAO CAT YGP sing 406 n n C4' O4' YGP sing 407 n n C4' C3' YGP sing 408 n n CAK CAT YGP doub 409 n n O3' C3' YGP sing 410 n n CAT CAA YGP sing 411 n n O4' C1' YGP sing 412 n n C3' C2' YGP sing 413 n n O2' C2' YGP sing 414 n n C2' C1' YGP sing 415 n n C1' N9 YGP sing 416 n n C8 N9 YGP sing 417 n y C8 N7 YGP doub 418 n y N9 C4 YGP sing 419 n y N7 C5 YGP sing 420 n y C4 C5 YGP doub 421 n y C4 N3 YGP sing 422 n n C5 C6 YGP sing 423 n n N3 C2 YGP doub 424 n n C6 O6 YGP doub 425 n n C6 N1 YGP sing 426 n n C2 N1 YGP sing 427 n n C2 N2 YGP sing 428 n n N2 H1 YGP sing 429 n n N2 H2 YGP sing 430 n n N1 H3 YGP sing 431 n n C8 H4 YGP sing 432 n n C1' H5 YGP sing 433 n n C2' H6 YGP sing 434 n n O2' H7 YGP sing 435 n n C3' H8 YGP sing 436 n n O3' H9 YGP sing 437 n n C4' H10 YGP sing 438 n n C5' H11 YGP sing 439 n n C5' H12 YGP sing 440 n n OAI H13 YGP sing 441 n n CAK H14 YGP sing 442 n n CAA H16 YGP sing 443 n n CAA H17 YGP sing 444 n n CAA H18 YGP sing 445 n n CAB H19 YGP sing 446 n n CAB H20 YGP sing 447 n n CAB H21 YGP sing 448 n n NAO H15 YGP sing 449 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 C C2 YGP . . . K 2 20.421 -9.395 -27.197 1 67.12 ? C2 YGP 202 C 1 HETATM 2 N N2 YGP . . . K 2 20.563 -8.352 -28.023 1 61.18 ? N2 YGP 202 C 1 HETATM 3 C C4 YGP . . . K 2 20.459 -10.292 -25.013 1 61.59 ? C4 YGP 202 C 1 HETATM 4 C C5 YGP . . . K 2 20.161 -11.512 -25.481 1 63.01 ? C5 YGP 202 C 1 HETATM 5 C C6 YGP . . . K 2 19.98 -11.73 -26.795 1 64.15 ? C6 YGP 202 C 1 HETATM 6 O O6 YGP . . . K 2 19.715 -12.847 -27.219 1 72.77 ? O6 YGP 202 C 1 HETATM 7 N N1 YGP . . . K 2 20.099 -10.673 -27.708 1 66.58 ? N1 YGP 202 C 1 HETATM 8 N N3 YGP . . . K 2 20.586 -9.246 -25.862 1 63.22 ? N3 YGP 202 C 1 HETATM 9 N N7 YGP . . . K 2 20.09 -12.326 -24.442 1 56.7 ? N7 YGP 202 C 1 HETATM 10 C C8 YGP . . . K 2 20.343 -11.639 -23.34 1 60.65 ? C8 YGP 202 C 1 HETATM 11 N N9 YGP . . . K 2 20.583 -10.377 -23.685 1 62.3 ? N9 YGP 202 C 1 HETATM 12 C C1' YGP . . . K 2 20.902 -9.249 -22.695 1 58.68 ? C1' YGP 202 C 1 HETATM 13 O O4' YGP . . . K 2 21.252 -9.744 -21.347 1 56.15 ? O4' YGP 202 C 1 HETATM 14 C C2' YGP . . . K 2 19.644 -8.367 -22.506 1 55.73 ? C2' YGP 202 C 1 HETATM 15 O O2' YGP . . . K 2 20.006 -7.05 -22.083 1 63.51 ? O2' YGP 202 C 1 HETATM 16 C C3' YGP . . . K 2 18.934 -9.093 -21.4 1 56.45 ? C3' YGP 202 C 1 HETATM 17 O O3' YGP . . . K 2 17.95 -8.284 -20.81 1 54.47 ? O3' YGP 202 C 1 HETATM 18 C C4' YGP . . . K 2 20.117 -9.366 -20.45 1 58.13 ? C4' YGP 202 C 1 HETATM 19 C C5' YGP . . . K 2 19.734 -10.49 -19.505 1 52.78 ? C5' YGP 202 C 1 HETATM 20 O O5' YGP . . . K 2 19.373 -11.62 -20.305 1 47.95 ? O5' YGP 202 C 1 HETATM 21 P PBG YGP . . . K 2 18.764 -12.913 -19.589 1 50.6 ? PBG YGP 202 C 1 HETATM 22 O OAI YGP . . . K 2 18.206 -13.707 -20.825 1 49.44 ? OAI YGP 202 C 1 HETATM 23 O OAF YGP . . . K 2 17.651 -12.646 -18.624 1 45.85 ? OAF YGP 202 C 1 HETATM 24 O OAR YGP . . . K 2 20.055 -13.642 -18.871 1 43.28 ? OAR YGP 202 C 1 HETATM 25 C CAW YGP . . . K 2 21.362 -13.769 -19.284 1 45.22 ? CAW YGP 202 C 1 HETATM 26 C CAK YGP . . . K 2 21.66 -14.342 -20.54 1 46.14 ? CAK YGP 202 C 1 HETATM 27 C CAT YGP . . . K 2 23.009 -14.523 -20.919 1 47.23 ? CAT YGP 202 C 1 HETATM 28 C CAA YGP . . . K 2 23.378 -15.066 -22.189 1 48.95 ? CAA YGP 202 C 1 HETATM 29 N NAO YGP . . . K 2 24.034 -14.128 -20.039 1 40.9 ? NAO YGP 202 C 1 HETATM 30 C CAX YGP . . . K 2 23.768 -13.568 -18.776 1 43.98 ? CAX YGP 202 C 1 HETATM 31 O OAD YGP . . . K 2 24.744 -13.261 -18.07 1 40.06 ? OAD YGP 202 C 1 HETATM 32 C CAV YGP . . . K 2 22.41 -13.377 -18.371 1 45.39 ? CAV YGP 202 C 1 HETATM 33 C CAB YGP . . . K 2 22.143 -12.806 -17.082 1 38.78 ? CAB YGP 202 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 210 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 33 #