data_2GVZ # _model_server_result.job_id QpxrcBMet6NdGHP5oW1Qsw _model_server_result.datetime_utc '2024-11-23 07:13:00' _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 2gvz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":100}' # _entry.id 2GVZ # _exptl.entry_id 2GVZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 640.328 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-O-[2-(METHYLAMINO)BENZOYL]ADENOSINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)" _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 2GVZ _cell.length_a 116.8 _cell.length_b 132.1 _cell.length_c 69.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GVZ _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 ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 6 _struct_asym.id G _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 G O2A ONA . A ONA 100 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc2 G O1B ONA . A ONA 100 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc3 A OD2 ASP 41 A ASP 396 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc4 A O ILE 42 A ILE 397 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc5 A OD2 ASP 85 A ASP 440 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc6 C OG SER 54 C SER 54 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc7 C OG1 THR 204 C THR 204 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc8 J O3G GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc9 J O2G GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc10 J O2B GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _chem_comp.formula 'C18 H23 N6 O14 P3' _chem_comp.formula_weight 640.328 _chem_comp.id ONA _chem_comp.mon_nstd_flag . _chem_comp.name "3'-O-[2-(METHYLAMINO)BENZOYL]ADENOSINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'(3')-O-(N-METHYLANTHRANILOYL)-ADENOSINE 5'-TRIPHOSPHATE" # 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 CA7 NA1 ONA sing 377 n n CA7 HA71 ONA sing 378 n n CA7 HA72 ONA sing 379 n n CA7 HA73 ONA sing 380 n n NA1 CA6 ONA sing 381 n n NA1 HA1 ONA sing 382 n n CA6 CA5 ONA sing 383 n y CA6 CA1 ONA doub 384 n y CA5 CA4 ONA doub 385 n y CA5 HA5 ONA sing 386 n n CA4 CA3 ONA sing 387 n y CA4 HA4 ONA sing 388 n n CA3 CA2 ONA doub 389 n y CA3 HA3 ONA sing 390 n n CA2 CA1 ONA sing 391 n y CA2 HA2 ONA sing 392 n n CA1 CA ONA sing 393 n n CA OA ONA doub 394 n n CA O3' ONA sing 395 n n O3' C3' ONA sing 396 n n C3' C2' ONA sing 397 n n C3' C4' ONA sing 398 n n C3' H3' ONA sing 399 n n C2' O2' ONA sing 400 n n C2' C1' ONA sing 401 n n C2' H1 ONA sing 402 n n O2' H2' ONA sing 403 n n C4' C5' ONA sing 404 n n C4' O4' ONA sing 405 n n C4' H4' ONA sing 406 n n C5' O5' ONA sing 407 n n C5' "H5'1" ONA sing 408 n n C5' "H5'2" ONA sing 409 n n O5' PA ONA sing 410 n n PA O3A ONA doub 411 n n PA O2A ONA sing 412 n n PA O1A ONA sing 413 n n O2A H2A ONA sing 414 n n O1A PB ONA sing 415 n n PB O3B ONA doub 416 n n PB O2B ONA sing 417 n n PB O1B ONA sing 418 n n O2B H2B ONA sing 419 n n O1B PG ONA sing 420 n n PG O3G ONA doub 421 n n PG O1G ONA sing 422 n n PG O2G ONA sing 423 n n O1G H1G ONA sing 424 n n O2G H2G ONA sing 425 n n O4' C1' ONA sing 426 n n C1' N9 ONA sing 427 n n C1' H1' ONA sing 428 n n N9 C8 ONA sing 429 n y N9 C4 ONA sing 430 n y C8 N7 ONA doub 431 n y C8 H8 ONA sing 432 n n N7 C5 ONA sing 433 n y C5 C4 ONA sing 434 n y C5 C6 ONA doub 435 n y C4 N3 ONA doub 436 n y N3 C2 ONA sing 437 n y C2 N1 ONA doub 438 n y C2 H2 ONA sing 439 n n N1 C6 ONA sing 440 n y C6 N6 ONA sing 441 n n N6 HN61 ONA sing 442 n n N6 HN62 ONA sing 443 n n # _atom_sites.entry_id 2GVZ _atom_sites.fract_transf_matrix[1][1] 0.008562 _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] 0.00757 _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] 0.014368 _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 D 4 MN A 1 581 502 MN MN . E 4 MN A 1 582 503 MN MN . F 5 FKP A 1 1 1 FKP FKP . G 6 ONA A 1 100 100 ONA ONA . H 4 MN C 1 396 396 MN MN . I 7 CL C 1 397 397 CL CL . J 8 GSP C 1 395 395 GSP GSP . # 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 CA7 ONA . . . G 6 66.475 -13.831 54.267 1 89.6 ? CA7 ONA 100 A 1 HETATM 2 N NA1 ONA . . . G 6 65.09 -14.26 54.589 1 89.04 ? NA1 ONA 100 A 1 HETATM 3 C CA6 ONA . . . G 6 64.628 -15.497 54.949 1 88.69 ? CA6 ONA 100 A 1 HETATM 4 C CA5 ONA . . . G 6 65.633 -16.721 55.068 1 87.63 ? CA5 ONA 100 A 1 HETATM 5 C CA4 ONA . . . G 6 65.005 -18.167 55.288 1 86.27 ? CA4 ONA 100 A 1 HETATM 6 C CA3 ONA . . . G 6 63.51 -18.206 55.756 1 84.54 ? CA3 ONA 100 A 1 HETATM 7 C CA2 ONA . . . G 6 62.708 -16.875 55.575 1 85.14 ? CA2 ONA 100 A 1 HETATM 8 C CA1 ONA . . . G 6 63.225 -15.628 55.204 1 89.13 ? CA1 ONA 100 A 1 HETATM 9 C CA ONA . . . G 6 62.201 -14.479 55.109 1 92.58 ? CA ONA 100 A 1 HETATM 10 O OA ONA . . . G 6 62.203 -13.399 56.061 1 97.52 ? OA ONA 100 A 1 HETATM 11 O O3' ONA . . . G 6 61.307 -14.582 54.078 1 94.3 ? O3' ONA 100 A 1 HETATM 12 C C3' ONA . . . G 6 60.313 -13.554 53.683 1 99.49 ? C3' ONA 100 A 1 HETATM 13 C C2' ONA . . . G 6 59.556 -14.096 52.481 1 93.39 ? C2' ONA 100 A 1 HETATM 14 O O2' ONA . . . G 6 60.447 -14.71 51.547 1 95.27 ? O2' ONA 100 A 1 HETATM 15 C C4' ONA . . . G 6 59.171 -13.413 54.686 1 100.38 ? C4' ONA 100 A 1 HETATM 16 C C5' ONA . . . G 6 58.405 -12.048 54.874 1 98.14 ? C5' ONA 100 A 1 HETATM 17 O O5' ONA . . . G 6 58.783 -10.919 54.395 1 87.63 ? O5' ONA 100 A 1 HETATM 18 P PA ONA . . . G 6 57.536 -9.879 54.544 1 82.96 ? PA ONA 100 A 1 HETATM 19 O O3A ONA . . . G 6 58.055 -8.788 53.543 1 82.6 ? O3A ONA 100 A 1 HETATM 20 O O2A ONA . . . G 6 56.228 -10.484 54.233 1 83.52 ? O2A ONA 100 A 1 HETATM 21 O O1A ONA . . . G 6 57.773 -9.635 56.079 1 77.2 ? O1A ONA 100 A 1 HETATM 22 P PB ONA . . . G 6 56.789 -8.96 57.077 1 74.13 ? PB ONA 100 A 1 HETATM 23 O O3B ONA . . . G 6 55.616 -10.068 56.929 1 63.98 ? O3B ONA 100 A 1 HETATM 24 O O2B ONA . . . G 6 56.128 -7.593 56.89 1 65.06 ? O2B ONA 100 A 1 HETATM 25 O O1B ONA . . . G 6 57.688 -9.353 58.265 1 75.72 ? O1B ONA 100 A 1 HETATM 26 P PG ONA . . . G 6 58.456 -8.158 58.876 1 53.57 ? PG ONA 100 A 1 HETATM 27 O O3G ONA . . . G 6 58.949 -7.155 57.684 1 65.7 ? O3G ONA 100 A 1 HETATM 28 O O1G ONA . . . G 6 57.355 -7.464 59.843 1 61.47 ? O1G ONA 100 A 1 HETATM 29 O O2G ONA . . . G 6 59.63 -8.654 59.639 1 56.24 ? O2G ONA 100 A 1 HETATM 30 O O4' ONA . . . G 6 58.163 -14.444 54.343 1 82.92 ? O4' ONA 100 A 1 HETATM 31 C C1' ONA . . . G 6 58.619 -15.115 53.132 1 86.23 ? C1' ONA 100 A 1 HETATM 32 N N9 ONA . . . G 6 57.475 -15.55 52.253 1 90.32 ? N9 ONA 100 A 1 HETATM 33 C C8 ONA . . . G 6 57.203 -16.836 51.936 1 91.24 ? C8 ONA 100 A 1 HETATM 34 N N7 ONA . . . G 6 56.14 -16.894 51.13 1 92.67 ? N7 ONA 100 A 1 HETATM 35 C C5 ONA . . . G 6 55.723 -15.653 50.925 1 94.6 ? C5 ONA 100 A 1 HETATM 36 C C4 ONA . . . G 6 56.574 -14.778 51.644 1 92.69 ? C4 ONA 100 A 1 HETATM 37 N N3 ONA . . . G 6 56.395 -13.419 51.625 1 94.17 ? N3 ONA 100 A 1 HETATM 38 C C2 ONA . . . G 6 55.41 -12.808 50.933 1 96.39 ? C2 ONA 100 A 1 HETATM 39 N N1 ONA . . . G 6 54.516 -13.624 50.183 1 97.33 ? N1 ONA 100 A 1 HETATM 40 C C6 ONA . . . G 6 54.675 -15.06 50.177 1 96.54 ? C6 ONA 100 A 1 HETATM 41 N N6 ONA . . . G 6 53.836 -15.819 49.47 1 97.98 ? N6 ONA 100 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 41 #