data_5V60 # _model_server_result.job_id '_tuAu2tvm_jDPwhvqZgYoQ' _model_server_result.datetime_utc '2024-11-14 19:27:01' _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 5v60 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5V60 # _exptl.entry_id 5V60 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 5V60 _cell.length_a 41.757 _cell.length_b 78.516 _cell.length_c 152.566 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V60 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,K _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 2 _struct_asym.id B _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 covale ? covale1 A C LEU 180 A LEU 184 1_555 A N TPO 181 A TPO 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C TPO 181 A TPO 185 1_555 A N GLU 182 A GLU 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C GLU 182 A GLU 186 1_555 A N PTR 183 A PTR 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C PTR 183 A PTR 187 1_555 A N VAL 184 A VAL 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD1 ASN 150 A ASN 154 1_555 I MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc2 A OD2 ASP 163 A ASP 167 1_555 I MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc3 A OD1 ASP 163 A ASP 167 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc4 A OD2 ASP 163 A ASP 167 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc5 B O2G ACP . A ACP 401 1_555 I MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc6 B O2A ACP . A ACP 401 1_555 I MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc7 B O1G ACP . A ACP 401 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc8 B O2G ACP . A ACP 401 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc9 B O2B ACP . A ACP 401 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc10 I MG MG . A MG 408 1_555 K O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc11 I MG MG . A MG 408 1_555 K O HOH . A HOH 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc12 J MG MG . A MG 409 1_555 K O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc13 J MG MG . A MG 409 1_555 K O HOH . A HOH 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 5V60 _atom_sites.fract_transf_matrix[1][1] 0.023948 _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] 0.012736 _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] 0.006555 _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 B 2 ACP A 1 401 1 ACP ACP . C 3 GOL A 1 402 1 GOL GOL . D 3 GOL A 1 403 2 GOL GOL . E 3 GOL A 1 404 3 GOL GOL . F 3 GOL A 1 405 4 GOL GOL . G 3 GOL A 1 406 5 GOL GOL . H 3 GOL A 1 407 6 GOL GOL . I 4 MG A 1 408 1 MG MG . J 4 MG A 1 409 2 MG MG . K 5 HOH A 1 501 168 HOH HOH . K 5 HOH A 2 502 173 HOH HOH . K 5 HOH A 3 503 162 HOH HOH . K 5 HOH A 4 504 123 HOH HOH . K 5 HOH A 5 505 118 HOH HOH . K 5 HOH A 6 506 29 HOH HOH . K 5 HOH A 7 507 164 HOH HOH . K 5 HOH A 8 508 172 HOH HOH . K 5 HOH A 9 509 128 HOH HOH . K 5 HOH A 10 510 15 HOH HOH . K 5 HOH A 11 511 12 HOH HOH . K 5 HOH A 12 512 13 HOH HOH . K 5 HOH A 13 513 174 HOH HOH . K 5 HOH A 14 514 42 HOH HOH . K 5 HOH A 15 515 132 HOH HOH . K 5 HOH A 16 516 17 HOH HOH . K 5 HOH A 17 517 49 HOH HOH . K 5 HOH A 18 518 142 HOH HOH . K 5 HOH A 19 519 129 HOH HOH . K 5 HOH A 20 520 130 HOH HOH . K 5 HOH A 21 521 122 HOH HOH . K 5 HOH A 22 522 24 HOH HOH . K 5 HOH A 23 523 8 HOH HOH . K 5 HOH A 24 524 10 HOH HOH . K 5 HOH A 25 525 131 HOH HOH . K 5 HOH A 26 526 45 HOH HOH . K 5 HOH A 27 527 149 HOH HOH . K 5 HOH A 28 528 65 HOH HOH . K 5 HOH A 29 529 59 HOH HOH . K 5 HOH A 30 530 14 HOH HOH . K 5 HOH A 31 531 146 HOH HOH . K 5 HOH A 32 532 126 HOH HOH . K 5 HOH A 33 533 145 HOH HOH . K 5 HOH A 34 534 22 HOH HOH . K 5 HOH A 35 535 18 HOH HOH . K 5 HOH A 36 536 166 HOH HOH . K 5 HOH A 37 537 156 HOH HOH . K 5 HOH A 38 538 160 HOH HOH . K 5 HOH A 39 539 51 HOH HOH . K 5 HOH A 40 540 27 HOH HOH . K 5 HOH A 41 541 66 HOH HOH . K 5 HOH A 42 542 30 HOH HOH . K 5 HOH A 43 543 139 HOH HOH . K 5 HOH A 44 544 127 HOH HOH . K 5 HOH A 45 545 16 HOH HOH . K 5 HOH A 46 546 140 HOH HOH . K 5 HOH A 47 547 136 HOH HOH . K 5 HOH A 48 548 144 HOH HOH . K 5 HOH A 49 549 58 HOH HOH . K 5 HOH A 50 550 167 HOH HOH . K 5 HOH A 51 551 137 HOH HOH . K 5 HOH A 52 552 170 HOH HOH . K 5 HOH A 53 553 2 HOH HOH . K 5 HOH A 54 554 81 HOH HOH . K 5 HOH A 55 555 158 HOH HOH . K 5 HOH A 56 556 157 HOH HOH . K 5 HOH A 57 557 135 HOH HOH . K 5 HOH A 58 558 150 HOH HOH . K 5 HOH A 59 559 92 HOH HOH . K 5 HOH A 60 560 161 HOH HOH . K 5 HOH A 61 561 35 HOH HOH . K 5 HOH A 62 562 124 HOH HOH . K 5 HOH A 63 563 125 HOH HOH . K 5 HOH A 64 564 4 HOH HOH . K 5 HOH A 65 565 171 HOH HOH . K 5 HOH A 66 566 133 HOH HOH . K 5 HOH A 67 567 120 HOH HOH . K 5 HOH A 68 568 6 HOH HOH . K 5 HOH A 69 569 121 HOH HOH . K 5 HOH A 70 570 119 HOH HOH . K 5 HOH A 71 571 159 HOH HOH . K 5 HOH A 72 572 90 HOH HOH . K 5 HOH A 73 573 165 HOH HOH . K 5 HOH A 74 574 163 HOH HOH . K 5 HOH A 75 575 155 HOH HOH . K 5 HOH A 76 576 28 HOH HOH . K 5 HOH A 77 577 134 HOH HOH . K 5 HOH A 78 578 138 HOH HOH . K 5 HOH A 79 579 154 HOH HOH . K 5 HOH A 80 580 141 HOH HOH . K 5 HOH A 81 581 148 HOH HOH . K 5 HOH A 82 582 143 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 PG ACP . . . B 2 13.206 12.017 19.541 1 58.06 ? PG ACP 401 A 1 HETATM 2 O O1G ACP . . . B 2 12.167 10.798 19.4 1 57.97 ? O1G ACP 401 A 1 HETATM 3 O O2G ACP . . . B 2 12.268 13.243 20.059 1 60.92 ? O2G ACP 401 A 1 HETATM 4 O O3G ACP . . . B 2 14.362 11.685 20.401 1 57.57 ? O3G ACP 401 A 1 HETATM 5 P PB ACP . . . B 2 12.476 12.382 16.769 1 49.88 ? PB ACP 401 A 1 HETATM 6 O O1B ACP . . . B 2 12.778 11.018 15.973 1 49.84 ? O1B ACP 401 A 1 HETATM 7 O O2B ACP . . . B 2 11.157 12.242 17.432 1 48.26 ? O2B ACP 401 A 1 HETATM 8 C C3B ACP . . . B 2 13.796 12.651 17.964 1 54.5 ? C3B ACP 401 A 1 HETATM 9 P PA ACP . . . B 2 11.892 15.102 16.091 1 43.03 ? PA ACP 401 A 1 HETATM 10 O O1A ACP . . . B 2 10.512 15.243 15.493 1 45.03 ? O1A ACP 401 A 1 HETATM 11 O O2A ACP . . . B 2 12.145 15.551 17.52 1 45.61 ? O2A ACP 401 A 1 HETATM 12 O O3A ACP . . . B 2 12.464 13.632 15.761 1 45.93 ? O3A ACP 401 A 1 HETATM 13 O O5' ACP . . . B 2 12.915 15.892 15.133 1 45.29 ? O5' ACP 401 A 1 HETATM 14 C C5' ACP . . . B 2 14.318 15.869 15.398 1 44.3 ? C5' ACP 401 A 1 HETATM 15 C C4' ACP . . . B 2 14.883 17.264 15.214 1 42.9 ? C4' ACP 401 A 1 HETATM 16 O O4' ACP . . . B 2 14.686 17.635 13.855 1 42.22 ? O4' ACP 401 A 1 HETATM 17 C C3' ACP . . . B 2 14.215 18.351 16.044 1 43.54 ? C3' ACP 401 A 1 HETATM 18 O O3' ACP . . . B 2 14.814 18.559 17.329 1 44.74 ? O3' ACP 401 A 1 HETATM 19 C C2' ACP . . . B 2 14.393 19.563 15.164 1 42.8 ? C2' ACP 401 A 1 HETATM 20 O O2' ACP . . . B 2 15.69 20.141 15.337 1 42.44 ? O2' ACP 401 A 1 HETATM 21 C C1' ACP . . . B 2 14.319 19.01 13.765 1 40.26 ? C1' ACP 401 A 1 HETATM 22 N N9 ACP . . . B 2 12.971 19.164 13.17 1 39.39 ? N9 ACP 401 A 1 HETATM 23 C C8 ACP . . . B 2 11.898 18.375 13.316 1 37.37 ? C8 ACP 401 A 1 HETATM 24 N N7 ACP . . . B 2 10.852 18.848 12.608 1 36.65 ? N7 ACP 401 A 1 HETATM 25 C C5 ACP . . . B 2 11.248 19.956 11.986 1 37.96 ? C5 ACP 401 A 1 HETATM 26 C C6 ACP . . . B 2 10.646 20.958 11.085 1 37.25 ? C6 ACP 401 A 1 HETATM 27 N N6 ACP . . . B 2 9.372 20.844 10.703 1 36.78 ? N6 ACP 401 A 1 HETATM 28 N N1 ACP . . . B 2 11.415 21.985 10.663 1 38.28 ? N1 ACP 401 A 1 HETATM 29 C C2 ACP . . . B 2 12.7 22.096 11.055 1 39.16 ? C2 ACP 401 A 1 HETATM 30 N N3 ACP . . . B 2 13.298 21.227 11.878 1 39.44 ? N3 ACP 401 A 1 HETATM 31 C C4 ACP . . . B 2 12.643 20.157 12.362 1 38.75 ? C4 ACP 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 385 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #