data_4XC0 # _model_server_result.job_id 5K0lo4eET9eAUzpjvEIX5Q _model_server_result.datetime_utc '2024-11-16 15:49:26' _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 4xc0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4XC0 # _exptl.entry_id 4XC0 _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 107.54 _cell.angle_gamma 90 _cell.entry_id 4XC0 _cell.length_a 41.68 _cell.length_b 46.08 _cell.length_c 59.33 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XC0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 metalc ? metalc1 A OD1 ASN 76 A ASN 40 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc2 B O1G ACP . A ACP 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc3 B O1B ACP . A ACP 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc4 B O2A ACP . A ACP 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc5 C MG MG . A MG 302 1_555 E O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 C MG MG . A MG 302 1_555 E O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? # _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 4XC0 _atom_sites.fract_transf_matrix[1][1] 0.023992 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007583 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021701 _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] 0.017677 _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 1 301 1 ACP ACP . C 3 MG A 1 302 1 MG MG . D 4 PEG A 1 303 1 PEG PEG . E 5 HOH A 1 401 133 HOH HOH . E 5 HOH A 2 402 89 HOH HOH . E 5 HOH A 3 403 103 HOH HOH . E 5 HOH A 4 404 36 HOH HOH . E 5 HOH A 5 405 141 HOH HOH . E 5 HOH A 6 406 65 HOH HOH . E 5 HOH A 7 407 50 HOH HOH . E 5 HOH A 8 408 83 HOH HOH . E 5 HOH A 9 409 93 HOH HOH . E 5 HOH A 10 410 16 HOH HOH . E 5 HOH A 11 411 147 HOH HOH . E 5 HOH A 12 412 95 HOH HOH . E 5 HOH A 13 413 73 HOH HOH . E 5 HOH A 14 414 30 HOH HOH . E 5 HOH A 15 415 45 HOH HOH . E 5 HOH A 16 416 146 HOH HOH . E 5 HOH A 17 417 120 HOH HOH . E 5 HOH A 18 418 6 HOH HOH . E 5 HOH A 19 419 149 HOH HOH . E 5 HOH A 20 420 106 HOH HOH . E 5 HOH A 21 421 64 HOH HOH . E 5 HOH A 22 422 157 HOH HOH . E 5 HOH A 23 423 5 HOH HOH . E 5 HOH A 24 424 88 HOH HOH . E 5 HOH A 25 425 27 HOH HOH . E 5 HOH A 26 426 67 HOH HOH . E 5 HOH A 27 427 31 HOH HOH . E 5 HOH A 28 428 82 HOH HOH . E 5 HOH A 29 429 111 HOH HOH . E 5 HOH A 30 430 116 HOH HOH . E 5 HOH A 31 431 78 HOH HOH . E 5 HOH A 32 432 135 HOH HOH . E 5 HOH A 33 433 118 HOH HOH . E 5 HOH A 34 434 105 HOH HOH . E 5 HOH A 35 435 107 HOH HOH . E 5 HOH A 36 436 152 HOH HOH . E 5 HOH A 37 437 122 HOH HOH . E 5 HOH A 38 438 153 HOH HOH . E 5 HOH A 39 439 134 HOH HOH . E 5 HOH A 40 440 3 HOH HOH . E 5 HOH A 41 441 4 HOH HOH . E 5 HOH A 42 442 7 HOH HOH . E 5 HOH A 43 443 11 HOH HOH . E 5 HOH A 44 444 13 HOH HOH . E 5 HOH A 45 445 14 HOH HOH . E 5 HOH A 46 446 15 HOH HOH . E 5 HOH A 47 447 17 HOH HOH . E 5 HOH A 48 448 18 HOH HOH . E 5 HOH A 49 449 19 HOH HOH . E 5 HOH A 50 450 22 HOH HOH . E 5 HOH A 51 451 23 HOH HOH . E 5 HOH A 52 452 24 HOH HOH . E 5 HOH A 53 453 25 HOH HOH . E 5 HOH A 54 454 26 HOH HOH . E 5 HOH A 55 455 28 HOH HOH . E 5 HOH A 56 456 29 HOH HOH . E 5 HOH A 57 457 33 HOH HOH . E 5 HOH A 58 458 34 HOH HOH . E 5 HOH A 59 459 35 HOH HOH . E 5 HOH A 60 460 37 HOH HOH . E 5 HOH A 61 461 38 HOH HOH . E 5 HOH A 62 462 40 HOH HOH . E 5 HOH A 63 463 41 HOH HOH . E 5 HOH A 64 464 42 HOH HOH . E 5 HOH A 65 465 43 HOH HOH . E 5 HOH A 66 466 44 HOH HOH . E 5 HOH A 67 467 51 HOH HOH . E 5 HOH A 68 468 53 HOH HOH . E 5 HOH A 69 469 54 HOH HOH . E 5 HOH A 70 470 55 HOH HOH . E 5 HOH A 71 471 56 HOH HOH . E 5 HOH A 72 472 57 HOH HOH . E 5 HOH A 73 473 59 HOH HOH . E 5 HOH A 74 474 60 HOH HOH . E 5 HOH A 75 475 62 HOH HOH . E 5 HOH A 76 476 66 HOH HOH . E 5 HOH A 77 477 68 HOH HOH . E 5 HOH A 78 478 69 HOH HOH . E 5 HOH A 79 479 70 HOH HOH . E 5 HOH A 80 480 71 HOH HOH . E 5 HOH A 81 481 72 HOH HOH . E 5 HOH A 82 482 74 HOH HOH . E 5 HOH A 83 483 75 HOH HOH . E 5 HOH A 84 484 76 HOH HOH . E 5 HOH A 85 485 79 HOH HOH . E 5 HOH A 86 486 80 HOH HOH . E 5 HOH A 87 487 81 HOH HOH . E 5 HOH A 88 488 84 HOH HOH . E 5 HOH A 89 489 86 HOH HOH . E 5 HOH A 90 490 90 HOH HOH . E 5 HOH A 91 491 91 HOH HOH . E 5 HOH A 92 492 94 HOH HOH . E 5 HOH A 93 493 97 HOH HOH . E 5 HOH A 94 494 98 HOH HOH . E 5 HOH A 95 495 100 HOH HOH . E 5 HOH A 96 496 101 HOH HOH . E 5 HOH A 97 497 104 HOH HOH . E 5 HOH A 98 498 108 HOH HOH . E 5 HOH A 99 499 109 HOH HOH . E 5 HOH A 100 500 110 HOH HOH . E 5 HOH A 101 501 113 HOH HOH . E 5 HOH A 102 502 115 HOH HOH . E 5 HOH A 103 503 117 HOH HOH . E 5 HOH A 104 504 119 HOH HOH . E 5 HOH A 105 505 124 HOH HOH . E 5 HOH A 106 506 125 HOH HOH . E 5 HOH A 107 507 126 HOH HOH . E 5 HOH A 108 508 127 HOH HOH . E 5 HOH A 109 509 128 HOH HOH . E 5 HOH A 110 510 129 HOH HOH . E 5 HOH A 111 511 130 HOH HOH . E 5 HOH A 112 512 132 HOH HOH . E 5 HOH A 113 513 137 HOH HOH . E 5 HOH A 114 514 138 HOH HOH . E 5 HOH A 115 515 139 HOH HOH . E 5 HOH A 116 516 142 HOH HOH . E 5 HOH A 117 517 143 HOH HOH . E 5 HOH A 118 518 144 HOH HOH . E 5 HOH A 119 519 145 HOH HOH . E 5 HOH A 120 520 150 HOH HOH . E 5 HOH A 121 521 151 HOH HOH . E 5 HOH A 122 522 154 HOH HOH . E 5 HOH A 123 523 155 HOH HOH . E 5 HOH A 124 524 156 HOH HOH . E 5 HOH A 125 525 158 HOH HOH . E 5 HOH A 126 526 159 HOH HOH . E 5 HOH A 127 527 1 HOH HOH . E 5 HOH A 128 528 2 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 19.859 11.527 81.042 1 21.58 ? PG ACP 301 A 1 HETATM 2 O O1G ACP . . . B 2 20.501 10.912 79.832 1 20.78 ? O1G ACP 301 A 1 HETATM 3 O O2G ACP . . . B 2 20.164 10.76 82.307 1 23.02 ? O2G ACP 301 A 1 HETATM 4 O O3G ACP . . . B 2 20.114 12.997 81.179 1 19.97 ? O3G ACP 301 A 1 HETATM 5 P PB ACP . . . B 2 17.481 11.139 79.194 1 18.51 ? PB ACP 301 A 1 HETATM 6 O O1B ACP . . . B 2 18.146 9.956 78.539 1 17.52 ? O1B ACP 301 A 1 HETATM 7 O O2B ACP . . . B 2 15.973 11.142 79.229 1 19.28 ? O2B ACP 301 A 1 HETATM 8 C C3B ACP . . . B 2 18.061 11.283 80.907 1 20.07 ? C3B ACP 301 A 1 HETATM 9 P PA ACP . . . B 2 18.791 12.681 77.15 1 17.92 ? PA ACP 301 A 1 HETATM 10 O O1A ACP . . . B 2 19.103 14.148 77.06 1 15.81 ? O1A ACP 301 A 1 HETATM 11 O O2A ACP . . . B 2 19.907 11.655 77.123 1 16.77 ? O2A ACP 301 A 1 HETATM 12 O O3A ACP . . . B 2 17.907 12.518 78.493 1 17.07 ? O3A ACP 301 A 1 HETATM 13 O O5' ACP . . . B 2 17.756 12.299 75.986 1 16.29 ? O5' ACP 301 A 1 HETATM 14 C C5' ACP . . . B 2 16.6 13.137 75.838 1 17.67 ? C5' ACP 301 A 1 HETATM 15 C C4' ACP . . . B 2 15.429 12.317 75.318 1 16.46 ? C4' ACP 301 A 1 HETATM 16 O O4' ACP . . . B 2 15.619 12.127 73.918 1 16.95 ? O4' ACP 301 A 1 HETATM 17 C C3' ACP . . . B 2 15.31 10.923 75.917 1 18.45 ? C3' ACP 301 A 1 HETATM 18 O O3' ACP . . . B 2 14.478 10.936 77.079 1 17.44 ? O3' ACP 301 A 1 HETATM 19 C C2' ACP . . . B 2 14.689 10.118 74.801 1 18.08 ? C2' ACP 301 A 1 HETATM 20 O O2' ACP . . . B 2 13.265 10.278 74.83 1 20.39 ? O2' ACP 301 A 1 HETATM 21 C C1' ACP . . . B 2 15.213 10.808 73.553 1 16.84 ? C1' ACP 301 A 1 HETATM 22 N N9 ACP . . . B 2 16.326 10.019 72.962 1 17.05 ? N9 ACP 301 A 1 HETATM 23 C C8 ACP . . . B 2 17.64 10.315 72.982 1 17.2 ? C8 ACP 301 A 1 HETATM 24 N N7 ACP . . . B 2 18.365 9.373 72.32 1 16.16 ? N7 ACP 301 A 1 HETATM 25 C C5 ACP . . . B 2 17.494 8.441 71.881 1 16.24 ? C5 ACP 301 A 1 HETATM 26 C C6 ACP . . . B 2 17.561 7.18 71.117 1 15.69 ? C6 ACP 301 A 1 HETATM 27 N N6 ACP . . . B 2 18.754 6.689 70.683 1 16.43 ? N6 ACP 301 A 1 HETATM 28 N N1 ACP . . . B 2 16.399 6.523 70.866 1 15.8 ? N1 ACP 301 A 1 HETATM 29 C C2 ACP . . . B 2 15.199 6.979 71.286 1 16.16 ? C2 ACP 301 A 1 HETATM 30 N N3 ACP . . . B 2 15.066 8.116 71.978 1 15.53 ? N3 ACP 301 A 1 HETATM 31 C C4 ACP . . . B 2 16.151 8.877 72.297 1 16.27 ? C4 ACP 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 31 #