data_6E2U # _model_server_result.job_id bOanGSxiAPqr_QFHCxWt2w _model_server_result.datetime_utc '2024-10-19 00:52:15' _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 6e2u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 6E2U # _exptl.entry_id 6E2U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _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 6E2U _cell.length_a 80.037 _cell.length_b 97.036 _cell.length_c 46.018 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6E2U _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 OG SER 130 A SER 106 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc2 B O1A DP6 . A DP6 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc3 C O2G ACP . A ACP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc4 C O2B ACP . A ACP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc5 C O2A ACP . A ACP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? # _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 6E2U _atom_sites.fract_transf_matrix[1][1] 0.012494 _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] 0.010305 _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] 0.021731 _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 DP6 A 1 401 401 DP6 DP6 . C 3 ACP A 1 402 402 ACP ACP . D 4 MG A 1 403 403 MG MG . E 5 HOH A 1 501 501 HOH HOH . E 5 HOH A 2 502 502 HOH HOH . E 5 HOH A 3 503 503 HOH HOH . E 5 HOH A 4 504 504 HOH HOH . E 5 HOH A 5 505 505 HOH HOH . E 5 HOH A 6 506 506 HOH HOH . E 5 HOH A 7 507 507 HOH HOH . E 5 HOH A 8 508 508 HOH HOH . E 5 HOH A 9 509 509 HOH HOH . E 5 HOH A 10 510 510 HOH HOH . E 5 HOH A 11 511 511 HOH HOH . E 5 HOH A 12 512 512 HOH HOH . E 5 HOH A 13 513 513 HOH HOH . E 5 HOH A 14 514 514 HOH HOH . E 5 HOH A 15 515 515 HOH HOH . E 5 HOH A 16 516 516 HOH HOH . E 5 HOH A 17 517 517 HOH HOH . E 5 HOH A 18 518 518 HOH HOH . E 5 HOH A 19 519 519 HOH HOH . E 5 HOH A 20 520 520 HOH HOH . E 5 HOH A 21 521 521 HOH HOH . E 5 HOH A 22 522 522 HOH HOH . E 5 HOH A 23 523 523 HOH HOH . E 5 HOH A 24 524 524 HOH HOH . E 5 HOH A 25 525 525 HOH HOH . E 5 HOH A 26 526 526 HOH HOH . E 5 HOH A 27 527 527 HOH HOH . E 5 HOH A 28 528 528 HOH HOH . E 5 HOH A 29 529 529 HOH HOH . E 5 HOH A 30 530 530 HOH HOH . E 5 HOH A 31 531 531 HOH HOH . E 5 HOH A 32 532 532 HOH HOH . E 5 HOH A 33 533 533 HOH HOH . E 5 HOH A 34 534 534 HOH HOH . E 5 HOH A 35 535 535 HOH HOH . E 5 HOH A 36 536 536 HOH HOH . E 5 HOH A 37 537 537 HOH HOH . E 5 HOH A 38 538 538 HOH HOH . E 5 HOH A 39 539 539 HOH HOH . E 5 HOH A 40 540 540 HOH HOH . E 5 HOH A 41 541 541 HOH HOH . E 5 HOH A 42 542 542 HOH HOH . E 5 HOH A 43 543 543 HOH HOH . E 5 HOH A 44 544 544 HOH HOH . E 5 HOH A 45 545 545 HOH HOH . E 5 HOH A 46 546 546 HOH HOH . E 5 HOH A 47 547 547 HOH HOH . E 5 HOH A 48 548 548 HOH HOH . E 5 HOH A 49 549 549 HOH HOH . E 5 HOH A 50 550 550 HOH HOH . E 5 HOH A 51 551 551 HOH HOH . E 5 HOH A 52 552 552 HOH HOH . E 5 HOH A 53 553 553 HOH HOH . E 5 HOH A 54 554 554 HOH HOH . E 5 HOH A 55 555 555 HOH HOH . E 5 HOH A 56 556 556 HOH HOH . E 5 HOH A 57 557 557 HOH HOH . E 5 HOH A 58 558 558 HOH HOH . E 5 HOH A 59 559 559 HOH HOH . E 5 HOH A 60 560 560 HOH HOH . E 5 HOH A 61 561 561 HOH HOH . E 5 HOH A 62 562 562 HOH HOH . E 5 HOH A 63 563 563 HOH HOH . E 5 HOH A 64 564 564 HOH HOH . E 5 HOH A 65 565 565 HOH HOH . E 5 HOH A 66 566 566 HOH HOH . E 5 HOH A 67 567 567 HOH HOH . E 5 HOH A 68 568 568 HOH HOH . E 5 HOH A 69 569 569 HOH HOH . E 5 HOH A 70 570 570 HOH HOH . E 5 HOH A 71 571 571 HOH HOH . E 5 HOH A 72 572 572 HOH HOH . E 5 HOH A 73 573 573 HOH HOH . E 5 HOH A 74 574 574 HOH HOH . E 5 HOH A 75 575 575 HOH HOH . E 5 HOH A 76 576 576 HOH HOH . E 5 HOH A 77 577 577 HOH HOH . E 5 HOH A 78 578 578 HOH HOH . E 5 HOH A 79 579 579 HOH HOH . E 5 HOH A 80 580 580 HOH HOH . E 5 HOH A 81 581 581 HOH HOH . E 5 HOH A 82 582 582 HOH HOH . E 5 HOH A 83 583 583 HOH HOH . E 5 HOH A 84 584 584 HOH HOH . E 5 HOH A 85 585 585 HOH HOH . E 5 HOH A 86 586 586 HOH HOH . E 5 HOH A 87 587 587 HOH HOH . E 5 HOH A 88 588 588 HOH HOH . E 5 HOH A 89 589 589 HOH HOH . E 5 HOH A 90 590 590 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 . . . C 3 12.69 12.984 12.859 0.75 41.3 ? PG ACP 402 A 1 HETATM 2 O O1G ACP . . . C 3 11.725 11.859 12.678 0.75 40.4 ? O1G ACP 402 A 1 HETATM 3 O O2G ACP . . . C 3 13.766 12.612 13.891 0.75 38.65 ? O2G ACP 402 A 1 HETATM 4 O O3G ACP . . . C 3 11.906 14.277 13.237 0.75 30.92 ? O3G ACP 402 A 1 HETATM 5 P PB ACP . . . C 3 14.939 14.302 11.392 0.75 36.76 ? PB ACP 402 A 1 HETATM 6 O O1B ACP . . . C 3 15.585 14.567 10.082 0.75 41.16 ? O1B ACP 402 A 1 HETATM 7 O O2B ACP . . . C 3 16.011 13.786 12.409 0.75 37.12 ? O2B ACP 402 A 1 HETATM 8 C C3B ACP . . . C 3 13.553 13.196 11.302 0.75 42.78 ? C3B ACP 402 A 1 HETATM 9 P PA ACP . . . C 3 14.635 16.392 13.326 0.75 42.73 ? PA ACP 402 A 1 HETATM 10 O O1A ACP . . . C 3 13.415 17.374 13.734 0.75 40.23 ? O1A ACP 402 A 1 HETATM 11 O O2A ACP . . . C 3 15.017 15.451 14.407 0.75 35.31 ? O2A ACP 402 A 1 HETATM 12 O O3A ACP . . . C 3 14.301 15.609 11.981 0.75 39.35 ? O3A ACP 402 A 1 HETATM 13 O O5' ACP . . . C 3 15.885 17.264 12.828 0.75 40.95 ? O5' ACP 402 A 1 HETATM 14 C C5' ACP . . . C 3 15.71 18.118 11.701 0.75 40.31 ? C5' ACP 402 A 1 HETATM 15 C C4' ACP . . . C 3 16.516 19.372 11.982 0.75 39.95 ? C4' ACP 402 A 1 HETATM 16 O O4' ACP . . . C 3 17.881 18.974 12.241 0.75 40.56 ? O4' ACP 402 A 1 HETATM 17 C C3' ACP . . . C 3 16.58 20.304 10.758 0.75 38.52 ? C3' ACP 402 A 1 HETATM 18 O O3' ACP . . . C 3 15.433 21.149 10.728 0.75 36.81 ? O3' ACP 402 A 1 HETATM 19 C C2' ACP . . . C 3 17.876 21.08 11.1 0.75 42.03 ? C2' ACP 402 A 1 HETATM 20 O O2' ACP . . . C 3 17.647 22.099 12.093 0.75 30.35 ? O2' ACP 402 A 1 HETATM 21 C C1' ACP . . . C 3 18.775 19.959 11.675 0.75 36.42 ? C1' ACP 402 A 1 HETATM 22 N N9 ACP . . . C 3 19.599 19.314 10.635 0.75 36.55 ? N9 ACP 402 A 1 HETATM 23 C C8 ACP . . . C 3 19.227 18.396 9.69 0.75 39.65 ? C8 ACP 402 A 1 HETATM 24 N N7 ACP . . . C 3 20.214 18.019 8.919 0.75 39.94 ? N7 ACP 402 A 1 HETATM 25 C C5 ACP . . . C 3 21.284 18.729 9.369 0.75 36.8 ? C5 ACP 402 A 1 HETATM 26 C C6 ACP . . . C 3 22.634 18.814 8.995 0.75 32.49 ? C6 ACP 402 A 1 HETATM 27 N N6 ACP . . . C 3 23.133 18.052 7.952 0.75 37.11 ? N6 ACP 402 A 1 HETATM 28 N N1 ACP . . . C 3 23.425 19.631 9.696 0.75 35.2 ? N1 ACP 402 A 1 HETATM 29 C C2 ACP . . . C 3 22.951 20.344 10.693 0.75 36.93 ? C2 ACP 402 A 1 HETATM 30 N N3 ACP . . . C 3 21.706 20.359 11.138 0.75 36.95 ? N3 ACP 402 A 1 HETATM 31 C C4 ACP . . . C 3 20.929 19.534 10.451 0.75 33.63 ? C4 ACP 402 A 1 HETATM 32 H H3B1 ACP . . . C 3 12.848 13.585 10.568 0.75 51.37 ? H3B1 ACP 402 A 1 HETATM 33 H H3B2 ACP . . . C 3 13.902 12.222 10.964 0.75 51.37 ? H3B2 ACP 402 A 1 HETATM 34 H "H5'1" ACP . . . C 3 14.657 18.372 11.582 0.75 48.41 ? "H5'1" ACP 402 A 1 HETATM 35 H "H5'2" ACP . . . C 3 16.082 17.63 10.8 0.75 48.41 ? "H5'2" ACP 402 A 1 HETATM 36 H H4' ACP . . . C 3 16.106 19.902 12.842 0.75 47.98 ? H4' ACP 402 A 1 HETATM 37 H H3' ACP . . . C 3 16.686 19.738 9.831 0.75 46.26 ? H3' ACP 402 A 1 HETATM 38 H HO3' ACP . . . C 3 14.772 20.704 10.178 0.75 44.2 ? HO3' ACP 402 A 1 HETATM 39 H H2' ACP . . . C 3 18.32 21.508 10.201 0.75 50.47 ? H2' ACP 402 A 1 HETATM 40 H HO2' ACP . . . C 3 18.135 22.883 11.807 0.75 36.45 ? HO2' ACP 402 A 1 HETATM 41 H H1' ACP . . . C 3 19.419 20.366 12.456 0.75 43.74 ? H1' ACP 402 A 1 HETATM 42 H H8 ACP . . . C 3 18.22 18.017 9.595 0.75 47.62 ? H8 ACP 402 A 1 HETATM 43 H HN61 ACP . . . C 3 23.075 17.084 7.987 0.75 44.56 ? HN61 ACP 402 A 1 HETATM 44 H HN62 ACP . . . C 3 23.541 18.485 7.186 0.75 44.56 ? HN62 ACP 402 A 1 HETATM 45 H H2 ACP . . . C 3 23.652 20.987 11.204 0.75 44.35 ? H2 ACP 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 45 #