data_1U3D # _model_server_result.job_id lz-17L9iNfae9pKTp6-_xQ _model_server_result.datetime_utc '2024-11-28 07:15:13' _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 1u3d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":511}' # _entry.id 1U3D # _exptl.entry_id 1U3D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 120 _cell.entry_id 1U3D _cell.length_a 169.213 _cell.length_b 169.213 _cell.length_c 104.521 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1U3D _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _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 _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 5 _struct_asym.id H _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 disulf ? disulf1 A SG CYS 80 A CYS 80 1_555 A SG CYS 190 A CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc1 A O ASN 219 A ASN 219 1_555 E MG MG . A MG 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc2 A O ASN 238 A ASN 238 1_555 C MG MG . A MG 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc3 A O SER 244 A SER 244 1_555 D MG MG . A MG 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc4 A N SER 244 A SER 244 1_555 D MG MG . A MG 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc5 A OG1 THR 246 A THR 246 1_555 C MG MG . A MG 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? metalc ? metalc6 A OG1 THR 246 A THR 246 1_555 D MG MG . A MG 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc7 A NE2 HIS 358 A HIS 358 1_555 C MG MG . A MG 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.066 ? metalc ? metalc8 H N3B ANP . A ANP 511 1_555 B MG MG . A MG 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc9 H O2A ANP . A ANP 511 1_555 B MG MG . A MG 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc10 I O1 NDS . A NDS 512 1_555 E MG MG . A MG 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 PG O1G ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 1U3D _atom_sites.fract_transf_matrix[1][1] 0.00591 _atom_sites.fract_transf_matrix[1][2] 0.003412 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006824 _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] 0.009567 _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 MG A 1 514 514 MG MG2 . C 2 MG A 1 515 515 MG MG2 . D 2 MG A 1 516 516 MG MG2 . E 2 MG A 1 517 517 MG MG2 . F 3 CL A 1 518 518 CL CL1 . G 4 FAD A 1 510 510 FAD FAD . H 5 ANP A 1 511 511 ANP ANP . I 6 NDS A 1 512 512 NDS SB . J 7 HOH A 1 519 1 HOH HOH . J 7 HOH A 2 520 2 HOH HOH . J 7 HOH A 3 521 3 HOH HOH . J 7 HOH A 4 522 4 HOH HOH . J 7 HOH A 5 523 5 HOH HOH . J 7 HOH A 6 524 6 HOH HOH . J 7 HOH A 7 525 7 HOH HOH . J 7 HOH A 8 526 8 HOH HOH . J 7 HOH A 9 527 9 HOH HOH . J 7 HOH A 10 528 10 HOH HOH . J 7 HOH A 11 529 11 HOH HOH . J 7 HOH A 12 530 12 HOH HOH . J 7 HOH A 13 531 13 HOH HOH . J 7 HOH A 14 532 14 HOH HOH . J 7 HOH A 15 533 15 HOH HOH . J 7 HOH A 16 534 16 HOH HOH . J 7 HOH A 17 535 17 HOH HOH . J 7 HOH A 18 536 18 HOH HOH . J 7 HOH A 19 537 19 HOH HOH . J 7 HOH A 20 538 20 HOH HOH . J 7 HOH A 21 539 21 HOH HOH . J 7 HOH A 22 540 22 HOH HOH . J 7 HOH A 23 541 23 HOH HOH . J 7 HOH A 24 542 24 HOH HOH . J 7 HOH A 25 543 25 HOH HOH . J 7 HOH A 26 544 26 HOH HOH . J 7 HOH A 27 545 27 HOH HOH . J 7 HOH A 28 546 28 HOH HOH . J 7 HOH A 29 547 29 HOH HOH . J 7 HOH A 30 548 30 HOH HOH . J 7 HOH A 31 549 31 HOH HOH . J 7 HOH A 32 550 32 HOH HOH . J 7 HOH A 33 551 33 HOH HOH . J 7 HOH A 34 552 34 HOH HOH . J 7 HOH A 35 553 35 HOH HOH . J 7 HOH A 36 554 36 HOH HOH . J 7 HOH A 37 555 37 HOH HOH . J 7 HOH A 38 556 38 HOH HOH . J 7 HOH A 39 557 39 HOH HOH . J 7 HOH A 40 558 40 HOH HOH . J 7 HOH A 41 559 41 HOH HOH . J 7 HOH A 42 560 42 HOH HOH . J 7 HOH A 43 561 43 HOH HOH . J 7 HOH A 44 562 47 HOH HOH . J 7 HOH A 45 563 48 HOH HOH . J 7 HOH A 46 564 50 HOH HOH . J 7 HOH A 47 565 51 HOH HOH . J 7 HOH A 48 566 52 HOH HOH . J 7 HOH A 49 567 53 HOH HOH . J 7 HOH A 50 568 54 HOH HOH . J 7 HOH A 51 569 55 HOH HOH . J 7 HOH A 52 570 56 HOH HOH . J 7 HOH A 53 571 57 HOH HOH . J 7 HOH A 54 572 58 HOH HOH . J 7 HOH A 55 573 59 HOH HOH . J 7 HOH A 56 574 60 HOH HOH . J 7 HOH A 57 575 61 HOH HOH . J 7 HOH A 58 576 62 HOH HOH . J 7 HOH A 59 577 63 HOH HOH . J 7 HOH A 60 578 64 HOH HOH . J 7 HOH A 61 579 65 HOH HOH . J 7 HOH A 62 580 66 HOH HOH . J 7 HOH A 63 581 67 HOH HOH . J 7 HOH A 64 582 68 HOH HOH . J 7 HOH A 65 583 69 HOH HOH . J 7 HOH A 66 584 70 HOH HOH . J 7 HOH A 67 585 71 HOH HOH . J 7 HOH A 68 586 72 HOH HOH . J 7 HOH A 69 587 73 HOH HOH . J 7 HOH A 70 588 74 HOH HOH . J 7 HOH A 71 589 76 HOH HOH . J 7 HOH A 72 590 77 HOH HOH . J 7 HOH A 73 591 78 HOH HOH . J 7 HOH A 74 592 79 HOH HOH . J 7 HOH A 75 593 80 HOH HOH . J 7 HOH A 76 594 81 HOH HOH . J 7 HOH A 77 595 82 HOH HOH . J 7 HOH A 78 596 83 HOH HOH . J 7 HOH A 79 597 84 HOH HOH . J 7 HOH A 80 598 85 HOH HOH . J 7 HOH A 81 599 86 HOH HOH . J 7 HOH A 82 600 87 HOH HOH . J 7 HOH A 83 601 88 HOH HOH . J 7 HOH A 84 602 89 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 ANP . . . H 5 63.279 -8.017 59.227 0.79 115.83 ? PG ANP 511 A 1 HETATM 2 O O1G ANP . . . H 5 62.396 -8.68 58.245 0.79 115.18 ? O1G ANP 511 A 1 HETATM 3 O O2G ANP . . . H 5 64.765 -7.811 58.638 0.79 111.27 ? O2G ANP 511 A 1 HETATM 4 O O3G ANP . . . H 5 63.441 -8.898 60.567 0.79 110.52 ? O3G ANP 511 A 1 HETATM 5 P PB ANP . . . H 5 63.326 -5.75 60.929 0.79 120.04 ? PB ANP 511 A 1 HETATM 6 O O1B ANP . . . H 5 64.782 -6.016 61.042 0.79 118.56 ? O1B ANP 511 A 1 HETATM 7 O O2B ANP . . . H 5 62.474 -6.072 62.092 0.79 119.89 ? O2B ANP 511 A 1 HETATM 8 N N3B ANP . . . H 5 62.746 -6.555 59.658 0.79 116.97 ? N3B ANP 511 A 1 HETATM 9 P PA ANP . . . H 5 61.805 -3.354 60.907 0.79 118.05 ? PA ANP 511 A 1 HETATM 10 O O1A ANP . . . H 5 61.715 -2.237 59.957 0.79 115.25 ? O1A ANP 511 A 1 HETATM 11 O O2A ANP . . . H 5 60.637 -4.277 61.017 0.79 116.02 ? O2A ANP 511 A 1 HETATM 12 O O3A ANP . . . H 5 63.117 -4.206 60.515 0.79 117.68 ? O3A ANP 511 A 1 HETATM 13 O O5' ANP . . . H 5 62.149 -2.784 62.375 0.79 108.79 ? O5' ANP 511 A 1 HETATM 14 C C5' ANP . . . H 5 62.306 -3.673 63.486 0.79 97.34 ? C5' ANP 511 A 1 HETATM 15 C C4' ANP . . . H 5 61.534 -3.197 64.719 0.79 86.37 ? C4' ANP 511 A 1 HETATM 16 O O4' ANP . . . H 5 61.962 -1.914 65.204 0.79 83.79 ? O4' ANP 511 A 1 HETATM 17 C C3' ANP . . . H 5 60.046 -3.02 64.42 0.79 78.2 ? C3' ANP 511 A 1 HETATM 18 O O3' ANP . . . H 5 59.41 -4.299 64.443 0.79 84.83 ? O3' ANP 511 A 1 HETATM 19 C C2' ANP . . . H 5 59.661 -2.191 65.642 0.79 76.31 ? C2' ANP 511 A 1 HETATM 20 O O2' ANP . . . H 5 59.791 -2.932 66.86 0.79 63.07 ? O2' ANP 511 A 1 HETATM 21 C C1' ANP . . . H 5 60.792 -1.162 65.582 0.79 77.56 ? C1' ANP 511 A 1 HETATM 22 N N9 ANP . . . H 5 60.54 -0.143 64.538 0.79 68.47 ? N9 ANP 511 A 1 HETATM 23 C C8 ANP . . . H 5 60.906 -0.235 63.258 0.79 69.16 ? C8 ANP 511 A 1 HETATM 24 N N7 ANP . . . H 5 60.63 0.912 62.636 0.79 69.98 ? N7 ANP 511 A 1 HETATM 25 C C5 ANP . . . H 5 60.085 1.727 63.519 0.79 65.59 ? C5 ANP 511 A 1 HETATM 26 C C6 ANP . . . H 5 59.621 3.043 63.439 0.79 59.7 ? C6 ANP 511 A 1 HETATM 27 N N6 ANP . . . H 5 59.708 3.703 62.298 0.79 62.91 ? N6 ANP 511 A 1 HETATM 28 N N1 ANP . . . H 5 59.09 3.633 64.594 0.79 58 ? N1 ANP 511 A 1 HETATM 29 C C2 ANP . . . H 5 59.042 2.893 65.786 0.79 61.91 ? C2 ANP 511 A 1 HETATM 30 N N3 ANP . . . H 5 59.493 1.659 65.823 0.79 61.53 ? N3 ANP 511 A 1 HETATM 31 C C4 ANP . . . H 5 60.012 1.058 64.736 0.79 65.11 ? C4 ANP 511 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #