data_6LY6 # _model_server_result.job_id K9p9mZZwkHskXmyDU2qvjQ _model_server_result.datetime_utc '2025-01-11 07:03:45' _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 6ly6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6LY6 # _exptl.entry_id 6LY6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _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 6LY6 _cell.length_a 105.723 _cell.length_b 105.723 _cell.length_c 71.597 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LY6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall 'P 64' _symmetry.space_group_name_H-M 'P 64' # _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,F _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' 4_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 -52.8615 91.558804 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 OE1 GLU 219 A GLU 396 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc2 A OG SER 222 A SER 399 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc3 B O1B ANP . A ANP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc4 B O2A ANP . A ANP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc5 B O2G ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? metalc ? metalc6 B O2B ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? metalc ? metalc7 D MG MG . A MG 503 1_555 F O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc8 D MG MG . A MG 503 1_555 F O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc9 D MG MG . A MG 503 1_555 F O HOH . A HOH 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc10 D MG MG . A MG 503 1_555 F O HOH . A HOH 623 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? # _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 43 n n PG O2G ANP sing 44 n n PG O3G ANP sing 45 n n PG N3B ANP sing 46 n n O2G HOG2 ANP sing 47 n n O3G HOG3 ANP sing 48 n n PB O1B ANP doub 49 n n PB O2B ANP sing 50 n n PB N3B ANP sing 51 n n PB O3A ANP sing 52 n n O2B HOB2 ANP sing 53 n n N3B HNB1 ANP sing 54 n n PA O1A ANP doub 55 n n PA O2A ANP sing 56 n n PA O3A ANP sing 57 n n PA O5' ANP sing 58 n n O2A HOA2 ANP sing 59 n n O5' C5' ANP sing 60 n n C5' C4' ANP sing 61 n n C5' "H5'1" ANP sing 62 n n C5' "H5'2" ANP sing 63 n n C4' O4' ANP sing 64 n n C4' C3' ANP sing 65 n n C4' H4' ANP sing 66 n n O4' C1' ANP sing 67 n n C3' O3' ANP sing 68 n n C3' C2' ANP sing 69 n n C3' H3' ANP sing 70 n n O3' HO3' ANP sing 71 n n C2' O2' ANP sing 72 n n C2' C1' ANP sing 73 n n C2' H2' ANP sing 74 n n O2' HO2' ANP sing 75 n n C1' N9 ANP sing 76 n n C1' H1' ANP sing 77 n n N9 C8 ANP sing 78 n y N9 C4 ANP sing 79 n y C8 N7 ANP doub 80 n y C8 H8 ANP sing 81 n n N7 C5 ANP sing 82 n y C5 C6 ANP sing 83 n y C5 C4 ANP doub 84 n y C6 N6 ANP sing 85 n n C6 N1 ANP doub 86 n y N6 HN61 ANP sing 87 n n N6 HN62 ANP sing 88 n n N1 C2 ANP sing 89 n y C2 N3 ANP doub 90 n y C2 H2 ANP sing 91 n n N3 C4 ANP sing 92 n y # _atom_sites.entry_id 6LY6 _atom_sites.fract_transf_matrix[1][1] 0.009459 _atom_sites.fract_transf_matrix[1][2] 0.005461 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010922 _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] 0.013967 _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 ANP A 1 501 1 ANP ANP . C 3 MG A 1 502 1 MG MG . D 3 MG A 1 503 2 MG MG . E 4 ALN A 1 504 1 ALN NAP . F 5 HOH A 1 601 67 HOH HOH . F 5 HOH A 2 602 55 HOH HOH . F 5 HOH A 3 603 13 HOH HOH . F 5 HOH A 4 604 9 HOH HOH . F 5 HOH A 5 605 1 HOH HOH . F 5 HOH A 6 606 24 HOH HOH . F 5 HOH A 7 607 75 HOH HOH . F 5 HOH A 8 608 73 HOH HOH . F 5 HOH A 9 609 14 HOH HOH . F 5 HOH A 10 610 8 HOH HOH . F 5 HOH A 11 611 48 HOH HOH . F 5 HOH A 12 612 47 HOH HOH . F 5 HOH A 13 613 11 HOH HOH . F 5 HOH A 14 614 7 HOH HOH . F 5 HOH A 15 615 74 HOH HOH . F 5 HOH A 16 616 63 HOH HOH . F 5 HOH A 17 617 16 HOH HOH . F 5 HOH A 18 618 10 HOH HOH . F 5 HOH A 19 619 4 HOH HOH . F 5 HOH A 20 620 6 HOH HOH . F 5 HOH A 21 621 20 HOH HOH . F 5 HOH A 22 622 19 HOH HOH . F 5 HOH A 23 623 77 HOH HOH . F 5 HOH A 24 624 57 HOH HOH . F 5 HOH A 25 625 2 HOH HOH . F 5 HOH A 26 626 35 HOH HOH . F 5 HOH A 27 627 18 HOH HOH . F 5 HOH A 28 628 22 HOH HOH . F 5 HOH A 29 629 32 HOH HOH . F 5 HOH A 30 630 15 HOH HOH . F 5 HOH A 31 631 3 HOH HOH . F 5 HOH A 32 632 17 HOH HOH . F 5 HOH A 33 633 68 HOH HOH . F 5 HOH A 34 634 26 HOH HOH . F 5 HOH A 35 635 56 HOH HOH . F 5 HOH A 36 636 21 HOH HOH . F 5 HOH A 37 637 65 HOH HOH . F 5 HOH A 38 638 27 HOH HOH . F 5 HOH A 39 639 12 HOH HOH . F 5 HOH A 40 640 70 HOH HOH . F 5 HOH A 41 641 50 HOH HOH . F 5 HOH A 42 642 23 HOH HOH . F 5 HOH A 43 643 37 HOH HOH . F 5 HOH A 44 644 44 HOH HOH . F 5 HOH A 45 645 31 HOH HOH . F 5 HOH A 46 646 34 HOH HOH . F 5 HOH A 47 647 41 HOH HOH . F 5 HOH A 48 648 36 HOH HOH . F 5 HOH A 49 649 38 HOH HOH . F 5 HOH A 50 650 69 HOH HOH . F 5 HOH A 51 651 46 HOH HOH . F 5 HOH A 52 652 64 HOH HOH . F 5 HOH A 53 653 39 HOH HOH . F 5 HOH A 54 654 29 HOH HOH . F 5 HOH A 55 655 49 HOH HOH . F 5 HOH A 56 656 53 HOH HOH . F 5 HOH A 57 657 43 HOH HOH . F 5 HOH A 58 658 52 HOH HOH . F 5 HOH A 59 659 25 HOH HOH . F 5 HOH A 60 660 28 HOH HOH . F 5 HOH A 61 661 59 HOH HOH . F 5 HOH A 62 662 72 HOH HOH . F 5 HOH A 63 663 58 HOH HOH . F 5 HOH A 64 664 71 HOH HOH . F 5 HOH A 65 665 54 HOH HOH . F 5 HOH A 66 666 60 HOH HOH . F 5 HOH A 67 667 51 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 . . . B 2 -25.402 25.705 -1.032 1 45.52 ? PG ANP 501 A 1 HETATM 2 O O1G ANP . . . B 2 -24.098 25.832 -1.714 1 41.22 ? O1G ANP 501 A 1 HETATM 3 O O2G ANP . . . B 2 -25.436 26.633 0.237 1 47.26 ? O2G ANP 501 A 1 HETATM 4 O O3G ANP . . . B 2 -25.617 24.207 -0.617 1 46.36 ? O3G ANP 501 A 1 HETATM 5 P PB ANP . . . B 2 -27.927 26.856 -1.27 1 41.69 ? PB ANP 501 A 1 HETATM 6 O O1B ANP . . . B 2 -28.986 25.861 -1.032 1 44.95 ? O1B ANP 501 A 1 HETATM 7 O O2B ANP . . . B 2 -27.431 27.385 0.096 1 54.69 ? O2B ANP 501 A 1 HETATM 8 N N3B ANP . . . B 2 -26.644 26.154 -2.08 1 49.86 ? N3B ANP 501 A 1 HETATM 9 P PA ANP . . . B 2 -29.883 28.276 -2.683 1 41.23 ? PA ANP 501 A 1 HETATM 10 O O1A ANP . . . B 2 -30.791 28.69 -1.614 1 44.57 -1 O1A ANP 501 A 1 HETATM 11 O O2A ANP . . . B 2 -30.362 27.032 -3.418 1 46.14 ? O2A ANP 501 A 1 HETATM 12 O O3A ANP . . . B 2 -28.425 28.03 -2.15 1 53.56 ? O3A ANP 501 A 1 HETATM 13 O O5' ANP . . . B 2 -29.667 29.501 -3.613 1 40.52 ? O5' ANP 501 A 1 HETATM 14 C C5' ANP . . . B 2 -29.767 29.432 -5.04 1 46.98 ? C5' ANP 501 A 1 HETATM 15 C C4' ANP . . . B 2 -28.399 29.466 -5.678 1 38.2 ? C4' ANP 501 A 1 HETATM 16 O O4' ANP . . . B 2 -27.662 30.617 -5.227 1 40.41 ? O4' ANP 501 A 1 HETATM 17 C C3' ANP . . . B 2 -27.481 28.299 -5.358 1 40.69 ? C3' ANP 501 A 1 HETATM 18 O O3' ANP . . . B 2 -27.811 27.145 -6.118 1 42.86 ? O3' ANP 501 A 1 HETATM 19 C C2' ANP . . . B 2 -26.112 28.88 -5.707 1 38.56 ? C2' ANP 501 A 1 HETATM 20 O O2' ANP . . . B 2 -25.823 28.818 -7.095 1 35.86 ? O2' ANP 501 A 1 HETATM 21 C C1' ANP . . . B 2 -26.273 30.342 -5.282 1 31.58 ? C1' ANP 501 A 1 HETATM 22 N N9 ANP . . . B 2 -25.692 30.628 -3.979 1 45.15 ? N9 ANP 501 A 1 HETATM 23 C C8 ANP . . . B 2 -26.248 30.375 -2.753 1 44.86 ? C8 ANP 501 A 1 HETATM 24 N N7 ANP . . . B 2 -25.494 30.725 -1.742 1 42.06 ? N7 ANP 501 A 1 HETATM 25 C C5 ANP . . . B 2 -24.358 31.241 -2.343 1 40.2 ? C5 ANP 501 A 1 HETATM 26 C C6 ANP . . . B 2 -23.166 31.789 -1.82 1 42.37 ? C6 ANP 501 A 1 HETATM 27 N N6 ANP . . . B 2 -22.92 31.914 -0.516 1 40.4 ? N6 ANP 501 A 1 HETATM 28 N N1 ANP . . . B 2 -22.221 32.214 -2.7 1 39.71 ? N1 ANP 501 A 1 HETATM 29 C C2 ANP . . . B 2 -22.464 32.094 -4.01 1 40.61 ? C2 ANP 501 A 1 HETATM 30 N N3 ANP . . . B 2 -23.549 31.594 -4.613 1 42.13 ? N3 ANP 501 A 1 HETATM 31 C C4 ANP . . . B 2 -24.464 31.181 -3.723 1 42.02 ? C4 ANP 501 A 1 HETATM 32 H HOG2 ANP . . . B 2 -24.816 26.366 0.815 1 56.15 ? HOG2 ANP 501 A 1 HETATM 33 H HOG3 ANP . . . B 2 -24.838 23.831 -0.462 1 55.06 ? HOG3 ANP 501 A 1 HETATM 34 H HOB2 ANP . . . B 2 -28.086 27.331 0.69 1 65.06 ? HOB2 ANP 501 A 1 HETATM 35 H HNB1 ANP . . . B 2 -26.936 25.424 -2.535 1 59.27 ? HNB1 ANP 501 A 1 HETATM 36 H HOA2 ANP . . . B 2 -31.207 26.871 -3.206 1 54.81 ? HOA2 ANP 501 A 1 HETATM 37 H "H5'1" ANP . . . B 2 -30.291 30.187 -5.36 1 55.81 ? "H5'1" ANP 501 A 1 HETATM 38 H "H5'2" ANP . . . B 2 -30.218 28.599 -5.292 1 55.81 ? "H5'2" ANP 501 A 1 HETATM 39 H H4' ANP . . . B 2 -28.478 29.542 -6.651 1 45.27 ? H4' ANP 501 A 1 HETATM 40 H H3' ANP . . . B 2 -27.525 28.116 -4.417 1 48.26 ? H3' ANP 501 A 1 HETATM 41 H HO3' ANP . . . B 2 -27.111 26.901 -6.604 1 50.86 ? HO3' ANP 501 A 1 HETATM 42 H H2' ANP . . . B 2 -25.421 28.469 -5.174 1 45.71 ? H2' ANP 501 A 1 HETATM 43 H HO2' ANP . . . B 2 -25.339 28.093 -7.266 1 42.47 ? HO2' ANP 501 A 1 HETATM 44 H H1' ANP . . . B 2 -25.858 30.898 -5.96 1 37.33 ? H1' ANP 501 A 1 HETATM 45 H H8 ANP . . . B 2 -27.113 29.982 -2.646 1 53.26 ? H8 ANP 501 A 1 HETATM 46 H HN61 ANP . . . B 2 -23.337 32.579 -0.029 1 47.92 ? HN61 ANP 501 A 1 HETATM 47 H HN62 ANP . . . B 2 -22.339 31.342 -0.103 1 47.92 ? HN62 ANP 501 A 1 HETATM 48 H H2 ANP . . . B 2 -21.761 32.41 -4.6 1 48.16 ? H2 ANP 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #