data_6VPJ # _model_server_result.job_id 8n_zCsdbgNXlBfWi2LejUg _model_server_result.datetime_utc '2024-11-04 22:17:01' _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 6vpj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6VPJ # _exptl.entry_id 6VPJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _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 90 _cell.entry_id 6VPJ _cell.length_a 90.941 _cell.length_b 90.941 _cell.length_c 118.882 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VPJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 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 _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' 7_555 y,x,-z 0 1 0 1 0 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 # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 GLC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O1 _pdbx_entity_branch_link.leaving_atom_id_2 HO1 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC D 1 TRE 2 n B GLC 2 B 2 GLC D 1 TRE # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id C1 _struct_conn.ptnr1_label_comp_id GLC _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id GLC _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id O1 _struct_conn.ptnr2_label_comp_id GLC _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id GLC _struct_conn.ptnr2_auth_seq_id 2 _struct_conn.ptnr2_symmetry 1_555 _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 1.373 _struct_conn.pdbx_value_order sing # _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 6VPJ _atom_sites.fract_transf_matrix[1][1] 0.010996 _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] 0.010996 _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] 0.008412 _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 C 3 ANP A 1 401 1 ANP ANP . D 4 HOH A 1 501 26 HOH HOH . D 4 HOH A 2 502 92 HOH HOH . D 4 HOH A 3 503 9 HOH HOH . D 4 HOH A 4 504 109 HOH HOH . D 4 HOH A 5 505 60 HOH HOH . D 4 HOH A 6 506 111 HOH HOH . D 4 HOH A 7 507 55 HOH HOH . D 4 HOH A 8 508 79 HOH HOH . D 4 HOH A 9 509 64 HOH HOH . D 4 HOH A 10 510 20 HOH HOH . D 4 HOH A 11 511 2 HOH HOH . D 4 HOH A 12 512 31 HOH HOH . D 4 HOH A 13 513 6 HOH HOH . D 4 HOH A 14 514 108 HOH HOH . D 4 HOH A 15 515 81 HOH HOH . D 4 HOH A 16 516 48 HOH HOH . D 4 HOH A 17 517 104 HOH HOH . D 4 HOH A 18 518 110 HOH HOH . D 4 HOH A 19 519 80 HOH HOH . D 4 HOH A 20 520 84 HOH HOH . D 4 HOH A 21 521 52 HOH HOH . D 4 HOH A 22 522 87 HOH HOH . D 4 HOH A 23 523 27 HOH HOH . D 4 HOH A 24 524 77 HOH HOH . D 4 HOH A 25 525 86 HOH HOH . D 4 HOH A 26 526 29 HOH HOH . D 4 HOH A 27 527 12 HOH HOH . D 4 HOH A 28 528 53 HOH HOH . D 4 HOH A 29 529 63 HOH HOH . D 4 HOH A 30 530 13 HOH HOH . D 4 HOH A 31 531 91 HOH HOH . D 4 HOH A 32 532 113 HOH HOH . D 4 HOH A 33 533 73 HOH HOH . D 4 HOH A 34 534 88 HOH HOH . D 4 HOH A 35 535 10 HOH HOH . D 4 HOH A 36 536 57 HOH HOH . D 4 HOH A 37 537 43 HOH HOH . D 4 HOH A 38 538 47 HOH HOH . D 4 HOH A 39 539 67 HOH HOH . D 4 HOH A 40 540 83 HOH HOH . D 4 HOH A 41 541 106 HOH HOH . D 4 HOH A 42 542 14 HOH HOH . D 4 HOH A 43 543 70 HOH HOH . D 4 HOH A 44 544 98 HOH HOH . D 4 HOH A 45 545 4 HOH HOH . D 4 HOH A 46 546 96 HOH HOH . D 4 HOH A 47 547 74 HOH HOH . D 4 HOH A 48 548 89 HOH HOH . D 4 HOH A 49 549 56 HOH HOH . D 4 HOH A 50 550 5 HOH HOH . D 4 HOH A 51 551 101 HOH HOH . D 4 HOH A 52 552 11 HOH HOH . D 4 HOH A 53 553 112 HOH HOH . D 4 HOH A 54 554 8 HOH HOH . D 4 HOH A 55 555 97 HOH HOH . D 4 HOH A 56 556 15 HOH HOH . D 4 HOH A 57 557 69 HOH HOH . D 4 HOH A 58 558 16 HOH HOH . D 4 HOH A 59 559 46 HOH HOH . D 4 HOH A 60 560 23 HOH HOH . D 4 HOH A 61 561 62 HOH HOH . D 4 HOH A 62 562 51 HOH HOH . D 4 HOH A 63 563 3 HOH HOH . D 4 HOH A 64 564 37 HOH HOH . D 4 HOH A 65 565 22 HOH HOH . D 4 HOH A 66 566 59 HOH HOH . D 4 HOH A 67 567 103 HOH HOH . D 4 HOH A 68 568 102 HOH HOH . D 4 HOH A 69 569 85 HOH HOH . D 4 HOH A 70 570 66 HOH HOH . D 4 HOH A 71 571 21 HOH HOH . D 4 HOH A 72 572 44 HOH HOH . D 4 HOH A 73 573 40 HOH HOH . D 4 HOH A 74 574 30 HOH HOH . D 4 HOH A 75 575 93 HOH HOH . D 4 HOH A 76 576 72 HOH HOH . D 4 HOH A 77 577 25 HOH HOH . D 4 HOH A 78 578 58 HOH HOH . D 4 HOH A 79 579 94 HOH HOH . D 4 HOH A 80 580 28 HOH HOH . D 4 HOH A 81 581 39 HOH HOH . D 4 HOH A 82 582 17 HOH HOH . D 4 HOH A 83 583 32 HOH HOH . D 4 HOH A 84 584 34 HOH HOH . D 4 HOH A 85 585 18 HOH HOH . D 4 HOH A 86 586 78 HOH HOH . D 4 HOH A 87 587 76 HOH HOH . D 4 HOH A 88 588 7 HOH HOH . D 4 HOH A 89 589 1 HOH HOH . D 4 HOH A 90 590 24 HOH HOH . D 4 HOH A 91 591 49 HOH HOH . D 4 HOH A 92 592 50 HOH HOH . D 4 HOH A 93 593 19 HOH HOH . D 4 HOH A 94 594 35 HOH HOH . D 4 HOH A 95 595 82 HOH HOH . D 4 HOH A 96 596 95 HOH HOH . D 4 HOH A 97 597 36 HOH HOH . D 4 HOH A 98 598 90 HOH HOH . D 4 HOH A 99 599 65 HOH HOH . D 4 HOH A 100 600 45 HOH HOH . D 4 HOH A 101 601 107 HOH HOH . D 4 HOH A 102 602 75 HOH HOH . D 4 HOH A 103 603 71 HOH HOH . D 4 HOH A 104 604 68 HOH HOH . D 4 HOH A 105 605 38 HOH HOH . D 4 HOH A 106 606 105 HOH HOH . D 4 HOH A 107 607 42 HOH HOH . D 4 HOH A 108 608 54 HOH HOH . D 4 HOH A 109 609 33 HOH HOH . D 4 HOH A 110 610 61 HOH HOH . D 4 HOH A 111 611 99 HOH HOH . D 4 HOH A 112 612 41 HOH HOH . D 4 HOH A 113 613 100 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 . . . C 3 16.852 -1.528 -1.213 1 66.98 ? PG ANP 401 A 1 HETATM 2 O O1G ANP . . . C 3 15.759 -1.087 -2.135 1 71.19 ? O1G ANP 401 A 1 HETATM 3 O O2G ANP . . . C 3 18.212 -1.588 -2.005 1 61.58 ? O2G ANP 401 A 1 HETATM 4 O O3G ANP . . . C 3 16.511 -2.965 -0.648 1 66.39 ? O3G ANP 401 A 1 HETATM 5 P PB ANP . . . C 3 18.398 -0.498 0.924 1 67.94 ? PB ANP 401 A 1 HETATM 6 O O1B ANP . . . C 3 19.56 -0.623 -0.011 1 60.84 ? O1B ANP 401 A 1 HETATM 7 O O2B ANP . . . C 3 18.53 0.834 1.712 1 66.85 ? O2B ANP 401 A 1 HETATM 8 N N3B ANP . . . C 3 16.949 -0.432 0.077 1 66.94 ? N3B ANP 401 A 1 HETATM 9 P PA ANP . . . C 3 19 -3.109 1.662 1 61.54 ? PA ANP 401 A 1 HETATM 10 O O1A ANP . . . C 3 18.09 -3.896 0.799 1 58.8 ? O1A ANP 401 A 1 HETATM 11 O O2A ANP . . . C 3 20.417 -2.932 1.105 1 58.69 ? O2A ANP 401 A 1 HETATM 12 O O3A ANP . . . C 3 18.396 -1.666 1.961 1 69.25 ? O3A ANP 401 A 1 HETATM 13 O O5' ANP . . . C 3 19.044 -3.809 3.084 1 63.69 ? O5' ANP 401 A 1 HETATM 14 C C5' ANP . . . C 3 17.841 -4.049 3.838 1 62.79 ? C5' ANP 401 A 1 HETATM 15 C C4' ANP . . . C 3 18.215 -4.352 5.267 1 64.78 ? C4' ANP 401 A 1 HETATM 16 O O4' ANP . . . C 3 18.911 -5.615 5.331 1 63.34 ? O4' ANP 401 A 1 HETATM 17 C C3' ANP . . . C 3 19.154 -3.35 5.929 1 65.31 ? C3' ANP 401 A 1 HETATM 18 O O3' ANP . . . C 3 18.44 -2.252 6.485 1 68.12 ? O3' ANP 401 A 1 HETATM 19 C C2' ANP . . . C 3 19.828 -4.203 7.004 1 61.41 ? C2' ANP 401 A 1 HETATM 20 O O2' ANP . . . C 3 19.013 -4.323 8.165 1 59.59 ? O2' ANP 401 A 1 HETATM 21 C C1' ANP . . . C 3 19.948 -5.556 6.295 1 60.42 ? C1' ANP 401 A 1 HETATM 22 N N9 ANP . . . C 3 21.221 -5.753 5.61 1 57.93 ? N9 ANP 401 A 1 HETATM 23 C C8 ANP . . . C 3 21.567 -5.301 4.364 1 56.28 ? C8 ANP 401 A 1 HETATM 24 N N7 ANP . . . C 3 22.784 -5.625 3.997 1 54.23 ? N7 ANP 401 A 1 HETATM 25 C C5 ANP . . . C 3 23.273 -6.339 5.079 1 54.95 ? C5 ANP 401 A 1 HETATM 26 C C6 ANP . . . C 3 24.514 -6.962 5.321 1 54.52 ? C6 ANP 401 A 1 HETATM 27 N N6 ANP . . . C 3 25.526 -6.963 4.452 1 48.81 ? N6 ANP 401 A 1 HETATM 28 N N1 ANP . . . C 3 24.678 -7.593 6.507 1 55.82 ? N1 ANP 401 A 1 HETATM 29 C C2 ANP . . . C 3 23.667 -7.595 7.381 1 56.97 ? C2 ANP 401 A 1 HETATM 30 N N3 ANP . . . C 3 22.456 -7.044 7.262 1 59.46 ? N3 ANP 401 A 1 HETATM 31 C C4 ANP . . . C 3 22.322 -6.427 6.081 1 57.1 ? C4 ANP 401 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #