data_5NVA # _model_server_result.job_id 2PNxgBkgg2SdKf5XIpNKJg _model_server_result.datetime_utc '2024-11-23 05:27:08' _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 5nva # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 5NVA # _exptl.entry_id 5NVA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.27 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'N-acetyl-beta-neuraminic acid' _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 5NVA _cell.length_a 48.788 _cell.length_b 97.764 _cell.length_c 151.69 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NVA _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _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 3 _struct_asym.id D _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 O ALA 56 A ALA 56 1_555 B NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc2 A O LEU 59 A LEU 59 1_555 B NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc3 A OD1 ASP 182 A ASP 182 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc4 A OD2 ASP 182 A ASP 182 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc5 A O ALA 339 A ALA 339 1_555 B NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc6 A OG SER 342 A SER 342 1_555 B NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc7 A O SER 342 A SER 342 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc8 A OG SER 343 A SER 343 1_555 B NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc9 A OG SER 345 A SER 345 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc10 A OG SER 346 A SER 346 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? # _chem_comp.formula 'C11 H19 N O9' _chem_comp.formula_weight 309.27 _chem_comp.id SLB _chem_comp.mon_nstd_flag . _chem_comp.name 'N-acetyl-beta-neuraminic acid' _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms 'N-acetylneuraminic acid;sialic acid;O-sialic acid;5-N-ACETYL-BETA-D-NEURAMINIC ACID;BETA-SIALIC ACID' # 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 C1 C2 SLB sing 290 n n C1 O1A SLB doub 291 n n C1 O1B SLB sing 292 n n C2 C3 SLB sing 293 n n C2 O2 SLB sing 294 n n C2 O6 SLB sing 295 n n C3 C4 SLB sing 296 n n C3 H32 SLB sing 297 n n C3 H31 SLB sing 298 n n C4 C5 SLB sing 299 n n C4 O4 SLB sing 300 n n C4 H4 SLB sing 301 n n C5 C6 SLB sing 302 n n C5 N5 SLB sing 303 n n C5 H5 SLB sing 304 n n C6 C7 SLB sing 305 n n C6 O6 SLB sing 306 n n C6 H6 SLB sing 307 n n C7 C8 SLB sing 308 n n C7 O7 SLB sing 309 n n C7 H7 SLB sing 310 n n C8 C9 SLB sing 311 n n C8 O8 SLB sing 312 n n C8 H8 SLB sing 313 n n C9 O9 SLB sing 314 n n C9 H92 SLB sing 315 n n C9 H91 SLB sing 316 n n C10 C11 SLB sing 317 n n C10 N5 SLB sing 318 n n C10 O10 SLB doub 319 n n C11 H111 SLB sing 320 n n C11 H113 SLB sing 321 n n C11 H112 SLB sing 322 n n N5 HN5 SLB sing 323 n n O1B HO1B SLB sing 324 n n O2 HO2 SLB sing 325 n n O4 HO4 SLB sing 326 n n O7 HO7 SLB sing 327 n n O8 HO8 SLB sing 328 n n O9 HO9 SLB sing 329 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version SLB DNeup5Acb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 SLB 'N-acetyl-b-D-neuraminic acid' 'COMMON NAME' GMML 1 SLB b-D-Neup5Ac 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 SLB Neu5Ac 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5NVA _atom_sites.fract_transf_matrix[1][1] 0.020497 _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] 0.010229 _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] 0.006592 _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 NA A 1 501 1 NA NA . C 2 NA A 1 502 2 NA NA . D 3 SLB A 1 503 1 SLB SLB . E 4 HOH A 1 601 232 HOH HOH . E 4 HOH A 2 602 161 HOH HOH . E 4 HOH A 3 603 144 HOH HOH . E 4 HOH A 4 604 114 HOH HOH . E 4 HOH A 5 605 83 HOH HOH . E 4 HOH A 6 606 57 HOH HOH . E 4 HOH A 7 607 136 HOH HOH . E 4 HOH A 8 608 40 HOH HOH . E 4 HOH A 9 609 116 HOH HOH . E 4 HOH A 10 610 69 HOH HOH . E 4 HOH A 11 611 52 HOH HOH . E 4 HOH A 12 612 5 HOH HOH . E 4 HOH A 13 613 187 HOH HOH . E 4 HOH A 14 614 74 HOH HOH . E 4 HOH A 15 615 42 HOH HOH . E 4 HOH A 16 616 99 HOH HOH . E 4 HOH A 17 617 104 HOH HOH . E 4 HOH A 18 618 156 HOH HOH . E 4 HOH A 19 619 8 HOH HOH . E 4 HOH A 20 620 2 HOH HOH . E 4 HOH A 21 621 141 HOH HOH . E 4 HOH A 22 622 97 HOH HOH . E 4 HOH A 23 623 16 HOH HOH . E 4 HOH A 24 624 182 HOH HOH . E 4 HOH A 25 625 39 HOH HOH . E 4 HOH A 26 626 26 HOH HOH . E 4 HOH A 27 627 12 HOH HOH . E 4 HOH A 28 628 106 HOH HOH . E 4 HOH A 29 629 226 HOH HOH . E 4 HOH A 30 630 11 HOH HOH . E 4 HOH A 31 631 3 HOH HOH . E 4 HOH A 32 632 173 HOH HOH . E 4 HOH A 33 633 14 HOH HOH . E 4 HOH A 34 634 86 HOH HOH . E 4 HOH A 35 635 21 HOH HOH . E 4 HOH A 36 636 25 HOH HOH . E 4 HOH A 37 637 7 HOH HOH . E 4 HOH A 38 638 72 HOH HOH . E 4 HOH A 39 639 233 HOH HOH . E 4 HOH A 40 640 67 HOH HOH . E 4 HOH A 41 641 76 HOH HOH . E 4 HOH A 42 642 224 HOH HOH . E 4 HOH A 43 643 24 HOH HOH . E 4 HOH A 44 644 27 HOH HOH . E 4 HOH A 45 645 229 HOH HOH . E 4 HOH A 46 646 22 HOH HOH . E 4 HOH A 47 647 191 HOH HOH . E 4 HOH A 48 648 1 HOH HOH . E 4 HOH A 49 649 18 HOH HOH . E 4 HOH A 50 650 32 HOH HOH . E 4 HOH A 51 651 35 HOH HOH . E 4 HOH A 52 652 23 HOH HOH . E 4 HOH A 53 653 15 HOH HOH . E 4 HOH A 54 654 94 HOH HOH . E 4 HOH A 55 655 4 HOH HOH . E 4 HOH A 56 656 105 HOH HOH . E 4 HOH A 57 657 98 HOH HOH . E 4 HOH A 58 658 44 HOH HOH . E 4 HOH A 59 659 164 HOH HOH . E 4 HOH A 60 660 73 HOH HOH . E 4 HOH A 61 661 119 HOH HOH . E 4 HOH A 62 662 112 HOH HOH . E 4 HOH A 63 663 6 HOH HOH . E 4 HOH A 64 664 62 HOH HOH . E 4 HOH A 65 665 96 HOH HOH . E 4 HOH A 66 666 54 HOH HOH . E 4 HOH A 67 667 9 HOH HOH . E 4 HOH A 68 668 64 HOH HOH . E 4 HOH A 69 669 221 HOH HOH . E 4 HOH A 70 670 122 HOH HOH . E 4 HOH A 71 671 37 HOH HOH . E 4 HOH A 72 672 202 HOH HOH . E 4 HOH A 73 673 28 HOH HOH . E 4 HOH A 74 674 201 HOH HOH . E 4 HOH A 75 675 180 HOH HOH . E 4 HOH A 76 676 127 HOH HOH . E 4 HOH A 77 677 45 HOH HOH . E 4 HOH A 78 678 79 HOH HOH . E 4 HOH A 79 679 30 HOH HOH . E 4 HOH A 80 680 101 HOH HOH . E 4 HOH A 81 681 56 HOH HOH . E 4 HOH A 82 682 78 HOH HOH . E 4 HOH A 83 683 46 HOH HOH . E 4 HOH A 84 684 38 HOH HOH . E 4 HOH A 85 685 185 HOH HOH . E 4 HOH A 86 686 10 HOH HOH . E 4 HOH A 87 687 13 HOH HOH . E 4 HOH A 88 688 150 HOH HOH . E 4 HOH A 89 689 203 HOH HOH . E 4 HOH A 90 690 87 HOH HOH . E 4 HOH A 91 691 55 HOH HOH . E 4 HOH A 92 692 36 HOH HOH . E 4 HOH A 93 693 200 HOH HOH . E 4 HOH A 94 694 186 HOH HOH . E 4 HOH A 95 695 71 HOH HOH . E 4 HOH A 96 696 113 HOH HOH . E 4 HOH A 97 697 147 HOH HOH . E 4 HOH A 98 698 77 HOH HOH . E 4 HOH A 99 699 149 HOH HOH . E 4 HOH A 100 700 168 HOH HOH . E 4 HOH A 101 701 155 HOH HOH . E 4 HOH A 102 702 115 HOH HOH . E 4 HOH A 103 703 66 HOH HOH . E 4 HOH A 104 704 68 HOH HOH . E 4 HOH A 105 705 58 HOH HOH . E 4 HOH A 106 706 82 HOH HOH . E 4 HOH A 107 707 171 HOH HOH . E 4 HOH A 108 708 181 HOH HOH . E 4 HOH A 109 709 121 HOH HOH . E 4 HOH A 110 710 216 HOH HOH . E 4 HOH A 111 711 174 HOH HOH . E 4 HOH A 112 712 43 HOH HOH . E 4 HOH A 113 713 70 HOH HOH . E 4 HOH A 114 714 212 HOH HOH . E 4 HOH A 115 715 130 HOH HOH . E 4 HOH A 116 716 80 HOH HOH . E 4 HOH A 117 717 143 HOH HOH . E 4 HOH A 118 718 95 HOH HOH . E 4 HOH A 119 719 163 HOH HOH . E 4 HOH A 120 720 222 HOH HOH . E 4 HOH A 121 721 100 HOH HOH . E 4 HOH A 122 722 90 HOH HOH . E 4 HOH A 123 723 48 HOH HOH . E 4 HOH A 124 724 167 HOH HOH . E 4 HOH A 125 725 211 HOH HOH . E 4 HOH A 126 726 20 HOH HOH . E 4 HOH A 127 727 85 HOH HOH . E 4 HOH A 128 728 228 HOH HOH . E 4 HOH A 129 729 53 HOH HOH . E 4 HOH A 130 730 184 HOH HOH . E 4 HOH A 131 731 17 HOH HOH . E 4 HOH A 132 732 166 HOH HOH . E 4 HOH A 133 733 194 HOH HOH . E 4 HOH A 134 734 236 HOH HOH . E 4 HOH A 135 735 178 HOH HOH . E 4 HOH A 136 736 153 HOH HOH . E 4 HOH A 137 737 61 HOH HOH . E 4 HOH A 138 738 49 HOH HOH . E 4 HOH A 139 739 208 HOH HOH . E 4 HOH A 140 740 110 HOH HOH . E 4 HOH A 141 741 162 HOH HOH . E 4 HOH A 142 742 135 HOH HOH . E 4 HOH A 143 743 231 HOH HOH . E 4 HOH A 144 744 175 HOH HOH . E 4 HOH A 145 745 133 HOH HOH . E 4 HOH A 146 746 131 HOH HOH . E 4 HOH A 147 747 50 HOH HOH . E 4 HOH A 148 748 235 HOH HOH . E 4 HOH A 149 749 195 HOH HOH . E 4 HOH A 150 750 199 HOH HOH . E 4 HOH A 151 751 88 HOH HOH . E 4 HOH A 152 752 214 HOH HOH . E 4 HOH A 153 753 19 HOH HOH . E 4 HOH A 154 754 206 HOH HOH . E 4 HOH A 155 755 33 HOH HOH . E 4 HOH A 156 756 230 HOH HOH . E 4 HOH A 157 757 128 HOH HOH . E 4 HOH A 158 758 91 HOH HOH . E 4 HOH A 159 759 29 HOH HOH . E 4 HOH A 160 760 165 HOH HOH . E 4 HOH A 161 761 123 HOH HOH . E 4 HOH A 162 762 93 HOH HOH . E 4 HOH A 163 763 134 HOH HOH . E 4 HOH A 164 764 120 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 C C1 SLB . . . D 3 5.044 105.884 23.244 1 34.58 ? C1 SLB 503 A 1 HETATM 2 C C2 SLB . . . D 3 4.95 105.571 24.737 1 32.98 ? C2 SLB 503 A 1 HETATM 3 C C3 SLB . . . D 3 4.131 106.632 25.45 1 26.12 ? C3 SLB 503 A 1 HETATM 4 C C4 SLB . . . D 3 4.187 106.48 26.92 1 26.68 ? C4 SLB 503 A 1 HETATM 5 C C5 SLB . . . D 3 5.602 106.398 27.413 1 24.92 ? C5 SLB 503 A 1 HETATM 6 C C6 SLB . . . D 3 6.357 105.274 26.717 1 27.52 ? C6 SLB 503 A 1 HETATM 7 C C7 SLB . . . D 3 7.78 105.228 27.213 1 26.41 ? C7 SLB 503 A 1 HETATM 8 C C8 SLB . . . D 3 8.53 104.116 26.476 1 30.76 ? C8 SLB 503 A 1 HETATM 9 C C9 SLB . . . D 3 9.948 104.004 27.024 1 29.04 ? C9 SLB 503 A 1 HETATM 10 C C10 SLB . . . D 3 6.259 107.106 29.758 1 31.87 ? C10 SLB 503 A 1 HETATM 11 C C11 SLB . . . D 3 6.315 106.841 31.261 1 32.54 ? C11 SLB 503 A 1 HETATM 12 N N5 SLB . . . D 3 5.64 106.136 28.873 1 29.75 ? N5 SLB 503 A 1 HETATM 13 O O1A SLB . . . D 3 4.103 105.558 22.472 1 34.6 ? O1A SLB 503 A 1 HETATM 14 O O1B SLB . . . D 3 6.072 106.449 22.785 1 26.19 ? O1B SLB 503 A 1 HETATM 15 O O2 SLB . . . D 3 4.341 104.362 24.9 1 30.82 ? O2 SLB 503 A 1 HETATM 16 O O4 SLB . . . D 3 3.529 107.626 27.534 1 29.46 ? O4 SLB 503 A 1 HETATM 17 O O6 SLB . . . D 3 6.353 105.467 25.269 1 32.73 ? O6 SLB 503 A 1 HETATM 18 O O7 SLB . . . D 3 8.405 106.465 26.969 1 33.52 ? O7 SLB 503 A 1 HETATM 19 O O8 SLB . . . D 3 7.864 102.904 26.672 1 29.05 ? O8 SLB 503 A 1 HETATM 20 O O9 SLB . . . D 3 9.901 103.474 28.32 1 32.48 ? O9 SLB 503 A 1 HETATM 21 O O10 SLB . . . D 3 6.722 108.102 29.314 1 26.5 ? O10 SLB 503 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #