data_6H76 # _model_server_result.job_id RJXLCbKGX7QqjNgsPJ3Mbg _model_server_result.datetime_utc '2024-11-27 18:31:48' _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 6h76 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6H76 # _exptl.entry_id 6H76 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.27 _entity.id 2 _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 6H76 _cell.length_a 47.788 _cell.length_b 75.31 _cell.length_c 87.774 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6H76 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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,F,G _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 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 O LEU 177 A LEU 177 1_555 F CS CS . A CS 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.277 ? metalc ? metalc2 A OD1 ASN 180 A ASN 180 1_555 F CS CS . A CS 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.046 ? metalc ? metalc3 A O VAL 200 A VAL 200 1_555 F CS CS . A CS 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.073 ? metalc ? metalc4 A O LYS 224 A LYS 224 1_555 E CS CS . A CS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.016 ? metalc ? metalc5 A O LEU 226 A LEU 226 1_555 E CS CS . A CS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? metalc ? metalc6 E CS CS . A CS 404 1_555 G O HOH . A HOH 529 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.486 ? metalc ? metalc7 E CS CS . A CS 404 1_555 G O HOH . A HOH 646 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.45 ? metalc ? metalc8 E CS CS . A CS 404 1_555 G O HOH . A HOH 656 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.243 ? metalc ? metalc9 E CS CS . A CS 404 1_555 G O HOH . A HOH 665 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? # _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 277 n n C1 O1A SLB doub 278 n n C1 O1B SLB sing 279 n n C2 C3 SLB sing 280 n n C2 O2 SLB sing 281 n n C2 O6 SLB sing 282 n n C3 C4 SLB sing 283 n n C3 H32 SLB sing 284 n n C3 H31 SLB sing 285 n n C4 C5 SLB sing 286 n n C4 O4 SLB sing 287 n n C4 H4 SLB sing 288 n n C5 C6 SLB sing 289 n n C5 N5 SLB sing 290 n n C5 H5 SLB sing 291 n n C6 C7 SLB sing 292 n n C6 O6 SLB sing 293 n n C6 H6 SLB sing 294 n n C7 C8 SLB sing 295 n n C7 O7 SLB sing 296 n n C7 H7 SLB sing 297 n n C8 C9 SLB sing 298 n n C8 O8 SLB sing 299 n n C8 H8 SLB sing 300 n n C9 O9 SLB sing 301 n n C9 H92 SLB sing 302 n n C9 H91 SLB sing 303 n n C10 C11 SLB sing 304 n n C10 N5 SLB sing 305 n n C10 O10 SLB doub 306 n n C11 H111 SLB sing 307 n n C11 H113 SLB sing 308 n n C11 H112 SLB sing 309 n n N5 HN5 SLB sing 310 n n O1B HO1B SLB sing 311 n n O2 HO2 SLB sing 312 n n O4 HO4 SLB sing 313 n n O7 HO7 SLB sing 314 n n O8 HO8 SLB sing 315 n n O9 HO9 SLB sing 316 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 6H76 _atom_sites.fract_transf_matrix[1][1] 0.020926 _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] 0.013278 _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] 0.011393 _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 SLB A 1 401 1 SLB SLB . C 3 CL A 1 402 1 CL CL . D 3 CL A 1 403 1 CL CL . E 4 CS A 1 404 1 CS CS . F 4 CS A 1 405 2 CS CS . G 5 HOH A 1 501 111 HOH HOH . G 5 HOH A 2 502 130 HOH HOH . G 5 HOH A 3 503 160 HOH HOH . G 5 HOH A 4 504 184 HOH HOH . G 5 HOH A 5 505 77 HOH HOH . G 5 HOH A 6 506 180 HOH HOH . G 5 HOH A 7 507 107 HOH HOH . G 5 HOH A 8 508 133 HOH HOH . G 5 HOH A 9 509 22 HOH HOH . G 5 HOH A 10 510 122 HOH HOH . G 5 HOH A 11 511 64 HOH HOH . G 5 HOH A 12 512 11 HOH HOH . G 5 HOH A 13 513 42 HOH HOH . G 5 HOH A 14 514 17 HOH HOH . G 5 HOH A 15 515 5 HOH HOH . G 5 HOH A 16 516 170 HOH HOH . G 5 HOH A 17 517 65 HOH HOH . G 5 HOH A 18 518 173 HOH HOH . G 5 HOH A 19 519 84 HOH HOH . G 5 HOH A 20 520 88 HOH HOH . G 5 HOH A 21 521 183 HOH HOH . G 5 HOH A 22 522 69 HOH HOH . G 5 HOH A 23 523 35 HOH HOH . G 5 HOH A 24 524 131 HOH HOH . G 5 HOH A 25 525 163 HOH HOH . G 5 HOH A 26 526 118 HOH HOH . G 5 HOH A 27 527 105 HOH HOH . G 5 HOH A 28 528 54 HOH HOH . G 5 HOH A 29 529 75 HOH HOH . G 5 HOH A 30 530 109 HOH HOH . G 5 HOH A 31 531 39 HOH HOH . G 5 HOH A 32 532 128 HOH HOH . G 5 HOH A 33 533 8 HOH HOH . G 5 HOH A 34 534 48 HOH HOH . G 5 HOH A 35 535 59 HOH HOH . G 5 HOH A 36 536 106 HOH HOH . G 5 HOH A 37 537 151 HOH HOH . G 5 HOH A 38 538 121 HOH HOH . G 5 HOH A 39 539 61 HOH HOH . G 5 HOH A 40 540 138 HOH HOH . G 5 HOH A 41 541 101 HOH HOH . G 5 HOH A 42 542 103 HOH HOH . G 5 HOH A 43 543 24 HOH HOH . G 5 HOH A 44 544 125 HOH HOH . G 5 HOH A 45 545 142 HOH HOH . G 5 HOH A 46 546 6 HOH HOH . G 5 HOH A 47 547 55 HOH HOH . G 5 HOH A 48 548 96 HOH HOH . G 5 HOH A 49 549 52 HOH HOH . G 5 HOH A 50 550 143 HOH HOH . G 5 HOH A 51 551 51 HOH HOH . G 5 HOH A 52 552 79 HOH HOH . G 5 HOH A 53 553 56 HOH HOH . G 5 HOH A 54 554 18 HOH HOH . G 5 HOH A 55 555 14 HOH HOH . G 5 HOH A 56 556 172 HOH HOH . G 5 HOH A 57 557 108 HOH HOH . G 5 HOH A 58 558 177 HOH HOH . G 5 HOH A 59 559 15 HOH HOH . G 5 HOH A 60 560 47 HOH HOH . G 5 HOH A 61 561 53 HOH HOH . G 5 HOH A 62 562 139 HOH HOH . G 5 HOH A 63 563 140 HOH HOH . G 5 HOH A 64 564 147 HOH HOH . G 5 HOH A 65 565 12 HOH HOH . G 5 HOH A 66 566 28 HOH HOH . G 5 HOH A 67 567 99 HOH HOH . G 5 HOH A 68 568 21 HOH HOH . G 5 HOH A 69 569 60 HOH HOH . G 5 HOH A 70 570 70 HOH HOH . G 5 HOH A 71 571 73 HOH HOH . G 5 HOH A 72 572 148 HOH HOH . G 5 HOH A 73 573 182 HOH HOH . G 5 HOH A 74 574 9 HOH HOH . G 5 HOH A 75 575 19 HOH HOH . G 5 HOH A 76 576 123 HOH HOH . G 5 HOH A 77 577 136 HOH HOH . G 5 HOH A 78 578 141 HOH HOH . G 5 HOH A 79 579 13 HOH HOH . G 5 HOH A 80 580 116 HOH HOH . G 5 HOH A 81 581 113 HOH HOH . G 5 HOH A 82 582 83 HOH HOH . G 5 HOH A 83 583 20 HOH HOH . G 5 HOH A 84 584 81 HOH HOH . G 5 HOH A 85 585 34 HOH HOH . G 5 HOH A 86 586 144 HOH HOH . G 5 HOH A 87 587 37 HOH HOH . G 5 HOH A 88 588 90 HOH HOH . G 5 HOH A 89 589 164 HOH HOH . G 5 HOH A 90 590 68 HOH HOH . G 5 HOH A 91 591 57 HOH HOH . G 5 HOH A 92 592 165 HOH HOH . G 5 HOH A 93 593 134 HOH HOH . G 5 HOH A 94 594 16 HOH HOH . G 5 HOH A 95 595 85 HOH HOH . G 5 HOH A 96 596 93 HOH HOH . G 5 HOH A 97 597 31 HOH HOH . G 5 HOH A 98 598 33 HOH HOH . G 5 HOH A 99 599 112 HOH HOH . G 5 HOH A 100 600 89 HOH HOH . G 5 HOH A 101 601 50 HOH HOH . G 5 HOH A 102 602 32 HOH HOH . G 5 HOH A 103 603 94 HOH HOH . G 5 HOH A 104 604 76 HOH HOH . G 5 HOH A 105 605 78 HOH HOH . G 5 HOH A 106 606 110 HOH HOH . G 5 HOH A 107 607 162 HOH HOH . G 5 HOH A 108 608 72 HOH HOH . G 5 HOH A 109 609 159 HOH HOH . G 5 HOH A 110 610 179 HOH HOH . G 5 HOH A 111 611 92 HOH HOH . G 5 HOH A 112 612 174 HOH HOH . G 5 HOH A 113 613 127 HOH HOH . G 5 HOH A 114 614 114 HOH HOH . G 5 HOH A 115 615 40 HOH HOH . G 5 HOH A 116 616 29 HOH HOH . G 5 HOH A 117 617 44 HOH HOH . G 5 HOH A 118 618 157 HOH HOH . G 5 HOH A 119 619 7 HOH HOH . G 5 HOH A 120 620 45 HOH HOH . G 5 HOH A 121 621 67 HOH HOH . G 5 HOH A 122 622 117 HOH HOH . G 5 HOH A 123 623 66 HOH HOH . G 5 HOH A 124 624 145 HOH HOH . G 5 HOH A 125 625 49 HOH HOH . G 5 HOH A 126 626 120 HOH HOH . G 5 HOH A 127 627 86 HOH HOH . G 5 HOH A 128 628 46 HOH HOH . G 5 HOH A 129 629 150 HOH HOH . G 5 HOH A 130 630 43 HOH HOH . G 5 HOH A 131 631 102 HOH HOH . G 5 HOH A 132 632 25 HOH HOH . G 5 HOH A 133 633 181 HOH HOH . G 5 HOH A 134 634 63 HOH HOH . G 5 HOH A 135 635 30 HOH HOH . G 5 HOH A 136 636 71 HOH HOH . G 5 HOH A 137 637 74 HOH HOH . G 5 HOH A 138 638 62 HOH HOH . G 5 HOH A 139 639 135 HOH HOH . G 5 HOH A 140 640 26 HOH HOH . G 5 HOH A 141 641 23 HOH HOH . G 5 HOH A 142 642 168 HOH HOH . G 5 HOH A 143 643 82 HOH HOH . G 5 HOH A 144 644 91 HOH HOH . G 5 HOH A 145 645 146 HOH HOH . G 5 HOH A 146 646 98 HOH HOH . G 5 HOH A 147 647 10 HOH HOH . G 5 HOH A 148 648 115 HOH HOH . G 5 HOH A 149 649 80 HOH HOH . G 5 HOH A 150 650 119 HOH HOH . G 5 HOH A 151 651 167 HOH HOH . G 5 HOH A 152 652 129 HOH HOH . G 5 HOH A 153 653 171 HOH HOH . G 5 HOH A 154 654 41 HOH HOH . G 5 HOH A 155 655 137 HOH HOH . G 5 HOH A 156 656 156 HOH HOH . G 5 HOH A 157 657 132 HOH HOH . G 5 HOH A 158 658 38 HOH HOH . G 5 HOH A 159 659 158 HOH HOH . G 5 HOH A 160 660 155 HOH HOH . G 5 HOH A 161 661 153 HOH HOH . G 5 HOH A 162 662 124 HOH HOH . G 5 HOH A 163 663 95 HOH HOH . G 5 HOH A 164 664 104 HOH HOH . G 5 HOH A 165 665 87 HOH HOH . G 5 HOH A 166 666 149 HOH HOH . G 5 HOH A 167 667 27 HOH HOH . G 5 HOH A 168 668 154 HOH HOH . G 5 HOH A 169 669 126 HOH HOH . G 5 HOH A 170 670 97 HOH HOH . G 5 HOH A 171 671 152 HOH HOH . G 5 HOH A 172 672 100 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 C C1 SLB . . . B 2 -7.963 -9.486 11.127 1 14.26 ? C1 SLB 401 A 1 HETATM 2 C C2 SLB . . . B 2 -9.205 -9.19 11.948 1 14.28 ? C2 SLB 401 A 1 HETATM 3 C C3 SLB . . . B 2 -10.336 -8.737 11.03 1 15.49 ? C3 SLB 401 A 1 HETATM 4 C C4 SLB . . . B 2 -11.488 -8.196 11.879 1 15.02 ? C4 SLB 401 A 1 HETATM 5 C C5 SLB . . . B 2 -10.959 -7.099 12.855 1 13.81 ? C5 SLB 401 A 1 HETATM 6 C C6 SLB . . . B 2 -9.874 -7.72 13.696 1 14.87 ? C6 SLB 401 A 1 HETATM 7 C C7 SLB . . . B 2 -9.253 -6.714 14.661 1 14.59 ? C7 SLB 401 A 1 HETATM 8 C C8 SLB . . . B 2 -8.069 -7.364 15.445 1 13.83 ? C8 SLB 401 A 1 HETATM 9 C C9 SLB . . . B 2 -7.456 -6.406 16.469 1 15.29 ? C9 SLB 401 A 1 HETATM 10 C C10 SLB . . . B 2 -12.574 -5.382 13.525 1 15.33 ? C10 SLB 401 A 1 HETATM 11 C C11 SLB . . . B 2 -13.627 -4.973 14.51 1 15.75 ? C11 SLB 401 A 1 HETATM 12 N N5 SLB . . . B 2 -12.047 -6.568 13.658 1 14.06 ? N5 SLB 401 A 1 HETATM 13 O O1A SLB . . . B 2 -7.358 -8.511 10.614 1 16.3 ? O1A SLB 401 A 1 HETATM 14 O O1B SLB . . . B 2 -7.561 -10.677 11.043 1 15.15 ? O1B SLB 401 A 1 HETATM 15 O O2 SLB . . . B 2 -9.64 -10.354 12.653 1 14.13 ? O2 SLB 401 A 1 HETATM 16 O O4 SLB . . . B 2 -12.556 -7.711 11.083 1 14.75 ? O4 SLB 401 A 1 HETATM 17 O O6 SLB . . . B 2 -8.826 -8.2 12.888 1 13.72 ? O6 SLB 401 A 1 HETATM 18 O O7 SLB . . . B 2 -8.686 -5.602 13.922 1 15.77 ? O7 SLB 401 A 1 HETATM 19 O O8 SLB . . . B 2 -8.545 -8.556 16.06 1 14.75 ? O8 SLB 401 A 1 HETATM 20 O O9 SLB . . . B 2 -8.383 -5.895 17.397 1 16.68 ? O9 SLB 401 A 1 HETATM 21 O O10 SLB . . . B 2 -12.207 -4.609 12.672 1 17.56 ? O10 SLB 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 21 #