data_1SOM # _model_server_result.job_id LdIkyphREarZ25XZDFvhSA _model_server_result.datetime_utc '2024-11-28 12:29:32' _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 1som # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":544}' # _entry.id 1SOM # _exptl.entry_id 1SOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 1SOM _cell.length_a 111.56 _cell.length_b 111.56 _cell.length_c 137.002 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SOM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O _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_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 137.002 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N 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 67 A CYS 67 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf2 A SG CYS 254 A CYS 254 1_555 A SG CYS 265 A CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 402 A CYS 402 1_555 A SG CYS 521 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 59 A ASN 59 1_555 C C1 NAG . A NAG 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale2 A OG SER 200 A SER 200 1_555 N P1 VXA . A VXA 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.528 ? covale ? covale3 A ND2 ASN 416 A ASN 416 1_555 B C1 NAG . A NAG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 1SOM _atom_sites.fract_transf_matrix[1][1] 0.008964 _atom_sites.fract_transf_matrix[1][2] 0.005175 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01035 _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] 0.007299 _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 NAG A 1 544 416 NAG NAG . C 2 NAG A 1 545 59 NAG NAG . D 3 UNX A 1 1000 1000 UNX DEN . E 3 UNX A 1 1001 1001 UNX DEN . F 3 UNX A 1 1002 1002 UNX DEN . G 3 UNX A 1 1003 1002 UNX DEN . H 3 UNX A 1 1004 1002 UNX DEN . I 3 UNX A 1 1005 1002 UNX DEN . J 3 UNX A 1 1006 1002 UNX DEN . K 3 UNX A 1 1007 1002 UNX DEN . L 3 UNX A 1 1008 1002 UNX DEN . M 3 UNX A 1 1009 1002 UNX DEN . N 4 VXA A 1 1010 200 VXA SOM . O 5 HOH A 1 600 600 HOH HOH . O 5 HOH A 2 601 601 HOH HOH . O 5 HOH A 3 602 602 HOH HOH . O 5 HOH A 4 603 603 HOH HOH . O 5 HOH A 5 604 604 HOH HOH . O 5 HOH A 6 605 605 HOH HOH . O 5 HOH A 7 606 606 HOH HOH . O 5 HOH A 8 607 607 HOH HOH . O 5 HOH A 9 608 608 HOH HOH . O 5 HOH A 10 609 609 HOH HOH . O 5 HOH A 11 610 610 HOH HOH . O 5 HOH A 12 611 611 HOH HOH . O 5 HOH A 13 612 612 HOH HOH . O 5 HOH A 14 613 613 HOH HOH . O 5 HOH A 15 614 614 HOH HOH . O 5 HOH A 16 615 615 HOH HOH . O 5 HOH A 17 616 616 HOH HOH . O 5 HOH A 18 617 617 HOH HOH . O 5 HOH A 19 618 618 HOH HOH . O 5 HOH A 20 619 619 HOH HOH . O 5 HOH A 21 620 620 HOH HOH . O 5 HOH A 22 621 621 HOH HOH . O 5 HOH A 23 622 622 HOH HOH . O 5 HOH A 24 623 623 HOH HOH . O 5 HOH A 25 624 624 HOH HOH . O 5 HOH A 26 625 625 HOH HOH . O 5 HOH A 27 626 626 HOH HOH . O 5 HOH A 28 627 627 HOH HOH . O 5 HOH A 29 628 628 HOH HOH . O 5 HOH A 30 629 629 HOH HOH . O 5 HOH A 31 630 630 HOH HOH . O 5 HOH A 32 631 631 HOH HOH . O 5 HOH A 33 632 632 HOH HOH . O 5 HOH A 34 633 633 HOH HOH . O 5 HOH A 35 634 634 HOH HOH . O 5 HOH A 36 635 635 HOH HOH . O 5 HOH A 37 636 636 HOH HOH . O 5 HOH A 38 637 637 HOH HOH . O 5 HOH A 39 638 638 HOH HOH . O 5 HOH A 40 639 639 HOH HOH . O 5 HOH A 41 640 640 HOH HOH . O 5 HOH A 42 641 641 HOH HOH . O 5 HOH A 43 642 642 HOH HOH . O 5 HOH A 44 643 643 HOH HOH . O 5 HOH A 45 644 644 HOH HOH . O 5 HOH A 46 645 645 HOH HOH . O 5 HOH A 47 646 646 HOH HOH . O 5 HOH A 48 647 647 HOH HOH . O 5 HOH A 49 648 648 HOH HOH . O 5 HOH A 50 649 649 HOH HOH . O 5 HOH A 51 650 650 HOH HOH . O 5 HOH A 52 651 651 HOH HOH . O 5 HOH A 53 652 652 HOH HOH . O 5 HOH A 54 653 653 HOH HOH . O 5 HOH A 55 654 654 HOH HOH . O 5 HOH A 56 655 655 HOH HOH . O 5 HOH A 57 656 656 HOH HOH . O 5 HOH A 58 657 657 HOH HOH . O 5 HOH A 59 658 658 HOH HOH . O 5 HOH A 60 659 659 HOH HOH . O 5 HOH A 61 660 660 HOH HOH . O 5 HOH A 62 661 661 HOH HOH . O 5 HOH A 63 662 662 HOH HOH . O 5 HOH A 64 663 663 HOH HOH . O 5 HOH A 65 664 664 HOH HOH . O 5 HOH A 66 665 665 HOH HOH . O 5 HOH A 67 666 666 HOH HOH . O 5 HOH A 68 667 667 HOH HOH . O 5 HOH A 69 668 668 HOH HOH . O 5 HOH A 70 669 669 HOH HOH . O 5 HOH A 71 670 670 HOH HOH . O 5 HOH A 72 671 671 HOH HOH . O 5 HOH A 73 672 672 HOH HOH . O 5 HOH A 74 673 673 HOH HOH . O 5 HOH A 75 674 674 HOH HOH . O 5 HOH A 76 675 675 HOH HOH . O 5 HOH A 77 676 676 HOH HOH . O 5 HOH A 78 677 677 HOH HOH . O 5 HOH A 79 678 678 HOH HOH . O 5 HOH A 80 679 679 HOH HOH . O 5 HOH A 81 680 680 HOH HOH . O 5 HOH A 82 681 681 HOH HOH . O 5 HOH A 83 682 682 HOH HOH . O 5 HOH A 84 683 683 HOH HOH . O 5 HOH A 85 684 684 HOH HOH . O 5 HOH A 86 685 685 HOH HOH . O 5 HOH A 87 686 686 HOH HOH . O 5 HOH A 88 687 687 HOH HOH . O 5 HOH A 89 688 688 HOH HOH . O 5 HOH A 90 689 689 HOH HOH . O 5 HOH A 91 690 690 HOH HOH . O 5 HOH A 92 691 691 HOH HOH . O 5 HOH A 93 692 692 HOH HOH . O 5 HOH A 94 693 693 HOH HOH . O 5 HOH A 95 694 694 HOH HOH . O 5 HOH A 96 695 695 HOH HOH . O 5 HOH A 97 696 696 HOH HOH . O 5 HOH A 98 697 697 HOH HOH . O 5 HOH A 99 698 698 HOH HOH . O 5 HOH A 100 699 699 HOH HOH . O 5 HOH A 101 700 700 HOH HOH . O 5 HOH A 102 701 701 HOH HOH . O 5 HOH A 103 702 702 HOH HOH . O 5 HOH A 104 703 703 HOH HOH . O 5 HOH A 105 704 704 HOH HOH . O 5 HOH A 106 705 705 HOH HOH . O 5 HOH A 107 706 706 HOH HOH . O 5 HOH A 108 707 707 HOH HOH . O 5 HOH A 109 708 708 HOH HOH . O 5 HOH A 110 709 709 HOH HOH . O 5 HOH A 111 710 710 HOH HOH . O 5 HOH A 112 711 711 HOH HOH . O 5 HOH A 113 712 712 HOH HOH . O 5 HOH A 114 713 713 HOH HOH . O 5 HOH A 115 714 714 HOH HOH . O 5 HOH A 116 715 715 HOH HOH . O 5 HOH A 117 716 716 HOH HOH . O 5 HOH A 118 717 717 HOH HOH . O 5 HOH A 119 718 718 HOH HOH . O 5 HOH A 120 719 719 HOH HOH . O 5 HOH A 121 720 720 HOH HOH . O 5 HOH A 122 721 721 HOH HOH . O 5 HOH A 123 722 722 HOH HOH . O 5 HOH A 124 723 723 HOH HOH . O 5 HOH A 125 724 724 HOH HOH . O 5 HOH A 126 725 725 HOH HOH . O 5 HOH A 127 726 726 HOH HOH . O 5 HOH A 128 727 727 HOH HOH . O 5 HOH A 129 728 728 HOH HOH . O 5 HOH A 130 729 729 HOH HOH . O 5 HOH A 131 730 730 HOH HOH . O 5 HOH A 132 731 731 HOH HOH . O 5 HOH A 133 732 732 HOH HOH . O 5 HOH A 134 733 733 HOH HOH . O 5 HOH A 135 734 734 HOH HOH . O 5 HOH A 136 735 735 HOH HOH . O 5 HOH A 137 736 736 HOH HOH . O 5 HOH A 138 737 737 HOH HOH . O 5 HOH A 139 738 738 HOH HOH . O 5 HOH A 140 739 739 HOH HOH . O 5 HOH A 141 740 740 HOH HOH . O 5 HOH A 142 741 741 HOH HOH . O 5 HOH A 143 742 742 HOH HOH . O 5 HOH A 144 743 743 HOH HOH . O 5 HOH A 145 744 744 HOH HOH . O 5 HOH A 146 745 745 HOH HOH . O 5 HOH A 147 746 746 HOH HOH . O 5 HOH A 148 747 747 HOH HOH . O 5 HOH A 149 748 748 HOH HOH . O 5 HOH A 150 749 749 HOH HOH . O 5 HOH A 151 750 750 HOH HOH . O 5 HOH A 152 751 751 HOH HOH . O 5 HOH A 153 752 752 HOH HOH . O 5 HOH A 154 753 753 HOH HOH . O 5 HOH A 155 754 754 HOH HOH . O 5 HOH A 156 755 755 HOH HOH . O 5 HOH A 157 756 756 HOH HOH . O 5 HOH A 158 757 757 HOH HOH . O 5 HOH A 159 758 758 HOH HOH . O 5 HOH A 160 759 759 HOH HOH . O 5 HOH A 161 760 760 HOH HOH . O 5 HOH A 162 761 761 HOH HOH . O 5 HOH A 163 762 762 HOH HOH . O 5 HOH A 164 763 763 HOH HOH . O 5 HOH A 165 764 764 HOH HOH . O 5 HOH A 166 765 765 HOH HOH . O 5 HOH A 167 766 766 HOH HOH . O 5 HOH A 168 767 767 HOH HOH . O 5 HOH A 169 768 768 HOH HOH . O 5 HOH A 170 769 769 HOH HOH . O 5 HOH A 171 770 770 HOH HOH . O 5 HOH A 172 771 771 HOH HOH . O 5 HOH A 173 772 772 HOH HOH . O 5 HOH A 174 773 773 HOH HOH . O 5 HOH A 175 774 774 HOH HOH . O 5 HOH A 176 775 775 HOH HOH . O 5 HOH A 177 776 776 HOH HOH . O 5 HOH A 178 777 777 HOH HOH . O 5 HOH A 179 778 778 HOH HOH . O 5 HOH A 180 779 779 HOH HOH . O 5 HOH A 181 780 780 HOH HOH . O 5 HOH A 182 781 781 HOH HOH . O 5 HOH A 183 782 782 HOH HOH . O 5 HOH A 184 783 783 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 NAG . . . B 2 18.866 61.99 33.562 1 42.66 ? C1 NAG 544 A 1 HETATM 2 C C2 NAG . . . B 2 20.365 61.799 33.561 1 43.59 ? C2 NAG 544 A 1 HETATM 3 C C3 NAG . . . B 2 21.016 62.281 32.259 1 44.81 ? C3 NAG 544 A 1 HETATM 4 C C4 NAG . . . B 2 20.232 61.812 31.006 1 45.28 ? C4 NAG 544 A 1 HETATM 5 C C5 NAG . . . B 2 18.754 62.114 31.181 1 45.07 ? C5 NAG 544 A 1 HETATM 6 C C6 NAG . . . B 2 17.89 61.644 29.987 1 45.4 ? C6 NAG 544 A 1 HETATM 7 C C7 NAG . . . B 2 21.318 61.944 35.764 1 43.18 ? C7 NAG 544 A 1 HETATM 8 C C8 NAG . . . B 2 21.887 62.805 36.883 1 43.01 ? C8 NAG 544 A 1 HETATM 9 N N2 NAG . . . B 2 20.918 62.559 34.661 1 43.51 ? N2 NAG 544 A 1 HETATM 10 O O3 NAG . . . B 2 22.342 61.769 32.213 1 45.33 ? O3 NAG 544 A 1 HETATM 11 O O4 NAG . . . B 2 20.719 62.481 29.849 1 46.75 ? O4 NAG 544 A 1 HETATM 12 O O5 NAG . . . B 2 18.284 61.451 32.377 1 43.89 ? O5 NAG 544 A 1 HETATM 13 O O6 NAG . . . B 2 17.741 60.226 29.929 1 45.4 ? O6 NAG 544 A 1 HETATM 14 O O7 NAG . . . B 2 21.229 60.728 35.906 1 43.63 ? O7 NAG 544 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 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #