data_7M2D # _model_server_result.job_id I_p57XHR43mc7rv5OrycLA _model_server_result.datetime_utc '2024-11-08 01:47:26' _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 7m2d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 7M2D # _exptl.entry_id 7M2D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _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 7M2D _cell.length_a 115.11 _cell.length_b 115.11 _cell.length_c 309.02 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7M2D _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -57.555 99.688184 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -115.11 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . 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 3 n C NAG 1 C 1 NAG C 1 NAG 3 n C NAG 2 C 2 NAG C 2 NAG 3 n C BMA 3 C 3 BMA C 3 BMA 3 n C MAN 4 C 4 MAN C 4 MAN # 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 26 A CYS 53 1_555 B SG CYS 108 B CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 81 A CYS 108 1_555 A SG CYS 108 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 A SG CYS 94 A CYS 121 1_555 A SG CYS 120 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 B SG CYS 10 B CYS 511 1_555 B SG CYS 55 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 B SG CYS 100 B CYS 601 1_555 B SG CYS 107 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A ND2 ASN 201 A ASN 228 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 211 A ASN 238 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A ND2 ASN 230 A ASN 257 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 241 A ASN 268 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B ND2 ASN 62 B ASN 563 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 7M2D _atom_sites.fract_transf_matrix[1][1] 0.008687 _atom_sites.fract_transf_matrix[1][2] 0.005016 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010031 _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] 0.003236 _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 D 4 NAG A 1 601 601 NAG NAG . E 4 NAG A 1 602 602 NAG NAG . F 4 NAG A 1 603 603 NAG NAG . G 4 NAG A 1 604 604 NAG NAG . H 5 YPS A 1 605 605 YPS 953 . I 6 HOH A 1 701 109 HOH HOH . I 6 HOH A 2 702 125 HOH HOH . I 6 HOH A 3 703 37 HOH HOH . I 6 HOH A 4 704 73 HOH HOH . I 6 HOH A 5 705 108 HOH HOH . I 6 HOH A 6 706 84 HOH HOH . I 6 HOH A 7 707 82 HOH HOH . I 6 HOH A 8 708 69 HOH HOH . I 6 HOH A 9 709 1 HOH HOH . I 6 HOH A 10 710 38 HOH HOH . I 6 HOH A 11 711 88 HOH HOH . I 6 HOH A 12 712 5 HOH HOH . I 6 HOH A 13 713 79 HOH HOH . I 6 HOH A 14 714 66 HOH HOH . I 6 HOH A 15 715 71 HOH HOH . I 6 HOH A 16 716 80 HOH HOH . I 6 HOH A 17 717 67 HOH HOH . I 6 HOH A 18 718 9 HOH HOH . I 6 HOH A 19 719 4 HOH HOH . I 6 HOH A 20 720 89 HOH HOH . I 6 HOH A 21 721 35 HOH HOH . I 6 HOH A 22 722 119 HOH HOH . I 6 HOH A 23 723 52 HOH HOH . I 6 HOH A 24 724 15 HOH HOH . I 6 HOH A 25 725 60 HOH HOH . I 6 HOH A 26 726 7 HOH HOH . I 6 HOH A 27 727 120 HOH HOH . I 6 HOH A 28 728 42 HOH HOH . I 6 HOH A 29 729 3 HOH HOH . I 6 HOH A 30 730 6 HOH HOH . I 6 HOH A 31 731 14 HOH HOH . I 6 HOH A 32 732 33 HOH HOH . I 6 HOH A 33 733 75 HOH HOH . I 6 HOH A 34 734 12 HOH HOH . I 6 HOH A 35 735 53 HOH HOH . I 6 HOH A 36 736 8 HOH HOH . I 6 HOH A 37 737 101 HOH HOH . I 6 HOH A 38 738 13 HOH HOH . I 6 HOH A 39 739 114 HOH HOH . I 6 HOH A 40 740 10 HOH HOH . I 6 HOH A 41 741 83 HOH HOH . I 6 HOH A 42 742 43 HOH HOH . I 6 HOH A 43 743 56 HOH HOH . I 6 HOH A 44 744 68 HOH HOH . I 6 HOH A 45 745 31 HOH HOH . I 6 HOH A 46 746 112 HOH HOH . I 6 HOH A 47 747 95 HOH HOH . I 6 HOH A 48 748 32 HOH HOH . I 6 HOH A 49 749 48 HOH HOH . I 6 HOH A 50 750 127 HOH HOH . I 6 HOH A 51 751 122 HOH HOH . I 6 HOH A 52 752 76 HOH HOH . I 6 HOH A 53 753 77 HOH HOH . I 6 HOH A 54 754 11 HOH HOH . I 6 HOH A 55 755 117 HOH HOH . I 6 HOH A 56 756 143 HOH HOH . I 6 HOH A 57 757 113 HOH HOH . I 6 HOH A 58 758 118 HOH HOH . I 6 HOH A 59 759 126 HOH HOH . J 6 HOH B 1 701 16 HOH HOH . J 6 HOH B 2 702 28 HOH HOH . J 6 HOH B 3 703 17 HOH HOH . J 6 HOH B 4 704 29 HOH HOH . J 6 HOH B 5 705 140 HOH HOH . J 6 HOH B 6 706 18 HOH HOH . J 6 HOH B 7 707 19 HOH HOH . J 6 HOH B 8 708 65 HOH HOH . J 6 HOH B 9 709 105 HOH HOH . J 6 HOH B 10 710 21 HOH HOH . J 6 HOH B 11 711 99 HOH HOH . J 6 HOH B 12 712 39 HOH HOH . J 6 HOH B 13 713 100 HOH HOH . J 6 HOH B 14 714 93 HOH HOH . J 6 HOH B 15 715 94 HOH HOH . J 6 HOH B 16 716 121 HOH HOH . J 6 HOH B 17 717 44 HOH HOH . J 6 HOH B 18 718 22 HOH HOH . J 6 HOH B 19 719 30 HOH HOH . J 6 HOH B 20 720 98 HOH HOH . J 6 HOH B 21 721 133 HOH HOH . J 6 HOH B 22 722 40 HOH HOH . J 6 HOH B 23 723 132 HOH HOH . J 6 HOH B 24 724 137 HOH HOH . J 6 HOH B 25 725 106 HOH HOH . J 6 HOH B 26 726 142 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 . . . D 4 -38.538 -0.421 -40.695 1 88.39 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . D 4 -38.401 0.845 -39.867 1 87.07 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . D 4 -37.579 1.872 -40.63 1 90.82 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . D 4 -36.212 1.286 -40.958 1 92.24 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . D 4 -36.37 -0.026 -41.728 1 94.01 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . D 4 -35.058 -0.747 -41.942 1 97.25 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . D 4 -40.088 1.552 -38.233 1 94 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . D 4 -41.465 2.113 -38.031 1 90.04 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . D 4 -39.701 1.385 -39.503 1 88.5 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . D 4 -37.442 3.059 -39.857 1 96.88 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . D 4 -35.458 2.211 -41.732 1 100.83 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . D 4 -37.226 -0.935 -41.015 1 91.64 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . D 4 -34.309 -0.852 -40.739 1 95.13 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . D 4 -39.359 1.264 -37.288 1 97.15 ? O7 NAG 601 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #