data_3RGX # _model_server_result.job_id W_Mi8EwwFpCjaVcfBFeY1Q _model_server_result.datetime_utc '2024-10-19 10:15:15' _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 3rgx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1121}' # _entry.id 3RGX # _exptl.entry_id 3RGX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 120.98 _cell.angle_gamma 90 _cell.entry_id 3RGX _cell.length_a 173.391 _cell.length_b 66.705 _cell.length_c 119.051 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RGX _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 G N N ? 5 H N N ? 5 I N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 4 3 2 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 4 4 3 NAG NAG C1 O1 . O4 HO4 . 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 NAG 1 B 1 NAG A 1541 NAG 2 n B NAG 2 B 2 NAG A 1542 NAG 2 n B NAG 3 B 3 NAG A 1543 NAG 3 n C NAG 1 C 1 NAG A 2751 NAG 3 n C NAG 2 C 2 NAG A 2752 NAG 4 n D NAG 1 D 1 NAG A 5451 NAG 4 n D NAG 2 D 2 NAG A 5452 NAG 4 n D NAG 3 D 3 NAG A 5453 NAG 4 n D NAG 4 D 4 NAG A 5454 NAG 3 n E NAG 1 E 1 NAG A 5731 NAG 3 n E NAG 2 E 2 NAG A 5732 NAG 3 n F NAG 1 F 1 NAG A 2331 NAG 3 n F NAG 2 F 2 NAG A 2332 NAG # 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 40 A CYS 62 1_555 A SG CYS 47 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 A SG CYS 98 A CYS 120 1_555 A SG CYS 125 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 177 A CYS 199 1_555 A SG CYS 199 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 A SG CYS 222 A CYS 244 1_555 A SG CYS 246 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 293 A CYS 315 1_555 A SG CYS 317 A CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf6 A SG CYS 389 A CYS 411 1_555 A SG CYS 417 A CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf7 A SG CYS 587 A CYS 609 1_555 A SG CYS 613 A CYS 635 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 A SG CYS 741 A CYS 763 1_555 A SG CYS 748 A CYS 770 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 90 A ASN 112 1_555 G C1 NAG . A NAG 1121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 A ND2 ASN 132 A ASN 154 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 211 A ASN 233 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale4 A ND2 ASN 253 A ASN 275 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 A ND2 ASN 329 A ASN 351 1_555 H C1 NAG . A NAG 3511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale6 A ND2 ASN 488 A ASN 510 1_555 I C1 NAG . A NAG 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 A ND2 ASN 523 A ASN 545 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 A ND2 ASN 551 A ASN 573 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale9 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 B O4 NAG . B NAG 2 1_555 B C1 NAG . B NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale11 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale12 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale13 D O4 NAG . D NAG 2 1_555 D C1 NAG . D NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale14 D O4 NAG . D NAG 3 1_555 D C1 NAG . D NAG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale15 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale16 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 3RGX _atom_sites.fract_transf_matrix[1][1] 0.005767 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003463 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014991 _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] 0.009798 _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 G 5 NAG A 1 1121 1121 NAG NAG . H 5 NAG A 1 3511 3511 NAG NAG . I 5 NAG A 1 5101 5101 NAG NAG . J 6 HOH A 1 1 1 HOH HOH . J 6 HOH A 2 2 2 HOH HOH . J 6 HOH A 3 3 3 HOH HOH . J 6 HOH A 4 4 4 HOH HOH . J 6 HOH A 5 5 5 HOH HOH . J 6 HOH A 6 6 6 HOH HOH . J 6 HOH A 7 7 7 HOH HOH . J 6 HOH A 8 8 8 HOH HOH . J 6 HOH A 9 9 9 HOH HOH . J 6 HOH A 10 10 10 HOH HOH . J 6 HOH A 11 11 11 HOH HOH . J 6 HOH A 12 12 12 HOH HOH . J 6 HOH A 13 13 13 HOH HOH . J 6 HOH A 14 14 14 HOH HOH . J 6 HOH A 15 15 15 HOH HOH . J 6 HOH A 16 16 16 HOH HOH . J 6 HOH A 17 17 17 HOH HOH . J 6 HOH A 18 18 18 HOH HOH . J 6 HOH A 19 19 19 HOH HOH . J 6 HOH A 20 20 20 HOH HOH . J 6 HOH A 21 21 21 HOH HOH . J 6 HOH A 22 22 22 HOH HOH . J 6 HOH A 23 791 23 HOH HOH . J 6 HOH A 24 792 24 HOH HOH . J 6 HOH A 25 793 25 HOH HOH . J 6 HOH A 26 794 26 HOH HOH . J 6 HOH A 27 795 27 HOH HOH . J 6 HOH A 28 796 28 HOH HOH . J 6 HOH A 29 797 29 HOH HOH . J 6 HOH A 30 798 30 HOH HOH . J 6 HOH A 31 799 31 HOH HOH . J 6 HOH A 32 800 32 HOH HOH . J 6 HOH A 33 801 33 HOH HOH . J 6 HOH A 34 802 34 HOH HOH . J 6 HOH A 35 803 35 HOH HOH . J 6 HOH A 36 804 36 HOH HOH . J 6 HOH A 37 805 37 HOH HOH . J 6 HOH A 38 806 38 HOH HOH . J 6 HOH A 39 807 39 HOH HOH . J 6 HOH A 40 808 40 HOH HOH . J 6 HOH A 41 809 41 HOH HOH . J 6 HOH A 42 810 42 HOH HOH . J 6 HOH A 43 811 43 HOH HOH . J 6 HOH A 44 812 44 HOH HOH . J 6 HOH A 45 813 45 HOH HOH . J 6 HOH A 46 814 46 HOH HOH . J 6 HOH A 47 815 47 HOH HOH . J 6 HOH A 48 816 48 HOH HOH . J 6 HOH A 49 817 49 HOH HOH . J 6 HOH A 50 818 50 HOH HOH . J 6 HOH A 51 819 51 HOH HOH . J 6 HOH A 52 820 52 HOH HOH . J 6 HOH A 53 821 53 HOH HOH . J 6 HOH A 54 822 54 HOH HOH . J 6 HOH A 55 823 55 HOH HOH . J 6 HOH A 56 824 56 HOH HOH . J 6 HOH A 57 825 57 HOH HOH . J 6 HOH A 58 826 58 HOH HOH . J 6 HOH A 59 827 59 HOH HOH . J 6 HOH A 60 828 60 HOH HOH . J 6 HOH A 61 829 61 HOH HOH . J 6 HOH A 62 830 62 HOH HOH . J 6 HOH A 63 831 63 HOH HOH . J 6 HOH A 64 832 64 HOH HOH . J 6 HOH A 65 833 65 HOH HOH . J 6 HOH A 66 834 66 HOH HOH . J 6 HOH A 67 835 67 HOH HOH . J 6 HOH A 68 836 68 HOH HOH . J 6 HOH A 69 837 69 HOH HOH . J 6 HOH A 70 838 70 HOH HOH . J 6 HOH A 71 839 71 HOH HOH . J 6 HOH A 72 840 72 HOH HOH . J 6 HOH A 73 841 73 HOH HOH . J 6 HOH A 74 842 74 HOH HOH . J 6 HOH A 75 843 75 HOH HOH . J 6 HOH A 76 844 76 HOH HOH . J 6 HOH A 77 845 77 HOH HOH . J 6 HOH A 78 846 78 HOH HOH . J 6 HOH A 79 847 79 HOH HOH . J 6 HOH A 80 848 80 HOH HOH . J 6 HOH A 81 849 81 HOH HOH . J 6 HOH A 82 850 82 HOH HOH . J 6 HOH A 83 851 83 HOH HOH . J 6 HOH A 84 852 85 HOH HOH . J 6 HOH A 85 853 86 HOH HOH . J 6 HOH A 86 854 87 HOH HOH . J 6 HOH A 87 855 88 HOH HOH . J 6 HOH A 88 856 89 HOH HOH . J 6 HOH A 89 857 90 HOH HOH . J 6 HOH A 90 858 91 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 . . . G 5 -0.485 21.006 59.049 1 82.07 ? C1 NAG 1121 A 1 HETATM 2 C C2 NAG . . . G 5 0.833 20.914 59.831 1 86.87 ? C2 NAG 1121 A 1 HETATM 3 C C3 NAG . . . G 5 1.46 22.292 60.047 1 91.55 ? C3 NAG 1121 A 1 HETATM 4 C C4 NAG . . . G 5 1.622 22.989 58.702 1 94.2 ? C4 NAG 1121 A 1 HETATM 5 C C5 NAG . . . G 5 0.291 23.004 57.949 1 94.3 ? C5 NAG 1121 A 1 HETATM 6 C C6 NAG . . . G 5 0.469 23.619 56.563 1 97.31 ? C6 NAG 1121 A 1 HETATM 7 C C7 NAG . . . G 5 1.076 18.971 61.269 1 86.18 ? C7 NAG 1121 A 1 HETATM 8 C C8 NAG . . . G 5 0.536 18.238 62.468 1 83.2 ? C8 NAG 1121 A 1 HETATM 9 N N2 NAG . . . G 5 0.645 20.223 61.096 1 87.11 ? N2 NAG 1121 A 1 HETATM 10 O O3 NAG . . . G 5 2.714 22.183 60.692 1 91.97 ? O3 NAG 1121 A 1 HETATM 11 O O4 NAG . . . G 5 2.087 24.311 58.883 1 96.02 ? O4 NAG 1121 A 1 HETATM 12 O O5 NAG . . . G 5 -0.268 21.703 57.828 1 89.48 ? O5 NAG 1121 A 1 HETATM 13 O O6 NAG . . . G 5 1.734 23.263 56.045 1 100.38 ? O6 NAG 1121 A 1 HETATM 14 O O7 NAG . . . G 5 1.87 18.42 60.497 1 85.54 ? O7 NAG 1121 A 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 14 #