data_4J6G # _model_server_result.job_id jKjc-haToFjzfQQHzg291A _model_server_result.datetime_utc '2024-10-12 23:21:08' _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 4j6g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":301}' # _entry.id 4J6G # _exptl.entry_id 4J6G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 4J6G _cell.length_a 149.058 _cell.length_b 149.058 _cell.length_c 149.058 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4J6G _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dodecameric 12 software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 PISA hexameric 6 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,H,K,M 1 1,2,3 B,D,G,I,J,L,N 1 4,5,6 A,C,E,F,H,K,M 2 1,2,3 B,D,G,I,J,L,N 3 1,7,8 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 4 'crystal symmetry operation' 4_545 x+1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 74.529 -74.529 0 5 'crystal symmetry operation' 8_554 -z,x+1/2,-y-1/2 0 0 -1 1 0 0 0 -1 0 0 74.529 -74.529 6 'crystal symmetry operation' 12_455 -y-1/2,-z,x+1/2 0 -1 0 0 0 -1 1 0 0 -74.529 0 74.529 7 'crystal symmetry operation' 7_445 -z-1/2,-x-1,y+1/2 0 0 -1 -1 0 0 0 1 0 -74.529 -149.058 74.529 8 'crystal symmetry operation' 10_444 -y-1,z-1/2,-x-1/2 0 -1 0 0 0 1 -1 0 0 -149.058 -74.529 -74.529 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 . O3 HO3 . 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 E NAG 1 E 1 NAG E 301 NAG 3 n E NAG 2 E 2 NAG E 302 NAG 3 n E BMA 3 E 3 BMA E 303 BMA 3 n E MAN 4 E 4 MAN E 304 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 79 A CYS 154 1_555 A SG CYS 112 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 B SG CYS 79 B CYS 154 1_555 B SG CYS 112 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? disulf ? disulf3 C SG CYS 20 C CYS 49 1_555 C SG CYS 33 C CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 C SG CYS 23 C CYS 52 1_555 C SG CYS 41 C CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? disulf ? disulf5 C SG CYS 44 C CYS 73 1_555 C SG CYS 59 C CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? disulf ? disulf6 C SG CYS 62 C CYS 91 1_555 C SG CYS 76 C CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? disulf ? disulf7 C SG CYS 66 C CYS 95 1_555 C SG CYS 84 C CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf8 C SG CYS 86 C CYS 115 1_555 C SG CYS 97 C CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? disulf ? disulf9 C SG CYS 103 C CYS 132 1_555 C SG CYS 121 C CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf10 C SG CYS 124 C CYS 153 1_555 C SG CYS 139 C CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? disulf ? disulf11 C SG CYS 145 C CYS 174 1_555 C SG CYS 164 C CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf12 D SG CYS 20 D CYS 49 1_555 D SG CYS 33 D CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf13 D SG CYS 23 D CYS 52 1_555 D SG CYS 41 D CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? disulf ? disulf14 D SG CYS 44 D CYS 73 1_555 D SG CYS 59 D CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? disulf ? disulf15 D SG CYS 62 D CYS 91 1_555 D SG CYS 76 D CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? disulf ? disulf16 D SG CYS 66 D CYS 95 1_555 D SG CYS 84 D CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf17 D SG CYS 86 D CYS 115 1_555 D SG CYS 97 D CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf18 D SG CYS 103 D CYS 132 1_555 D SG CYS 121 D CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf19 D SG CYS 124 D CYS 153 1_555 D SG CYS 139 D CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf20 D SG CYS 145 D CYS 174 1_555 D SG CYS 164 D CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? covale ? covale1 C ND2 ASN 144 C ASN 173 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 D ND2 ASN 144 D ASN 173 1_555 I C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? covale ? covale3 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale5 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 C O CYS 103 C CYS 132 1_555 H MG MG . C MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? metalc ? metalc2 C O PRO 104 C PRO 133 1_555 H MG MG . C MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc3 C O ALA 107 C ALA 136 1_555 H MG MG . C MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc4 C OG SER 130 C SER 159 1_555 H MG MG . C MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc5 C O SER 132 C SER 161 1_555 H MG MG . C MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc6 H MG MG . C MG 305 1_555 M O HOH . C HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? metalc ? metalc7 D O CYS 103 D CYS 132 1_555 J MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc8 D O PRO 104 D PRO 133 1_555 J MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc9 D O ALA 107 D ALA 136 1_555 J MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc10 D OG SER 130 D SER 159 1_555 J MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc11 D O SER 132 D SER 161 1_555 J MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc12 J MG MG . D MG 302 1_555 N O HOH . D HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? # _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 4J6G _atom_sites.fract_transf_matrix[1][1] 0.006709 _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] 0.006709 _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] 0.006709 _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 F 4 CL A 1 301 301 CL CL . G 4 CL B 1 301 301 CL CL . H 5 MG C 1 305 605 MG MG . I 6 NAG D 1 301 201 NAG NAG . J 5 MG D 1 302 202 MG MG . K 7 HOH A 1 401 401 HOH HOH . K 7 HOH A 2 402 402 HOH HOH . K 7 HOH A 3 403 403 HOH HOH . K 7 HOH A 4 404 404 HOH HOH . K 7 HOH A 5 405 405 HOH HOH . K 7 HOH A 6 406 406 HOH HOH . K 7 HOH A 7 407 407 HOH HOH . K 7 HOH A 8 408 408 HOH HOH . K 7 HOH A 9 409 409 HOH HOH . K 7 HOH A 10 410 410 HOH HOH . K 7 HOH A 11 411 411 HOH HOH . K 7 HOH A 12 412 412 HOH HOH . K 7 HOH A 13 413 413 HOH HOH . K 7 HOH A 14 414 414 HOH HOH . K 7 HOH A 15 415 415 HOH HOH . K 7 HOH A 16 416 416 HOH HOH . K 7 HOH A 17 417 417 HOH HOH . K 7 HOH A 18 418 418 HOH HOH . L 7 HOH B 1 401 401 HOH HOH . L 7 HOH B 2 402 402 HOH HOH . L 7 HOH B 3 403 403 HOH HOH . L 7 HOH B 4 404 404 HOH HOH . L 7 HOH B 5 405 405 HOH HOH . L 7 HOH B 6 406 406 HOH HOH . L 7 HOH B 7 407 407 HOH HOH . L 7 HOH B 8 408 408 HOH HOH . L 7 HOH B 9 409 409 HOH HOH . L 7 HOH B 10 410 410 HOH HOH . L 7 HOH B 11 411 411 HOH HOH . L 7 HOH B 12 412 412 HOH HOH . L 7 HOH B 13 413 413 HOH HOH . L 7 HOH B 14 414 414 HOH HOH . L 7 HOH B 15 415 415 HOH HOH . M 7 HOH C 1 701 701 HOH HOH . M 7 HOH C 2 702 702 HOH HOH . M 7 HOH C 3 703 703 HOH HOH . M 7 HOH C 4 704 704 HOH HOH . M 7 HOH C 5 705 705 HOH HOH . M 7 HOH C 6 706 706 HOH HOH . M 7 HOH C 7 707 707 HOH HOH . N 7 HOH D 1 401 301 HOH HOH . N 7 HOH D 2 402 302 HOH HOH . N 7 HOH D 3 403 303 HOH HOH . N 7 HOH D 4 404 304 HOH HOH . N 7 HOH D 5 405 305 HOH HOH . N 7 HOH D 6 406 306 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 . . . I 6 -76.444 -51.165 57.241 1 50.36 ? C1 NAG 301 D 1 HETATM 2 C C2 NAG . . . I 6 -77.03 -52.582 57.173 1 53.94 ? C2 NAG 301 D 1 HETATM 3 C C3 NAG . . . I 6 -77.79 -53.026 58.452 1 55.11 ? C3 NAG 301 D 1 HETATM 4 C C4 NAG . . . I 6 -76.973 -52.839 59.782 1 59.51 ? C4 NAG 301 D 1 HETATM 5 C C5 NAG . . . I 6 -76.311 -51.431 59.765 1 59.84 ? C5 NAG 301 D 1 HETATM 6 C C6 NAG . . . I 6 -75.42 -51.079 61.007 1 64.08 ? C6 NAG 301 D 1 HETATM 7 C C7 NAG . . . I 6 -77.55 -53.702 55.037 1 68.39 ? C7 NAG 301 D 1 HETATM 8 C C8 NAG . . . I 6 -78.392 -53.806 53.812 1 69.93 ? C8 NAG 301 D 1 HETATM 9 N N2 NAG . . . I 6 -77.819 -52.741 55.94 1 56.38 ? N2 NAG 301 D 1 HETATM 10 O O3 NAG . . . I 6 -78.371 -54.348 58.315 1 47.81 ? O3 NAG 301 D 1 HETATM 11 O O4 NAG . . . I 6 -77.736 -53.173 60.996 1 58.74 ? O4 NAG 301 D 1 HETATM 12 O O5 NAG . . . I 6 -75.679 -51.119 58.482 1 57.24 ? O5 NAG 301 D 1 HETATM 13 O O6 NAG . . . I 6 -74.084 -51.591 61.016 1 61.13 ? O6 NAG 301 D 1 HETATM 14 O O7 NAG . . . I 6 -76.646 -54.524 55.132 1 67.63 ? O7 NAG 301 D 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 14 #