data_6JBT # _model_server_result.job_id JUsSJJLm2HlP6uCwmryaGg _model_server_result.datetime_utc '2024-11-22 12:03:23' _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 6jbt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":307}' # _entry.id 6JBT # _exptl.entry_id 6JBT _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 113.36 _cell.angle_gamma 90 _cell.entry_id 6JBT _cell.length_a 75.768 _cell.length_b 64.197 _cell.length_c 78.722 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JBT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 1 FUC NAG 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 4 n D NAG 1 A 1 NAG F 301 NAG 4 n D NAG 2 A 2 NAG F 302 NAG 4 n D FUC 3 A 3 FUC F 303 FUC 4 n E NAG 1 B 1 NAG F 311 NAG 4 n E NAG 2 B 2 NAG F 312 NAG 4 n E FUC 3 B 3 FUC F 313 FUC # 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 35 F CYS 35 1_555 A SG CYS 104 F CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 152 H CYS 152 1_555 B SG CYS 208 H CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? disulf ? disulf4 C SG CYS 23 L CYS 23 1_555 C SG CYS 93 L CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf5 C SG CYS 139 L CYS 139 1_555 C SG CYS 199 L CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 A ND2 ASN 30 F ASN 30 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 39 F ASN 39 1_555 E C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 97 F ASN 97 1_555 F C1 NAG . F NAG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 D O6 NAG . A NAG 1 1_555 D C1 FUC . A FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale6 E O4 NAG . B NAG 1 1_555 E C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 E O6 NAG . B NAG 1 1_555 E C1 FUC . B FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? # _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 260 n n C1 O1 NAG sing 261 n n C1 O5 NAG sing 262 n n C1 H1 NAG sing 263 n n C2 C3 NAG sing 264 n n C2 N2 NAG sing 265 n n C2 H2 NAG sing 266 n n C3 C4 NAG sing 267 n n C3 O3 NAG sing 268 n n C3 H3 NAG sing 269 n n C4 C5 NAG sing 270 n n C4 O4 NAG sing 271 n n C4 H4 NAG sing 272 n n C5 C6 NAG sing 273 n n C5 O5 NAG sing 274 n n C5 H5 NAG sing 275 n n C6 O6 NAG sing 276 n n C6 H61 NAG sing 277 n n C6 H62 NAG sing 278 n n C7 C8 NAG sing 279 n n C7 N2 NAG sing 280 n n C7 O7 NAG doub 281 n n C8 H81 NAG sing 282 n n C8 H82 NAG sing 283 n n C8 H83 NAG sing 284 n n N2 HN2 NAG sing 285 n n O1 HO1 NAG sing 286 n n O3 HO3 NAG sing 287 n n O4 HO4 NAG sing 288 n n O6 HO6 NAG sing 289 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 6JBT _atom_sites.fract_transf_matrix[1][1] 0.013198 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005702 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015577 _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] 0.013838 _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 5 NAG F 1 307 321 NAG NAG . G 6 HOH F 1 401 33 HOH HOH . G 6 HOH F 2 402 88 HOH HOH . G 6 HOH F 3 403 49 HOH HOH . G 6 HOH F 4 404 4 HOH HOH . G 6 HOH F 5 405 79 HOH HOH . G 6 HOH F 6 406 30 HOH HOH . G 6 HOH F 7 407 73 HOH HOH . G 6 HOH F 8 408 100 HOH HOH . G 6 HOH F 9 409 25 HOH HOH . G 6 HOH F 10 410 117 HOH HOH . G 6 HOH F 11 411 22 HOH HOH . G 6 HOH F 12 412 66 HOH HOH . G 6 HOH F 13 413 106 HOH HOH . G 6 HOH F 14 414 78 HOH HOH . H 6 HOH H 1 301 102 HOH HOH . H 6 HOH H 2 302 75 HOH HOH . H 6 HOH H 3 303 90 HOH HOH . H 6 HOH H 4 304 57 HOH HOH . H 6 HOH H 5 305 18 HOH HOH . H 6 HOH H 6 306 69 HOH HOH . H 6 HOH H 7 307 95 HOH HOH . H 6 HOH H 8 308 68 HOH HOH . H 6 HOH H 9 309 118 HOH HOH . H 6 HOH H 10 310 107 HOH HOH . H 6 HOH H 11 311 23 HOH HOH . H 6 HOH H 12 312 10 HOH HOH . H 6 HOH H 13 313 36 HOH HOH . H 6 HOH H 14 314 35 HOH HOH . H 6 HOH H 15 315 16 HOH HOH . H 6 HOH H 16 316 103 HOH HOH . H 6 HOH H 17 317 58 HOH HOH . H 6 HOH H 18 318 47 HOH HOH . H 6 HOH H 19 319 31 HOH HOH . H 6 HOH H 20 320 37 HOH HOH . H 6 HOH H 21 321 34 HOH HOH . H 6 HOH H 22 322 56 HOH HOH . H 6 HOH H 23 323 98 HOH HOH . H 6 HOH H 24 324 83 HOH HOH . H 6 HOH H 25 325 63 HOH HOH . H 6 HOH H 26 326 12 HOH HOH . H 6 HOH H 27 327 11 HOH HOH . H 6 HOH H 28 328 74 HOH HOH . H 6 HOH H 29 329 5 HOH HOH . H 6 HOH H 30 330 52 HOH HOH . H 6 HOH H 31 331 61 HOH HOH . H 6 HOH H 32 332 112 HOH HOH . I 6 HOH L 1 301 7 HOH HOH . I 6 HOH L 2 302 59 HOH HOH . I 6 HOH L 3 303 123 HOH HOH . I 6 HOH L 4 304 13 HOH HOH . I 6 HOH L 5 305 93 HOH HOH . I 6 HOH L 6 306 39 HOH HOH . I 6 HOH L 7 307 41 HOH HOH . I 6 HOH L 8 308 3 HOH HOH . I 6 HOH L 9 309 71 HOH HOH . I 6 HOH L 10 310 67 HOH HOH . I 6 HOH L 11 311 19 HOH HOH . I 6 HOH L 12 312 8 HOH HOH . I 6 HOH L 13 313 60 HOH HOH . I 6 HOH L 14 314 53 HOH HOH . I 6 HOH L 15 315 20 HOH HOH . I 6 HOH L 16 316 81 HOH HOH . I 6 HOH L 17 317 29 HOH HOH . I 6 HOH L 18 318 2 HOH HOH . I 6 HOH L 19 319 92 HOH HOH . I 6 HOH L 20 320 46 HOH HOH . I 6 HOH L 21 321 9 HOH HOH . I 6 HOH L 22 322 6 HOH HOH . I 6 HOH L 23 323 108 HOH HOH . I 6 HOH L 24 324 45 HOH HOH . I 6 HOH L 25 325 94 HOH HOH . I 6 HOH L 26 326 96 HOH HOH . I 6 HOH L 27 327 85 HOH HOH . I 6 HOH L 28 328 80 HOH HOH . I 6 HOH L 29 329 51 HOH HOH . I 6 HOH L 30 330 17 HOH HOH . I 6 HOH L 31 331 114 HOH HOH . I 6 HOH L 32 332 27 HOH HOH . I 6 HOH L 33 333 89 HOH HOH . I 6 HOH L 34 334 82 HOH HOH . I 6 HOH L 35 335 109 HOH HOH . I 6 HOH L 36 336 48 HOH HOH . I 6 HOH L 37 337 76 HOH HOH . I 6 HOH L 38 338 64 HOH HOH . I 6 HOH L 39 339 55 HOH HOH . I 6 HOH L 40 340 38 HOH HOH . I 6 HOH L 41 341 32 HOH HOH . I 6 HOH L 42 342 14 HOH HOH . I 6 HOH L 43 343 84 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 . . . F 5 -14.25 -63.675 -20.296 1 65.13 ? C1 NAG 307 F 1 HETATM 2 C C2 NAG . . . F 5 -14.409 -63.281 -18.826 1 67.05 ? C2 NAG 307 F 1 HETATM 3 C C3 NAG . . . F 5 -13.508 -64.138 -17.927 1 74.85 ? C3 NAG 307 F 1 HETATM 4 C C4 NAG . . . F 5 -12.092 -64.256 -18.482 1 73.97 ? C4 NAG 307 F 1 HETATM 5 C C5 NAG . . . F 5 -12.105 -64.595 -19.97 1 75.5 ? C5 NAG 307 F 1 HETATM 6 C C6 NAG . . . F 5 -11.306 -65.834 -20.306 1 73.47 ? C6 NAG 307 F 1 HETATM 7 C C7 NAG . . . F 5 -15.001 -60.897 -18.953 1 71.15 ? C7 NAG 307 F 1 HETATM 8 C C8 NAG . . . F 5 -14.549 -59.494 -18.681 1 62.82 ? C8 NAG 307 F 1 HETATM 9 N N2 NAG . . . F 5 -14.135 -61.866 -18.632 1 75.71 ? N2 NAG 307 F 1 HETATM 10 O O3 NAG . . . F 5 -14.077 -65.433 -17.779 1 85.74 ? O3 NAG 307 F 1 HETATM 11 O O4 NAG . . . F 5 -11.394 -63.032 -18.283 1 77.75 ? O4 NAG 307 F 1 HETATM 12 O O5 NAG . . . F 5 -13.452 -64.839 -20.394 1 70.78 ? O5 NAG 307 F 1 HETATM 13 O O6 NAG . . . F 5 -10.193 -65.985 -19.435 1 76.2 ? O6 NAG 307 F 1 HETATM 14 O O7 NAG . . . F 5 -16.102 -61.142 -19.441 1 59.02 ? O7 NAG 307 F 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 434 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #