data_5E4K # _model_server_result.job_id c_jpaXP6WCy5xPWYR8d54A _model_server_result.datetime_utc '2024-10-19 16:23:07' _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 5e4k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":605}' # _entry.id 5E4K # _exptl.entry_id 5E4K _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 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 90 _cell.entry_id 5E4K _cell.length_a 74.94 _cell.length_b 74.94 _cell.length_c 224.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5E4K _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 F 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 26 A CYS 54 1_555 A SG CYS 40 A CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf2 A SG CYS 65 A CYS 93 1_555 A SG CYS 84 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 95 A CYS 123 1_555 A SG CYS 140 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf4 A SG CYS 159 A CYS 187 1_555 A SG CYS 185 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 173 A CYS 201 1_555 A SG CYS 200 A CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 A SG CYS 207 A CYS 235 1_555 A SG CYS 220 A CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 238 A CYS 266 1_555 A SG CYS 331 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf8 A SG CYS 307 A CYS 335 1_555 A SG CYS 323 A CYS 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf9 A SG CYS 354 A CYS 382 1_555 A SG CYS 365 A CYS 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf10 A SG CYS 382 A CYS 410 1_555 A SG CYS 476 A CYS 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf11 A SG CYS 453 A CYS 481 1_555 A SG CYS 468 A CYS 496 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? covale ? covale1 A ND2 ASN 41 A ASN 69 1_555 E C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 A ND2 ASN 469 A ASN 497 1_555 F C1 NAG . A NAG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? metalc ? metalc1 A OE1 GLN 298 A GLN 326 1_555 D NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.968 ? metalc ? metalc2 A OD1 ASP 300 A ASP 328 1_555 D NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc3 A OE1 GLU 305 A GLU 333 1_555 D NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc4 A O ASN 320 A ASN 348 1_555 D NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc5 A OD1 ASP 418 A ASP 446 1_555 B CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc6 A OD2 ASP 418 A ASP 446 1_555 B CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc7 A OE1 GLN 422 A GLN 450 1_555 B CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc8 A OE1 GLU 442 A GLU 470 1_555 C CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc9 A OD1 ASN 444 A ASN 472 1_555 C CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc10 A OD1 ASN 445 A ASN 473 1_555 B CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc11 A O GLU 451 A GLU 479 1_555 B CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc12 A OE1 GLU 451 A GLU 479 1_555 C CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc13 A OD1 ASP 452 A ASP 480 1_555 B CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc14 A OD1 ASN 464 A ASN 492 1_555 C CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc15 A O ASP 465 A ASP 493 1_555 C CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc16 A OD1 ASP 465 A ASP 493 1_555 C CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc17 B CA CA . A CA 601 1_555 I O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc18 C CA CA . A CA 602 1_555 I O HOH . A HOH 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.126 ? metalc ? metalc19 C CA CA . A CA 602 1_555 I O HOH . A HOH 726 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? # _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 274 n n C1 O1 NAG sing 275 n n C1 O5 NAG sing 276 n n C1 H1 NAG sing 277 n n C2 C3 NAG sing 278 n n C2 N2 NAG sing 279 n n C2 H2 NAG sing 280 n n C3 C4 NAG sing 281 n n C3 O3 NAG sing 282 n n C3 H3 NAG sing 283 n n C4 C5 NAG sing 284 n n C4 O4 NAG sing 285 n n C4 H4 NAG sing 286 n n C5 C6 NAG sing 287 n n C5 O5 NAG sing 288 n n C5 H5 NAG sing 289 n n C6 O6 NAG sing 290 n n C6 H61 NAG sing 291 n n C6 H62 NAG sing 292 n n C7 C8 NAG sing 293 n n C7 N2 NAG sing 294 n n C7 O7 NAG doub 295 n n C8 H81 NAG sing 296 n n C8 H82 NAG sing 297 n n C8 H83 NAG sing 298 n n N2 HN2 NAG sing 299 n n O1 HO1 NAG sing 300 n n O3 HO3 NAG sing 301 n n O4 HO4 NAG sing 302 n n O6 HO6 NAG sing 303 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 5E4K _atom_sites.fract_transf_matrix[1][1] 0.013344 _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] 0.013344 _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] 0.004453 _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 CA A 1 601 601 CA CA . C 2 CA A 1 602 602 CA CA . D 3 NA A 1 603 603 NA NA . E 4 NAG A 1 604 604 NAG NAG . F 4 NAG A 1 605 605 NAG NAG . G 5 1PE A 1 606 606 1PE 1PE . H 6 PE5 A 1 607 607 PE5 PE5 . I 7 HOH A 1 701 7 HOH HOH . I 7 HOH A 2 702 3 HOH HOH . I 7 HOH A 3 703 2 HOH HOH . I 7 HOH A 4 704 103 HOH HOH . I 7 HOH A 5 705 1 HOH HOH . I 7 HOH A 6 706 5 HOH HOH . I 7 HOH A 7 707 45 HOH HOH . I 7 HOH A 8 708 72 HOH HOH . I 7 HOH A 9 709 57 HOH HOH . I 7 HOH A 10 710 15 HOH HOH . I 7 HOH A 11 711 102 HOH HOH . I 7 HOH A 12 712 6 HOH HOH . I 7 HOH A 13 713 89 HOH HOH . I 7 HOH A 14 714 14 HOH HOH . I 7 HOH A 15 715 13 HOH HOH . I 7 HOH A 16 716 20 HOH HOH . I 7 HOH A 17 717 10 HOH HOH . I 7 HOH A 18 718 82 HOH HOH . I 7 HOH A 19 719 70 HOH HOH . I 7 HOH A 20 720 21 HOH HOH . I 7 HOH A 21 721 76 HOH HOH . I 7 HOH A 22 722 38 HOH HOH . I 7 HOH A 23 723 29 HOH HOH . I 7 HOH A 24 724 84 HOH HOH . I 7 HOH A 25 725 81 HOH HOH . I 7 HOH A 26 726 31 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 4 43.872 24.484 -38.535 1 107.95 ? C1 NAG 605 A 1 HETATM 2 C C2 NAG . . . F 4 45.093 23.594 -38.203 1 117 ? C2 NAG 605 A 1 HETATM 3 C C3 NAG . . . F 4 46.137 24.38 -37.398 1 120.13 ? C3 NAG 605 A 1 HETATM 4 C C4 NAG . . . F 4 46.52 25.67 -38.112 1 125.41 ? C4 NAG 605 A 1 HETATM 5 C C5 NAG . . . F 4 45.269 26.504 -38.378 1 126.04 ? C5 NAG 605 A 1 HETATM 6 C C6 NAG . . . F 4 45.543 27.794 -39.132 1 124.13 ? C6 NAG 605 A 1 HETATM 7 C C7 NAG . . . F 4 44.429 21.235 -38.066 1 118.1 ? C7 NAG 605 A 1 HETATM 8 C C8 NAG . . . F 4 44.006 20.117 -37.16 1 112.34 ? C8 NAG 605 A 1 HETATM 9 N N2 NAG . . . F 4 44.681 22.406 -37.474 1 120.52 ? N2 NAG 605 A 1 HETATM 10 O O3 NAG . . . F 4 47.303 23.59 -37.19 1 120.67 ? O3 NAG 605 A 1 HETATM 11 O O4 NAG . . . F 4 47.441 26.401 -37.308 1 125.73 ? O4 NAG 605 A 1 HETATM 12 O O5 NAG . . . F 4 44.329 25.742 -39.157 1 121.29 ? O5 NAG 605 A 1 HETATM 13 O O6 NAG . . . F 4 46.084 27.582 -40.43 1 120.44 ? O6 NAG 605 A 1 HETATM 14 O O7 NAG . . . F 4 44.538 21.086 -39.279 1 120.87 ? O7 NAG 605 A 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 369 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #