data_6CFG # _model_server_result.job_id cgjvRsgYi1QI1GjtNJnSwg _model_server_result.datetime_utc '2024-10-17 05:31:26' _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 6cfg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":403}' # _entry.id 6CFG # _exptl.entry_id 6CFG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _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 120 _cell.entry_id 6CFG _cell.length_a 102.197 _cell.length_b 102.197 _cell.length_c 454.053 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6CFG _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_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -51.0985 -88.505198 0 3 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.0985 -88.505198 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 # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 D 1 NAG 3 n C NAG 2 C 2 NAG D 2 NAG 3 n D NAG 1 D 1 NAG D 5 NAG 3 n D NAG 2 D 2 NAG D 6 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 8 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 278 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 A SG CYS 59 A CYS 64 1_555 A SG CYS 71 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf4 A SG CYS 94 A CYS 97 1_555 A SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf5 A SG CYS 282 A CYS 281 1_555 A SG CYS 306 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? covale ? covale1 A ND2 ASN 27 A ASN 33 1_555 E C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 169 A ASN 169 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale3 A ND2 ASN 290 A ASN 289 1_555 F C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 B ND2 ASN 154 B ASN 154 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 309 n n C1 O1 NAG sing 310 n n C1 O5 NAG sing 311 n n C1 H1 NAG sing 312 n n C2 C3 NAG sing 313 n n C2 N2 NAG sing 314 n n C2 H2 NAG sing 315 n n C3 C4 NAG sing 316 n n C3 O3 NAG sing 317 n n C3 H3 NAG sing 318 n n C4 C5 NAG sing 319 n n C4 O4 NAG sing 320 n n C4 H4 NAG sing 321 n n C5 C6 NAG sing 322 n n C5 O5 NAG sing 323 n n C5 H5 NAG sing 324 n n C6 O6 NAG sing 325 n n C6 H61 NAG sing 326 n n C6 H62 NAG sing 327 n n C7 C8 NAG sing 328 n n C7 N2 NAG sing 329 n n C7 O7 NAG doub 330 n n C8 H81 NAG sing 331 n n C8 H82 NAG sing 332 n n C8 H83 NAG sing 333 n n N2 HN2 NAG sing 334 n n O1 HO1 NAG sing 335 n n O3 HO3 NAG sing 336 n n O4 HO4 NAG sing 337 n n O6 HO6 NAG sing 338 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 6CFG _atom_sites.fract_transf_matrix[1][1] 0.009785 _atom_sites.fract_transf_matrix[1][2] 0.005649 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011299 _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] 0.002202 _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 E 4 NAG A 1 403 3 NAG NAG . F 4 NAG A 1 404 4 NAG NAG . G 5 EZ7 B 1 201 1 EZ7 PDB . H 6 PEG B 1 204 1 PEG PEG . I 7 HOH A 1 501 77 HOH HOH . I 7 HOH A 2 502 40 HOH HOH . I 7 HOH A 3 503 56 HOH HOH . I 7 HOH A 4 504 10 HOH HOH . I 7 HOH A 5 505 2 HOH HOH . I 7 HOH A 6 506 88 HOH HOH . I 7 HOH A 7 507 25 HOH HOH . I 7 HOH A 8 508 8 HOH HOH . I 7 HOH A 9 509 20 HOH HOH . I 7 HOH A 10 510 76 HOH HOH . I 7 HOH A 11 511 53 HOH HOH . I 7 HOH A 12 512 83 HOH HOH . I 7 HOH A 13 513 26 HOH HOH . I 7 HOH A 14 514 78 HOH HOH . I 7 HOH A 15 515 85 HOH HOH . I 7 HOH A 16 516 27 HOH HOH . I 7 HOH A 17 517 101 HOH HOH . I 7 HOH A 18 518 64 HOH HOH . I 7 HOH A 19 519 71 HOH HOH . I 7 HOH A 20 520 16 HOH HOH . I 7 HOH A 21 521 41 HOH HOH . I 7 HOH A 22 522 39 HOH HOH . I 7 HOH A 23 523 97 HOH HOH . I 7 HOH A 24 524 48 HOH HOH . I 7 HOH A 25 525 81 HOH HOH . I 7 HOH A 26 526 52 HOH HOH . I 7 HOH A 27 527 45 HOH HOH . I 7 HOH A 28 528 4 HOH HOH . I 7 HOH A 29 529 75 HOH HOH . I 7 HOH A 30 530 89 HOH HOH . I 7 HOH A 31 531 32 HOH HOH . I 7 HOH A 32 532 90 HOH HOH . I 7 HOH A 33 533 5 HOH HOH . I 7 HOH A 34 534 18 HOH HOH . I 7 HOH A 35 535 68 HOH HOH . I 7 HOH A 36 536 38 HOH HOH . I 7 HOH A 37 537 59 HOH HOH . I 7 HOH A 38 538 43 HOH HOH . I 7 HOH A 39 539 84 HOH HOH . I 7 HOH A 40 540 87 HOH HOH . I 7 HOH A 41 541 82 HOH HOH . I 7 HOH A 42 542 73 HOH HOH . I 7 HOH A 43 543 65 HOH HOH . I 7 HOH A 44 544 62 HOH HOH . I 7 HOH A 45 545 86 HOH HOH . I 7 HOH A 46 546 14 HOH HOH . I 7 HOH A 47 547 102 HOH HOH . J 7 HOH B 1 301 51 HOH HOH . J 7 HOH B 2 302 30 HOH HOH . J 7 HOH B 3 303 13 HOH HOH . J 7 HOH B 4 304 46 HOH HOH . J 7 HOH B 5 305 79 HOH HOH . J 7 HOH B 6 306 95 HOH HOH . J 7 HOH B 7 307 44 HOH HOH . J 7 HOH B 8 308 70 HOH HOH . J 7 HOH B 9 309 100 HOH HOH . J 7 HOH B 10 310 96 HOH HOH . J 7 HOH B 11 311 80 HOH HOH . J 7 HOH B 12 312 24 HOH HOH . J 7 HOH B 13 313 103 HOH HOH . J 7 HOH B 14 314 1 HOH HOH . J 7 HOH B 15 315 3 HOH HOH . J 7 HOH B 16 316 92 HOH HOH . J 7 HOH B 17 317 49 HOH HOH . J 7 HOH B 18 318 7 HOH HOH . J 7 HOH B 19 319 91 HOH HOH . J 7 HOH B 20 320 15 HOH HOH . J 7 HOH B 21 321 50 HOH HOH . J 7 HOH B 22 322 93 HOH HOH . J 7 HOH B 23 323 6 HOH HOH . J 7 HOH B 24 324 94 HOH HOH . J 7 HOH B 25 325 36 HOH HOH . J 7 HOH B 26 326 60 HOH HOH . J 7 HOH B 27 327 55 HOH HOH . J 7 HOH B 28 328 61 HOH HOH . J 7 HOH B 29 329 21 HOH HOH . J 7 HOH B 30 330 37 HOH HOH . J 7 HOH B 31 331 67 HOH HOH . J 7 HOH B 32 332 29 HOH HOH . J 7 HOH B 33 333 11 HOH HOH . J 7 HOH B 34 334 17 HOH HOH . J 7 HOH B 35 335 31 HOH HOH . J 7 HOH B 36 336 28 HOH HOH . J 7 HOH B 37 337 99 HOH HOH . J 7 HOH B 38 338 69 HOH HOH . J 7 HOH B 39 339 57 HOH HOH . J 7 HOH B 40 340 72 HOH HOH . J 7 HOH B 41 341 54 HOH HOH . J 7 HOH B 42 342 63 HOH HOH . J 7 HOH B 43 343 42 HOH HOH . J 7 HOH B 44 344 66 HOH HOH . J 7 HOH B 45 345 74 HOH HOH . J 7 HOH B 46 346 47 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 . . . E 4 -19.2 -46.119 43.02 1 98.9 ? C1 NAG 403 A 1 HETATM 2 C C2 NAG . . . E 4 -20.28 -47.047 42.435 1 113.76 ? C2 NAG 403 A 1 HETATM 3 C C3 NAG . . . E 4 -20.782 -46.509 41.093 1 120.73 ? C3 NAG 403 A 1 HETATM 4 C C4 NAG . . . E 4 -21.245 -45.066 41.234 1 120.67 ? C4 NAG 403 A 1 HETATM 5 C C5 NAG . . . E 4 -20.116 -44.217 41.804 1 109.58 ? C5 NAG 403 A 1 HETATM 6 C C6 NAG . . . E 4 -20.529 -42.783 42.041 1 105.83 ? C6 NAG 403 A 1 HETATM 7 C C7 NAG . . . E 4 -20.334 -49.464 42.868 1 120.6 ? C7 NAG 403 A 1 HETATM 8 C C8 NAG . . . E 4 -19.678 -50.788 42.599 1 112.59 ? C8 NAG 403 A 1 HETATM 9 N N2 NAG . . . E 4 -19.774 -48.401 42.28 1 116.79 ? N2 NAG 403 A 1 HETATM 10 O O3 NAG . . . E 4 -21.858 -47.317 40.627 1 124.25 ? O3 NAG 403 A 1 HETATM 11 O O4 NAG . . . E 4 -21.638 -44.542 39.97 1 128.78 ? O4 NAG 403 A 1 HETATM 12 O O5 NAG . . . E 4 -19.699 -44.753 43.071 1 102.79 ? O5 NAG 403 A 1 HETATM 13 O O6 NAG . . . E 4 -19.4 -41.938 42.206 1 103.17 ? O6 NAG 403 A 1 HETATM 14 O O7 NAG . . . E 4 -21.32 -49.361 43.59 1 128.87 ? O7 NAG 403 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #