data_1NCD # _model_server_result.job_id w69XMurpAWecOaEOkJ85MQ _model_server_result.datetime_utc '2024-10-16 10:26:28' _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 1ncd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":475}' # _entry.id 1NCD # _exptl.entry_id 1NCD _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 1NCD _cell.length_a 167 _cell.length_b 167 _cell.length_c 124 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NCD _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 1,2,3,4 # 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' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 83.5 83.5 0 3 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 83.5 -83.5 0 4 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 167 0 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 4 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 5 2 1 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 4 n D NAG 1 A 1 NAG N 200 NAG 4 n D NAG 2 A 2 NAG N 200 NAG 4 n D BMA 3 A 3 BMA N 200 MAN 4 n D MAN 4 A 4 MAN N 200 MAN 4 n D MAN 5 A 5 MAN N 200 MAN 4 n D MAN 6 A 6 MAN N 200 MAN 5 n E NAG 1 B 1 NAG N 146 NAG 5 n E NAG 2 B 2 NAG N 146 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 12 N CYS 92 1_555 A SG CYS 338 N CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf2 A SG CYS 44 N CYS 124 1_555 A SG CYS 49 N CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf3 A SG CYS 96 N CYS 175 1_555 A SG CYS 114 N CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? disulf ? disulf4 A SG CYS 104 N CYS 183 1_555 A SG CYS 151 N CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf5 A SG CYS 153 N CYS 232 1_555 A SG CYS 158 N CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? disulf ? disulf6 A SG CYS 199 N CYS 278 1_555 A SG CYS 212 N CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf7 A SG CYS 201 N CYS 280 1_555 A SG CYS 210 N CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf8 A SG CYS 239 N CYS 318 1_555 A SG CYS 257 N CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? disulf ? disulf9 A SG CYS 342 N CYS 421 1_555 A SG CYS 368 N CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf11 B SG CYS 134 L CYS 134 1_555 B SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf12 B SG CYS 214 L CYS 214 1_555 C SG CYS 135 H CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf13 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf14 C SG CYS 147 H CYS 142 1_555 C SG CYS 202 H CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? covale ? covale1 A ND2 ASN 6 N ASN 86 1_555 F C1 NAG . N NAG 475 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.462 ? covale ? covale2 A ND2 ASN 66 N ASN 146 1_555 E C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A ND2 ASN 121 N ASN 200 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale4 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 D O4 NAG . A NAG 2 1_555 D C1 BMA . A BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale6 D O3 BMA . A BMA 3 1_555 D C1 MAN . A MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 D O2 MAN . A MAN 4 1_555 D C1 MAN . A MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 D O2 MAN . A MAN 5 1_555 D C1 MAN . A MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale9 E O4 NAG . B NAG 1 1_555 E C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 G CA CA . N CA 0 1_555 A O ASP 214 N ASP 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.003 ? metalc ? metalc2 G CA CA . N CA 0 1_555 A O ASN 215 N ASN 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.207 ? metalc ? metalc3 G CA CA . N CA 0 1_555 A O GLY 218 N GLY 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.625 ? metalc ? metalc4 G CA CA . N CA 0 1_555 A OD2 ASP 245 N ASP 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.001 ? metalc ? metalc5 G CA CA . N CA 0 1_555 A O ASN 264 N ASN 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc6 G CA CA . N CA 0 1_555 A O ASN 267 N ASN 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? # _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 ? # 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 1NCD _atom_sites.fract_transf_matrix[1][1] 0.005988 _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] 0.005988 _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] 0.008065 _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 6 NAG N 1 475 86 NAG NAG A G 7 CA N 1 0 0 CA CA . H 8 HOH N 1 478 53 HOH HOH . H 8 HOH N 2 479 103 HOH HOH . H 8 HOH N 3 480 104 HOH HOH . H 8 HOH N 4 481 108 HOH HOH . H 8 HOH N 5 482 110 HOH HOH . H 8 HOH N 6 483 120 HOH HOH . H 8 HOH N 7 484 131 HOH HOH . H 8 HOH N 8 485 148 HOH HOH . H 8 HOH N 9 486 203 HOH HOH . H 8 HOH N 10 487 204 HOH HOH . H 8 HOH N 11 488 205 HOH HOH . H 8 HOH N 12 489 206 HOH HOH . H 8 HOH N 13 490 207 HOH HOH . H 8 HOH N 14 491 211 HOH HOH . H 8 HOH N 15 492 212 HOH HOH . H 8 HOH N 16 493 213 HOH HOH . H 8 HOH N 17 494 217 HOH HOH . H 8 HOH N 18 495 224 HOH HOH . H 8 HOH N 19 496 226 HOH HOH . H 8 HOH N 20 497 228 HOH HOH . H 8 HOH N 21 498 229 HOH HOH . H 8 HOH N 22 499 231 HOH HOH . H 8 HOH N 23 500 232 HOH HOH . H 8 HOH N 24 501 235 HOH HOH . H 8 HOH N 25 502 236 HOH HOH . H 8 HOH N 26 503 237 HOH HOH . H 8 HOH N 27 504 241 HOH HOH . H 8 HOH N 28 505 242 HOH HOH . H 8 HOH N 29 506 243 HOH HOH . H 8 HOH N 30 507 250 HOH HOH . H 8 HOH N 31 508 251 HOH HOH . H 8 HOH N 32 509 253 HOH HOH . H 8 HOH N 33 510 254 HOH HOH . H 8 HOH N 34 511 256 HOH HOH . H 8 HOH N 35 512 259 HOH HOH . H 8 HOH N 36 513 261 HOH HOH . H 8 HOH N 37 514 263 HOH HOH . H 8 HOH N 38 515 266 HOH HOH . H 8 HOH N 39 516 268 HOH HOH . H 8 HOH N 40 517 269 HOH HOH . H 8 HOH N 41 518 270 HOH HOH . H 8 HOH N 42 519 271 HOH HOH . H 8 HOH N 43 520 274 HOH HOH . H 8 HOH N 44 521 275 HOH HOH . H 8 HOH N 45 522 276 HOH HOH . H 8 HOH N 46 523 277 HOH HOH . H 8 HOH N 47 524 278 HOH HOH . H 8 HOH N 48 525 280 HOH HOH . H 8 HOH N 49 526 281 HOH HOH . H 8 HOH N 50 527 283 HOH HOH . H 8 HOH N 51 528 284 HOH HOH . H 8 HOH N 52 529 286 HOH HOH . H 8 HOH N 53 530 289 HOH HOH . H 8 HOH N 54 531 290 HOH HOH . H 8 HOH N 55 532 291 HOH HOH . H 8 HOH N 56 533 292 HOH HOH . H 8 HOH N 57 534 293 HOH HOH . H 8 HOH N 58 535 295 HOH HOH . H 8 HOH N 59 536 298 HOH HOH . H 8 HOH N 60 537 299 HOH HOH . H 8 HOH N 61 538 301 HOH HOH . H 8 HOH N 62 539 302 HOH HOH . H 8 HOH N 63 540 311 HOH HOH . I 8 HOH L 1 215 1 HOH HOH . I 8 HOH L 2 216 86 HOH HOH . J 8 HOH H 1 228 14 HOH HOH . J 8 HOH H 2 229 15 HOH HOH . J 8 HOH H 3 230 66 HOH HOH . J 8 HOH H 4 231 113 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 . . A F 6 59.628 12.664 160.488 1 37.5 ? C1 NAG 475 N 1 HETATM 2 C C2 NAG . . A F 6 60.249 12.519 161.883 1 40.5 ? C2 NAG 475 N 1 HETATM 3 C C3 NAG . . A F 6 59.255 11.676 162.73 1 40.98 ? C3 NAG 475 N 1 HETATM 4 C C4 NAG . . A F 6 57.914 12.448 162.832 1 39.95 ? C4 NAG 475 N 1 HETATM 5 C C5 NAG . . A F 6 57.349 12.555 161.394 1 39.17 ? C5 NAG 475 N 1 HETATM 6 C C6 NAG . . A F 6 56.018 13.303 161.244 1 38.67 ? C6 NAG 475 N 1 HETATM 7 C C7 NAG . . A F 6 62.709 12.676 161.686 1 44.14 ? C7 NAG 475 N 1 HETATM 8 C C8 NAG . . A F 6 64.107 12.077 161.719 1 43.62 ? C8 NAG 475 N 1 HETATM 9 N N2 NAG . . A F 6 61.599 11.931 161.872 1 42.86 ? N2 NAG 475 N 1 HETATM 10 O O3 NAG . . A F 6 59.751 11.401 164.036 1 42.26 ? O3 NAG 475 N 1 HETATM 11 O O4 NAG . . A F 6 57.027 11.782 163.729 1 41.47 ? O4 NAG 475 N 1 HETATM 12 O O5 NAG . . A F 6 58.31 13.236 160.574 1 38.51 ? O5 NAG 475 N 1 HETATM 13 O O6 NAG . . A F 6 55.769 13.494 159.86 1 39.2 ? O6 NAG 475 N 1 HETATM 14 O O7 NAG . . A F 6 62.577 13.884 161.474 1 46.52 ? O7 NAG 475 N 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #