data_5NN9 # _model_server_result.job_id JvKLAxVoJsDxzQHlZomJgA _model_server_result.datetime_utc '2024-11-28 20:24:18' _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 5nn9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":477}' # _entry.id 5NN9 # _exptl.entry_id 5NN9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 5NN9 _cell.length_a 185.1 _cell.length_b 185.1 _cell.length_c 185.1 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NN9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 211 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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' 15_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 3 'crystal symmetry operation' 16_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN MAN C1 O1 . O3 HO3 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 2 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 2 7 3 MAN MAN 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 2 n B NAG 1 B 1 NAG ? 200 NAG 2 n B NAG 2 B 2 NAG ? 200 NAG 2 n B MAN 3 B 3 MAN ? 200 MAN 2 n B MAN 4 B 4 MAN ? 200 MAN 2 n B MAN 5 B 5 MAN ? 200 MAN 2 n B MAN 6 B 6 MAN ? 200 MAN 2 n B MAN 7 B 7 MAN ? 200 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 11 A CYS 92 1_555 A SG CYS 337 A CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf2 A SG CYS 43 A CYS 124 1_555 A SG CYS 48 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf3 A SG CYS 95 A CYS 175 1_555 A SG CYS 113 A CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf4 A SG CYS 103 A CYS 183 1_555 A SG CYS 150 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? disulf ? disulf5 A SG CYS 152 A CYS 232 1_555 A SG CYS 157 A CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? disulf ? disulf6 A SG CYS 198 A CYS 278 1_555 A SG CYS 211 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf7 A SG CYS 200 A CYS 280 1_555 A SG CYS 209 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf8 A SG CYS 238 A CYS 318 1_555 A SG CYS 256 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 A SG CYS 341 A CYS 421 1_555 A SG CYS 367 A CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? covale ? covale1 A ND2 ASN 5 A ASN 86 1_555 D C1 NAG . A NAG 477 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 A ND2 ASN 65 A ASN 146 1_555 C C1 NAG . A NAG 476 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.461 ? covale ? covale3 A ND2 ASN 120 A ASN 200 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale6 B O3 MAN . B MAN 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale7 B O6 MAN . B MAN 3 1_555 B C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale8 B O2 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale9 B O2 MAN . B MAN 5 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? metalc ? metalc1 E CA CA . A CA 18 1_555 A O ASP 213 A ASP 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc2 E CA CA . A CA 18 1_555 A O GLY 217 A GLY 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc3 E CA CA . A CA 18 1_555 A OD2 ASP 244 A ASP 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc4 E CA CA . A CA 18 1_555 A O ASN 266 A ASN 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.022 ? metalc ? metalc5 E CA CA . A CA 18 1_555 F O HOH . A HOH 485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 5NN9 _atom_sites.fract_transf_matrix[1][1] 0.005402 _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] 0.005402 _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] 0.005402 _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 C 3 NAG A 1 476 146 NAG NAG A D 3 NAG A 1 477 86 NAG NAG A E 4 CA A 1 18 18 CA CA . F 5 HOH A 1 478 1 HOH HOH . F 5 HOH A 2 479 2 HOH HOH . F 5 HOH A 3 480 3 HOH HOH . F 5 HOH A 4 481 4 HOH HOH . F 5 HOH A 5 482 5 HOH HOH . F 5 HOH A 6 483 6 HOH HOH . F 5 HOH A 7 484 7 HOH HOH . F 5 HOH A 8 485 8 HOH HOH . F 5 HOH A 9 486 9 HOH HOH . F 5 HOH A 10 487 10 HOH HOH . F 5 HOH A 11 488 11 HOH HOH . F 5 HOH A 12 489 12 HOH HOH . F 5 HOH A 13 490 13 HOH HOH . F 5 HOH A 14 491 14 HOH HOH . F 5 HOH A 15 492 15 HOH HOH . F 5 HOH A 16 493 16 HOH HOH . F 5 HOH A 17 494 17 HOH HOH . F 5 HOH A 18 495 19 HOH HOH . F 5 HOH A 19 496 20 HOH HOH . F 5 HOH A 20 497 21 HOH HOH . F 5 HOH A 21 498 22 HOH HOH . F 5 HOH A 22 499 23 HOH HOH . F 5 HOH A 23 500 24 HOH HOH . F 5 HOH A 24 501 25 HOH HOH . F 5 HOH A 25 502 26 HOH HOH . F 5 HOH A 26 503 27 HOH HOH . F 5 HOH A 27 504 28 HOH HOH . F 5 HOH A 28 505 29 HOH HOH . F 5 HOH A 29 506 30 HOH HOH . F 5 HOH A 30 507 31 HOH HOH . F 5 HOH A 31 508 32 HOH HOH . F 5 HOH A 32 509 33 HOH HOH . F 5 HOH A 33 510 34 HOH HOH . F 5 HOH A 34 511 35 HOH HOH . F 5 HOH A 35 512 36 HOH HOH . F 5 HOH A 36 513 37 HOH HOH . F 5 HOH A 37 514 38 HOH HOH . F 5 HOH A 38 515 39 HOH HOH . F 5 HOH A 39 516 40 HOH HOH . F 5 HOH A 40 517 41 HOH HOH . F 5 HOH A 41 518 42 HOH HOH . F 5 HOH A 42 519 43 HOH HOH . F 5 HOH A 43 520 44 HOH HOH . F 5 HOH A 44 521 45 HOH HOH . F 5 HOH A 45 522 46 HOH HOH . F 5 HOH A 46 523 47 HOH HOH . F 5 HOH A 47 524 48 HOH HOH . F 5 HOH A 48 525 49 HOH HOH . F 5 HOH A 49 526 50 HOH HOH . F 5 HOH A 50 527 51 HOH HOH . F 5 HOH A 51 528 52 HOH HOH . F 5 HOH A 52 529 53 HOH HOH . F 5 HOH A 53 530 54 HOH HOH . F 5 HOH A 54 531 55 HOH HOH . F 5 HOH A 55 532 56 HOH HOH . F 5 HOH A 56 533 57 HOH HOH . F 5 HOH A 57 534 58 HOH HOH . F 5 HOH A 58 535 59 HOH HOH . F 5 HOH A 59 536 60 HOH HOH . F 5 HOH A 60 537 61 HOH HOH . F 5 HOH A 61 538 62 HOH HOH . F 5 HOH A 62 539 63 HOH HOH . F 5 HOH A 63 540 64 HOH HOH . F 5 HOH A 64 541 65 HOH HOH . F 5 HOH A 65 542 66 HOH HOH . F 5 HOH A 66 543 67 HOH HOH . F 5 HOH A 67 544 68 HOH HOH . F 5 HOH A 68 545 69 HOH HOH . F 5 HOH A 69 546 70 HOH HOH . F 5 HOH A 70 547 71 HOH HOH . F 5 HOH A 71 548 72 HOH HOH . F 5 HOH A 72 549 73 HOH HOH . F 5 HOH A 73 550 74 HOH HOH . F 5 HOH A 74 551 75 HOH HOH . F 5 HOH A 75 552 76 HOH HOH . F 5 HOH A 76 553 77 HOH HOH . F 5 HOH A 77 554 78 HOH HOH . F 5 HOH A 78 555 79 HOH HOH . F 5 HOH A 79 556 80 HOH HOH . F 5 HOH A 80 557 81 HOH HOH . F 5 HOH A 81 558 82 HOH HOH . F 5 HOH A 82 559 83 HOH HOH . F 5 HOH A 83 560 84 HOH HOH . F 5 HOH A 84 561 85 HOH HOH . F 5 HOH A 85 562 86 HOH HOH . F 5 HOH A 86 563 87 HOH HOH . F 5 HOH A 87 564 88 HOH HOH . F 5 HOH A 88 565 89 HOH HOH . F 5 HOH A 89 566 90 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 D 3 17.076 18.113 29.803 1 30.8 ? C1 NAG 477 A 1 HETATM 2 C C2 NAG . . A D 3 15.792 17.673 29.134 1 31.94 ? C2 NAG 477 A 1 HETATM 3 C C3 NAG . . A D 3 16.089 16.486 28.278 1 34.91 ? C3 NAG 477 A 1 HETATM 4 C C4 NAG . . A D 3 17.115 16.822 27.213 1 35.28 ? C4 NAG 477 A 1 HETATM 5 C C5 NAG . . A D 3 18.389 17.382 27.876 1 35.28 ? C5 NAG 477 A 1 HETATM 6 C C6 NAG . . A D 3 19.455 17.923 26.866 1 35.9 ? C6 NAG 477 A 1 HETATM 7 C C7 NAG . . A D 3 13.563 17.167 30.041 1 33.33 ? C7 NAG 477 A 1 HETATM 8 C C8 NAG . . A D 3 12.778 16.765 31.28 1 30.59 ? C8 NAG 477 A 1 HETATM 9 N N2 NAG . . A D 3 14.868 17.347 30.194 1 33.07 ? N2 NAG 477 A 1 HETATM 10 O O3 NAG . . A D 3 14.934 15.97 27.647 1 36.55 ? O3 NAG 477 A 1 HETATM 11 O O4 NAG . . A D 3 17.349 15.596 26.549 1 37.12 ? O4 NAG 477 A 1 HETATM 12 O O5 NAG . . A D 3 18.01 18.476 28.777 1 32.72 ? O5 NAG 477 A 1 HETATM 13 O O6 NAG . . A D 3 20.304 18.836 27.54 1 37.8 ? O6 NAG 477 A 1 HETATM 14 O O7 NAG . . A D 3 13.044 17.418 28.956 1 34.63 ? O7 NAG 477 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #