data_5KOQ # _model_server_result.job_id 1gyQ_oEhlpZhnhBhVJaFFg _model_server_result.datetime_utc '2024-11-22 05:40:13' _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 5koq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5KOQ # _exptl.entry_id 5KOQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _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 5KOQ _cell.length_a 138.562 _cell.length_b 138.562 _cell.length_c 138.562 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KOQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA hexameric 6 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,H 1 1 B,E,F,G,I 2 1 A,B,C,D,E,F,G,H,I 3 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' 6_445 z-1/2,-x-1/2,-y 0 0 1 -1 0 0 0 -1 0 -69.281 -69.281 0 3 'crystal symmetry operation' 12_455 -y-1/2,-z,x+1/2 0 -1 0 0 0 -1 1 0 0 -69.281 0 69.281 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 48 A CYS 51 1_555 A SG CYS 55 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 214 A CYS 217 1_555 A SG CYS 218 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 256 A CYS 259 1_555 A SG CYS 293 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 48 B CYS 51 1_555 B SG CYS 55 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf5 B SG CYS 214 B CYS 217 1_555 B SG CYS 218 B CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 B SG CYS 256 B CYS 259 1_555 B SG CYS 293 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 72 A ASN 75 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 B ND2 ASN 72 B ASN 75 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? # _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 304 n n C1 O1 NAG sing 305 n n C1 O5 NAG sing 306 n n C1 H1 NAG sing 307 n n C2 C3 NAG sing 308 n n C2 N2 NAG sing 309 n n C2 H2 NAG sing 310 n n C3 C4 NAG sing 311 n n C3 O3 NAG sing 312 n n C3 H3 NAG sing 313 n n C4 C5 NAG sing 314 n n C4 O4 NAG sing 315 n n C4 H4 NAG sing 316 n n C5 C6 NAG sing 317 n n C5 O5 NAG sing 318 n n C5 H5 NAG sing 319 n n C6 O6 NAG sing 320 n n C6 H61 NAG sing 321 n n C6 H62 NAG sing 322 n n C7 C8 NAG sing 323 n n C7 N2 NAG sing 324 n n C7 O7 NAG doub 325 n n C8 H81 NAG sing 326 n n C8 H82 NAG sing 327 n n C8 H83 NAG sing 328 n n N2 HN2 NAG sing 329 n n O1 HO1 NAG sing 330 n n O3 HO3 NAG sing 331 n n O4 HO4 NAG sing 332 n n O6 HO6 NAG sing 333 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 5KOQ _atom_sites.fract_transf_matrix[1][1] 0.007217 _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] 0.007217 _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] 0.007217 _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 2 NAG A 1 401 400 NAG NAG . D 3 6VR A 1 402 500 6VR LIG . E 2 NAG B 1 401 410 NAG NAG . F 3 6VR B 1 402 510 6VR LIG . G 4 PEG B 1 403 610 PEG PEG . H 5 HOH A 1 501 6 HOH HOH . H 5 HOH A 2 502 8 HOH HOH . H 5 HOH A 3 503 19 HOH HOH . H 5 HOH A 4 504 2 HOH HOH . H 5 HOH A 5 505 5 HOH HOH . H 5 HOH A 6 506 16 HOH HOH . H 5 HOH A 7 507 18 HOH HOH . H 5 HOH A 8 508 1 HOH HOH . H 5 HOH A 9 509 17 HOH HOH . H 5 HOH A 10 510 46 HOH HOH . H 5 HOH A 11 511 60 HOH HOH . H 5 HOH A 12 512 47 HOH HOH . H 5 HOH A 13 513 80 HOH HOH . H 5 HOH A 14 514 70 HOH HOH . H 5 HOH A 15 515 79 HOH HOH . H 5 HOH A 16 516 14 HOH HOH . H 5 HOH A 17 517 82 HOH HOH . H 5 HOH A 18 518 86 HOH HOH . H 5 HOH A 19 519 4 HOH HOH . H 5 HOH A 20 520 49 HOH HOH . H 5 HOH A 21 521 84 HOH HOH . H 5 HOH A 22 522 76 HOH HOH . H 5 HOH A 23 523 75 HOH HOH . H 5 HOH A 24 524 21 HOH HOH . H 5 HOH A 25 525 81 HOH HOH . H 5 HOH A 26 526 51 HOH HOH . H 5 HOH A 27 527 55 HOH HOH . H 5 HOH A 28 528 83 HOH HOH . H 5 HOH A 29 529 34 HOH HOH . H 5 HOH A 30 530 38 HOH HOH . H 5 HOH A 31 531 32 HOH HOH . H 5 HOH A 32 532 13 HOH HOH . H 5 HOH A 33 533 22 HOH HOH . H 5 HOH A 34 534 50 HOH HOH . H 5 HOH A 35 535 85 HOH HOH . H 5 HOH A 36 536 39 HOH HOH . H 5 HOH A 37 537 20 HOH HOH . H 5 HOH A 38 538 42 HOH HOH . H 5 HOH A 39 539 71 HOH HOH . H 5 HOH A 40 540 58 HOH HOH . H 5 HOH A 41 541 72 HOH HOH . H 5 HOH A 42 542 43 HOH HOH . H 5 HOH A 43 543 9 HOH HOH . H 5 HOH A 44 544 40 HOH HOH . H 5 HOH A 45 545 12 HOH HOH . H 5 HOH A 46 546 74 HOH HOH . H 5 HOH A 47 547 56 HOH HOH . H 5 HOH A 48 548 53 HOH HOH . H 5 HOH A 49 549 73 HOH HOH . H 5 HOH A 50 550 48 HOH HOH . H 5 HOH A 51 551 57 HOH HOH . H 5 HOH A 52 552 28 HOH HOH . H 5 HOH A 53 553 54 HOH HOH . H 5 HOH A 54 554 29 HOH HOH . I 5 HOH B 1 501 7 HOH HOH . I 5 HOH B 2 502 66 HOH HOH . I 5 HOH B 3 503 27 HOH HOH . I 5 HOH B 4 504 15 HOH HOH . I 5 HOH B 5 505 62 HOH HOH . I 5 HOH B 6 506 24 HOH HOH . I 5 HOH B 7 507 59 HOH HOH . I 5 HOH B 8 508 68 HOH HOH . I 5 HOH B 9 509 64 HOH HOH . I 5 HOH B 10 510 65 HOH HOH . I 5 HOH B 11 511 36 HOH HOH . I 5 HOH B 12 512 11 HOH HOH . I 5 HOH B 13 513 87 HOH HOH . I 5 HOH B 14 514 41 HOH HOH . I 5 HOH B 15 515 77 HOH HOH . I 5 HOH B 16 516 30 HOH HOH . I 5 HOH B 17 517 37 HOH HOH . I 5 HOH B 18 518 44 HOH HOH . I 5 HOH B 19 519 67 HOH HOH . I 5 HOH B 20 520 10 HOH HOH . I 5 HOH B 21 521 63 HOH HOH . I 5 HOH B 22 522 23 HOH HOH . I 5 HOH B 23 523 78 HOH HOH . I 5 HOH B 24 524 35 HOH HOH . I 5 HOH B 25 525 31 HOH HOH . I 5 HOH B 26 526 26 HOH HOH . I 5 HOH B 27 527 3 HOH HOH . I 5 HOH B 28 528 52 HOH HOH . I 5 HOH B 29 529 33 HOH HOH . I 5 HOH B 30 530 45 HOH HOH . I 5 HOH B 31 531 25 HOH HOH . I 5 HOH B 32 532 61 HOH HOH . I 5 HOH B 33 533 69 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 . . . C 2 -57.687 21.986 0.433 0.8 60.2 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . C 2 -58.568 23.122 -0.111 0.8 62.43 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . C 2 -57.997 23.666 -1.428 0.8 64.97 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . C 2 -56.55 24.131 -1.235 0.8 66.05 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . C 2 -55.698 22.999 -0.636 0.8 66.39 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . C 2 -54.304 23.487 -0.26 0.8 68.15 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . C 2 -60.939 23.138 0.553 0.8 60.44 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . C 2 -62.318 22.655 0.213 0.8 57.86 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . C 2 -59.966 22.742 -0.277 0.8 61.79 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . C 2 -58.794 24.756 -1.909 0.8 65.2 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . C 2 -56.021 24.584 -2.489 0.8 66.53 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . C 2 -56.317 22.428 0.54 0.8 63.73 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . C 2 -53.396 23.103 -1.298 0.8 73.17 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . C 2 -60.743 23.841 1.534 0.8 59.77 ? O7 NAG 401 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #