data_5W6T # _model_server_result.job_id V8UiqrxVSNEyxoyJI1QmPQ _model_server_result.datetime_utc '2024-11-28 13:23:42' _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 5w6t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":404}' # _entry.id 5W6T # _exptl.entry_id 5W6T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 5W6T _cell.length_a 164.331 _cell.length_b 164.331 _cell.length_c 164.331 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W6T _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,K,L _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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 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 ? 5 E N N ? 5 F N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 C 1 NAG A 401 NAG 4 n D NAG 2 C 2 NAG A 402 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 4 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 42 A CYS 52 1_555 A SG CYS 274 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf3 A SG CYS 55 A CYS 64 1_555 A SG CYS 67 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf4 A SG CYS 90 A CYS 97 1_555 A SG CYS 135 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf5 A SG CYS 278 A CYS 281 1_555 A SG CYS 302 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 11 A ASN 21 1_555 E C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 23 A ASN 33 1_555 D C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A NH2 ARG 220 A ARG 224 1_555 H O2 GOL . A GOL 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.29 ? covale ? covale4 A ND2 ASN 268 A ASN 271 1_555 F C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale5 C C ACE 1 F ACE 1 1_555 C N PH8 2 F PH8 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 C C PH8 2 F PH8 2 1_555 C N ORN 3 F ORN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale7 C C ORN 3 F ORN 3 1_555 C N MLE 4 F MLE 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 C NE ORN 3 F ORN 3 1_555 C C 9WV 12 F 9WV 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale9 C C MLE 4 F MLE 4 1_555 C N GLU 5 F GLU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale10 C C TYR 6 F TYR 6 1_555 C N ZCL 7 F ZCL 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale11 C C ZCL 7 F ZCL 7 1_555 C N GLU 8 F GLU 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale12 C C SER 11 F SER 11 1_555 C N 9WV 12 F 9WV 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale13 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _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 5W6T _atom_sites.fract_transf_matrix[1][1] 0.006085 _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] 0.006085 _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] 0.006085 _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 5 NAG A 1 403 403 NAG NAG . F 5 NAG A 1 404 404 NAG NAG . G 6 GOL A 1 405 405 GOL GOL . H 6 GOL A 1 406 406 GOL GOL . I 7 CL B 1 201 201 CL CL . J 8 HOH A 1 501 501 HOH HOH . J 8 HOH A 2 502 502 HOH HOH . J 8 HOH A 3 503 503 HOH HOH . J 8 HOH A 4 504 504 HOH HOH . J 8 HOH A 5 505 505 HOH HOH . J 8 HOH A 6 506 506 HOH HOH . J 8 HOH A 7 507 507 HOH HOH . J 8 HOH A 8 508 508 HOH HOH . J 8 HOH A 9 509 509 HOH HOH . J 8 HOH A 10 510 510 HOH HOH . J 8 HOH A 11 511 511 HOH HOH . J 8 HOH A 12 512 512 HOH HOH . J 8 HOH A 13 513 513 HOH HOH . J 8 HOH A 14 514 514 HOH HOH . J 8 HOH A 15 515 515 HOH HOH . J 8 HOH A 16 516 516 HOH HOH . J 8 HOH A 17 517 517 HOH HOH . J 8 HOH A 18 518 518 HOH HOH . J 8 HOH A 19 519 519 HOH HOH . J 8 HOH A 20 520 520 HOH HOH . J 8 HOH A 21 521 521 HOH HOH . J 8 HOH A 22 522 522 HOH HOH . J 8 HOH A 23 523 523 HOH HOH . J 8 HOH A 24 524 524 HOH HOH . J 8 HOH A 25 525 525 HOH HOH . J 8 HOH A 26 526 526 HOH HOH . J 8 HOH A 27 527 527 HOH HOH . J 8 HOH A 28 528 528 HOH HOH . J 8 HOH A 29 529 529 HOH HOH . J 8 HOH A 30 530 530 HOH HOH . J 8 HOH A 31 531 531 HOH HOH . J 8 HOH A 32 532 532 HOH HOH . J 8 HOH A 33 533 533 HOH HOH . J 8 HOH A 34 534 534 HOH HOH . J 8 HOH A 35 535 535 HOH HOH . J 8 HOH A 36 536 536 HOH HOH . J 8 HOH A 37 537 537 HOH HOH . J 8 HOH A 38 538 538 HOH HOH . J 8 HOH A 39 539 539 HOH HOH . J 8 HOH A 40 540 540 HOH HOH . J 8 HOH A 41 541 541 HOH HOH . J 8 HOH A 42 542 542 HOH HOH . J 8 HOH A 43 543 543 HOH HOH . J 8 HOH A 44 544 544 HOH HOH . J 8 HOH A 45 545 545 HOH HOH . J 8 HOH A 46 546 546 HOH HOH . J 8 HOH A 47 547 547 HOH HOH . J 8 HOH A 48 548 548 HOH HOH . K 8 HOH B 1 301 301 HOH HOH . K 8 HOH B 2 302 302 HOH HOH . K 8 HOH B 3 303 303 HOH HOH . K 8 HOH B 4 304 304 HOH HOH . K 8 HOH B 5 305 305 HOH HOH . K 8 HOH B 6 306 306 HOH HOH . K 8 HOH B 7 307 307 HOH HOH . K 8 HOH B 8 308 308 HOH HOH . K 8 HOH B 9 309 309 HOH HOH . K 8 HOH B 10 310 310 HOH HOH . K 8 HOH B 11 311 311 HOH HOH . K 8 HOH B 12 312 312 HOH HOH . K 8 HOH B 13 313 313 HOH HOH . K 8 HOH B 14 314 314 HOH HOH . K 8 HOH B 15 315 315 HOH HOH . K 8 HOH B 16 316 316 HOH HOH . K 8 HOH B 17 317 317 HOH HOH . K 8 HOH B 18 318 318 HOH HOH . K 8 HOH B 19 319 319 HOH HOH . L 8 HOH F 1 101 101 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 5 -27.654 -31.621 6.914 1 114.97 ? C1 NAG 404 A 1 HETATM 2 C C2 NAG . . . F 5 -28.842 -31.745 7.882 1 123.19 ? C2 NAG 404 A 1 HETATM 3 C C3 NAG . . . F 5 -30.066 -30.984 7.385 1 132.46 ? C3 NAG 404 A 1 HETATM 4 C C4 NAG . . . F 5 -29.702 -29.535 7.107 1 137.47 ? C4 NAG 404 A 1 HETATM 5 C C5 NAG . . . F 5 -28.612 -29.522 6.047 1 136.48 ? C5 NAG 404 A 1 HETATM 6 C C6 NAG . . . F 5 -28.154 -28.131 5.665 1 132.05 ? C6 NAG 404 A 1 HETATM 7 C C7 NAG . . . F 5 -29.642 -33.573 9.288 1 133.31 ? C7 NAG 404 A 1 HETATM 8 C C8 NAG . . . F 5 -29.92 -35.04 9.382 1 140.56 ? C8 NAG 404 A 1 HETATM 9 N N2 NAG . . . F 5 -29.171 -33.142 8.118 1 119.01 ? N2 NAG 404 A 1 HETATM 10 O O3 NAG . . . F 5 -31.076 -31.051 8.388 1 131.67 ? O3 NAG 404 A 1 HETATM 11 O O4 NAG . . . F 5 -30.844 -28.815 6.657 1 133.37 ? O4 NAG 404 A 1 HETATM 12 O O5 NAG . . . F 5 -27.463 -30.228 6.541 1 122.53 ? O5 NAG 404 A 1 HETATM 13 O O6 NAG . . . F 5 -28.098 -27.985 4.252 1 119.73 ? O6 NAG 404 A 1 HETATM 14 O O7 NAG . . . F 5 -29.84 -32.81 10.228 1 135.77 ? O7 NAG 404 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #