data_4JB9 # _model_server_result.job_id lyiD5nXqd_vT4x1jC9MGaQ _model_server_result.datetime_utc '2024-11-23 16:33:36' _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 4jb9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":506}' # _entry.id 4JB9 # _exptl.entry_id 4JB9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 10 _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 4JB9 _cell.length_a 64.244 _cell.length_b 68.924 _cell.length_c 224.225 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JB9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M 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 11 G CYS 54 1_555 A SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 76 G CYS 119 1_555 A SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 102 G CYS 218 1_555 A SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 A SG CYS 112 G CYS 228 1_555 A SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 180 G CYS 296 1_555 A SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 A SG CYS 245 G CYS 378 1_555 A SG CYS 306 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 A SG CYS 252 G CYS 385 1_555 A SG CYS 279 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 A SG CYS 262 G CYS 395 1_555 A SG CYS 271 G CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 22 H CYS 22 1_555 B SG CYS 103 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 B SG CYS 110 H CYS 98 1_555 B SG CYS 113 H CYS 100 1_555 ? ? ? A ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 B SG CYS 158 H CYS 140 1_555 B SG CYS 214 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 C SG CYS 23 L CYS 23 1_555 C SG CYS 87 L CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 118 G ASN 234 1_555 D C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 125 G ASN 241 1_555 E C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A ND2 ASN 125 G ASN 241 1_555 E C2 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale4 A ND2 ASN 146 G ASN 262 1_555 F C1 NAG . G NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 A ND2 ASN 160 G ASN 276 1_555 G C1 NAG . G NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 A ND2 ASN 173 G ASN 289 1_555 H C1 NAG . G NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 A ND2 ASN 179 G ASN 295 1_555 I C1 NAG . G NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 A ND2 ASN 202 G ASN 334 1_555 J C1 NAG . G NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 A ND2 ASN 253 G ASN 386 1_555 K C1 NAG . G NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale10 A ND2 ASN 259 G ASN 392 1_555 L C1 NAG . G NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 A ND2 ASN 309 G ASN 448 1_555 M C1 NAG . G NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 4JB9 _atom_sites.fract_transf_matrix[1][1] 0.015566 _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] 0.014509 _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] 0.00446 _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 D 4 NAG G 1 501 501 NAG NAG . E 4 NAG G 1 502 502 NAG NAG . F 4 NAG G 1 503 503 NAG NAG . G 4 NAG G 1 504 504 NAG NAG . H 4 NAG G 1 505 505 NAG NAG . I 4 NAG G 1 506 506 NAG NAG . J 4 NAG G 1 507 507 NAG NAG . K 4 NAG G 1 508 508 NAG NAG . L 4 NAG G 1 509 509 NAG NAG . M 4 NAG G 1 510 510 NAG NAG . N 5 HOH G 1 601 1 HOH HOH . N 5 HOH G 2 602 2 HOH HOH . N 5 HOH G 3 603 3 HOH HOH . N 5 HOH G 4 604 4 HOH HOH . N 5 HOH G 5 605 5 HOH HOH . N 5 HOH G 6 606 6 HOH HOH . N 5 HOH G 7 607 7 HOH HOH . N 5 HOH G 8 608 8 HOH HOH . N 5 HOH G 9 609 33 HOH HOH . N 5 HOH G 10 610 38 HOH HOH . N 5 HOH G 11 611 39 HOH HOH . O 5 HOH H 1 301 9 HOH HOH . O 5 HOH H 2 302 10 HOH HOH . O 5 HOH H 3 303 11 HOH HOH . O 5 HOH H 4 304 12 HOH HOH . O 5 HOH H 5 305 13 HOH HOH . O 5 HOH H 6 306 14 HOH HOH . O 5 HOH H 7 307 15 HOH HOH . O 5 HOH H 8 308 16 HOH HOH . O 5 HOH H 9 309 17 HOH HOH . O 5 HOH H 10 310 18 HOH HOH . O 5 HOH H 11 311 19 HOH HOH . O 5 HOH H 12 312 20 HOH HOH . O 5 HOH H 13 313 21 HOH HOH . O 5 HOH H 14 314 32 HOH HOH . O 5 HOH H 15 315 34 HOH HOH . O 5 HOH H 16 316 37 HOH HOH . O 5 HOH H 17 317 40 HOH HOH . P 5 HOH L 1 301 22 HOH HOH . P 5 HOH L 2 302 23 HOH HOH . P 5 HOH L 3 303 24 HOH HOH . P 5 HOH L 4 304 25 HOH HOH . P 5 HOH L 5 305 26 HOH HOH . P 5 HOH L 6 306 27 HOH HOH . P 5 HOH L 7 307 28 HOH HOH . P 5 HOH L 8 308 29 HOH HOH . P 5 HOH L 9 309 30 HOH HOH . P 5 HOH L 10 310 31 HOH HOH . P 5 HOH L 11 311 35 HOH HOH . P 5 HOH L 12 312 36 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 . . . I 4 19.449 -22.297 -68.052 1 83.42 ? C1 NAG 506 G 1 HETATM 2 C C2 NAG . . . I 4 20.496 -21.819 -69.05 1 97.17 ? C2 NAG 506 G 1 HETATM 3 C C3 NAG . . . I 4 19.917 -21.832 -70.463 1 115.74 ? C3 NAG 506 G 1 HETATM 4 C C4 NAG . . . I 4 19.319 -23.195 -70.784 1 129.89 ? C4 NAG 506 G 1 HETATM 5 C C5 NAG . . . I 4 18.347 -23.629 -69.688 1 127.04 ? C5 NAG 506 G 1 HETATM 6 C C6 NAG . . . I 4 17.837 -25.039 -69.876 1 129.72 ? C6 NAG 506 G 1 HETATM 7 C C7 NAG . . . I 4 22.087 -20.281 -67.989 1 98.76 ? C7 NAG 506 G 1 HETATM 8 C C8 NAG . . . I 4 22.433 -18.848 -67.723 1 101.66 ? C8 NAG 506 G 1 HETATM 9 N N2 NAG . . . I 4 20.976 -20.493 -68.705 1 96.62 ? N2 NAG 506 G 1 HETATM 10 O O3 NAG . . . I 4 20.944 -21.524 -71.399 1 121.02 ? O3 NAG 506 G 1 HETATM 11 O O4 NAG . . . I 4 18.626 -23.135 -72.026 1 130.61 ? O4 NAG 506 G 1 HETATM 12 O O5 NAG . . . I 4 19.002 -23.593 -68.411 1 107.98 ? O5 NAG 506 G 1 HETATM 13 O O6 NAG . . . I 4 17.027 -25.448 -68.783 1 134.65 ? O6 NAG 506 G 1 HETATM 14 O O7 NAG . . . I 4 22.778 -21.206 -67.575 1 101.03 ? O7 NAG 506 G 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #