data_3U7Y # _model_server_result.job_id HRMtmn73-1OCfC-lG8dY_Q _model_server_result.datetime_utc '2024-10-19 00:47:41' _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 3u7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":505}' # _entry.id 3U7Y # _exptl.entry_id 3U7Y _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 6 _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 3U7Y _cell.length_a 69.13 _cell.length_b 70.5 _cell.length_c 217.74 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U7Y _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 _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 ? 6 F N N ? 6 G N N ? 6 H N N ? 6 J N N ? 6 K N N ? 6 L N N # _pdbx_entity_branch.entity_id 4 _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 ? 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 # 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 B 1 NAG 4 n D NAG 2 A 2 NAG B 2 NAG 4 n D BMA 3 A 3 BMA B 3 BMA 4 n D MAN 4 A 4 MAN B 4 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 22 H CYS 22 1_555 A SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf2 A SG CYS 32 H CYS 32 1_555 A SG CYS 102 H CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 A SG CYS 152 H CYS 144 1_555 A SG CYS 208 H CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 11 G CYS 54 1_555 B SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 B SG CYS 22 G CYS 65 1_555 B SG CYS 72 G CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 B SG CYS 76 G CYS 119 1_555 B SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 102 G CYS 218 1_555 B SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf8 B SG CYS 112 G CYS 228 1_555 B SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 B SG CYS 180 G CYS 296 1_555 B SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 B SG CYS 245 G CYS 378 1_555 B SG CYS 306 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 B SG CYS 252 G CYS 385 1_555 B SG CYS 279 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 B SG CYS 262 G CYS 395 1_555 B SG CYS 271 G CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf13 C SG CYS 23 L CYS 23 1_555 C SG CYS 86 L CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf14 C SG CYS 130 L CYS 130 1_555 C SG CYS 190 L CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A C PCA 1 H PCA 1 1_555 A N VAL 2 H VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 B ND2 ASN 45 G ASN 88 1_555 K C1 NAG . G NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 B ND2 ASN 118 G ASN 234 1_555 J C1 NAG . G NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 B ND2 ASN 146 G ASN 262 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 B ND2 ASN 173 G ASN 289 1_555 H C1 NAG . G NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 B ND2 ASN 179 G ASN 295 1_555 G C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 B ND2 ASN 253 G ASN 386 1_555 F C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 C ND2 ASN 70 L ASN 70 1_555 L C1 NAG . L NAG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 D O4 NAG . A NAG 2 1_555 D C1 BMA . A BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 D O3 BMA . A BMA 3 1_555 D C1 MAN . A MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 302 n n C1 O1 NAG sing 303 n n C1 O5 NAG sing 304 n n C1 H1 NAG sing 305 n n C2 C3 NAG sing 306 n n C2 N2 NAG sing 307 n n C2 H2 NAG sing 308 n n C3 C4 NAG sing 309 n n C3 O3 NAG sing 310 n n C3 H3 NAG sing 311 n n C4 C5 NAG sing 312 n n C4 O4 NAG sing 313 n n C4 H4 NAG sing 314 n n C5 C6 NAG sing 315 n n C5 O5 NAG sing 316 n n C5 H5 NAG sing 317 n n C6 O6 NAG sing 318 n n C6 H61 NAG sing 319 n n C6 H62 NAG sing 320 n n C7 C8 NAG sing 321 n n C7 N2 NAG sing 322 n n C7 O7 NAG doub 323 n n C8 H81 NAG sing 324 n n C8 H82 NAG sing 325 n n C8 H83 NAG sing 326 n n N2 HN2 NAG sing 327 n n O1 HO1 NAG sing 328 n n O3 HO3 NAG sing 329 n n O4 HO4 NAG sing 330 n n O6 HO6 NAG sing 331 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 3U7Y _atom_sites.fract_transf_matrix[1][1] 0.014465 _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] 0.014184 _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] 0.004593 _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 FLC H 1 222 1 FLC FLC . F 6 NAG G 1 501 501 NAG NAG . G 6 NAG G 1 502 1 NAG NAG . H 6 NAG G 1 503 1 NAG NAG . I 7 CL G 1 504 1 CL CL . J 6 NAG G 1 505 1 NAG NAG . K 6 NAG G 1 506 1 NAG NAG . L 6 NAG L 1 211 1 NAG NAG . M 8 HOH H 1 223 1 HOH HOH . M 8 HOH H 2 224 2 HOH HOH . M 8 HOH H 3 225 4 HOH HOH . M 8 HOH H 4 226 5 HOH HOH . M 8 HOH H 5 227 7 HOH HOH . M 8 HOH H 6 228 8 HOH HOH . M 8 HOH H 7 229 14 HOH HOH . M 8 HOH H 8 230 15 HOH HOH . M 8 HOH H 9 231 17 HOH HOH . M 8 HOH H 10 232 20 HOH HOH . M 8 HOH H 11 233 23 HOH HOH . M 8 HOH H 12 234 25 HOH HOH . M 8 HOH H 13 235 26 HOH HOH . M 8 HOH H 14 236 28 HOH HOH . M 8 HOH H 15 237 31 HOH HOH . M 8 HOH H 16 238 43 HOH HOH . M 8 HOH H 17 239 46 HOH HOH . M 8 HOH H 18 240 47 HOH HOH . M 8 HOH H 19 241 49 HOH HOH . M 8 HOH H 20 242 53 HOH HOH . M 8 HOH H 21 243 55 HOH HOH . M 8 HOH H 22 244 57 HOH HOH . M 8 HOH H 23 245 59 HOH HOH . M 8 HOH H 24 246 63 HOH HOH . M 8 HOH H 25 247 67 HOH HOH . N 8 HOH G 1 6 6 HOH HOH . N 8 HOH G 2 11 11 HOH HOH . N 8 HOH G 3 12 12 HOH HOH . N 8 HOH G 4 13 13 HOH HOH . N 8 HOH G 5 18 18 HOH HOH . N 8 HOH G 6 19 19 HOH HOH . N 8 HOH G 7 21 21 HOH HOH . N 8 HOH G 8 22 22 HOH HOH . N 8 HOH G 9 24 24 HOH HOH . N 8 HOH G 10 29 29 HOH HOH . N 8 HOH G 11 30 30 HOH HOH . N 8 HOH G 12 32 32 HOH HOH . N 8 HOH G 13 33 33 HOH HOH . N 8 HOH G 14 34 34 HOH HOH . N 8 HOH G 15 35 35 HOH HOH . N 8 HOH G 16 36 36 HOH HOH . N 8 HOH G 17 37 37 HOH HOH . N 8 HOH G 18 39 39 HOH HOH . N 8 HOH G 19 41 41 HOH HOH . N 8 HOH G 20 42 42 HOH HOH . N 8 HOH G 21 507 3 HOH HOH . N 8 HOH G 22 508 50 HOH HOH . N 8 HOH G 23 509 52 HOH HOH . N 8 HOH G 24 510 54 HOH HOH . N 8 HOH G 25 511 56 HOH HOH . N 8 HOH G 26 512 58 HOH HOH . N 8 HOH G 27 513 60 HOH HOH . N 8 HOH G 28 514 62 HOH HOH . N 8 HOH G 29 515 66 HOH HOH . O 8 HOH L 1 212 9 HOH HOH . O 8 HOH L 2 213 10 HOH HOH . O 8 HOH L 3 214 16 HOH HOH . O 8 HOH L 4 215 27 HOH HOH . O 8 HOH L 5 216 38 HOH HOH . O 8 HOH L 6 217 40 HOH HOH . O 8 HOH L 7 218 44 HOH HOH . O 8 HOH L 8 219 45 HOH HOH . O 8 HOH L 9 220 48 HOH HOH . O 8 HOH L 10 221 51 HOH HOH . O 8 HOH L 11 222 61 HOH HOH . O 8 HOH L 12 223 64 HOH HOH . O 8 HOH L 13 224 65 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 . . . J 6 23.018 -10.567 -29.465 1 75.06 ? C1 NAG 505 G 1 HETATM 2 C C2 NAG . . . J 6 22.648 -11.758 -28.513 1 118.64 ? C2 NAG 505 G 1 HETATM 3 C C3 NAG . . . J 6 22.458 -11.172 -27.081 1 112.05 ? C3 NAG 505 G 1 HETATM 4 C C4 NAG . . . J 6 23.274 -9.835 -26.942 1 98.2 ? C4 NAG 505 G 1 HETATM 5 C C5 NAG . . . J 6 24.593 -9.864 -27.826 1 92.02 ? C5 NAG 505 G 1 HETATM 6 C C6 NAG . . . J 6 25.634 -10.869 -27.27 1 94.27 ? C6 NAG 505 G 1 HETATM 7 C C7 NAG . . . J 6 21.527 -13.452 -29.851 1 117.67 ? C7 NAG 505 G 1 HETATM 8 C C8 NAG . . . J 6 20.215 -14.023 -30.29 1 117.83 ? C8 NAG 505 G 1 HETATM 9 N N2 NAG . . . J 6 21.42 -12.367 -28.982 1 117.62 ? N2 NAG 505 G 1 HETATM 10 O O3 NAG . . . J 6 22.944 -12.12 -26.186 1 111.41 ? O3 NAG 505 G 1 HETATM 11 O O4 NAG . . . J 6 22.405 -8.794 -27.29 1 97.15 ? O4 NAG 505 G 1 HETATM 12 O O5 NAG . . . J 6 24.369 -10.206 -29.151 1 85.15 ? O5 NAG 505 G 1 HETATM 13 O O6 NAG . . . J 6 26.872 -10.435 -27.748 1 94.7 ? O6 NAG 505 G 1 HETATM 14 O O7 NAG . . . J 6 22.615 -13.883 -30.215 1 117.39 ? O7 NAG 505 G 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #