data_4P59 # _model_server_result.job_id XnQTzpRQgQoj668GG9WgnQ _model_server_result.datetime_utc '2024-11-02 06:26:32' _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 4p59 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":707}' # _entry.id 4P59 # _exptl.entry_id 4P59 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 4P59 _cell.length_a 124.226 _cell.length_b 140.939 _cell.length_c 180.247 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P59 _symmetry.cell_setting . _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _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 ? 5 F N N ? 5 G N N ? 5 H 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 B 1 NAG A 851 NAG 4 n D NAG 2 B 2 NAG A 852 NAG 4 n E NAG 1 C 1 NAG A 901 NAG 4 n E NAG 2 C 2 NAG A 902 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 10 A CYS 29 1_555 A SG CYS 37 A CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 137 A CYS 156 1_555 A SG CYS 164 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 A SG CYS 167 A CYS 186 1_555 A SG CYS 175 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 A SG CYS 171 A CYS 190 1_555 A SG CYS 183 A CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 A SG CYS 191 A CYS 210 1_555 A SG CYS 199 A CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf6 A SG CYS 195 A CYS 214 1_555 A SG CYS 207 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf7 A SG CYS 208 A CYS 227 1_555 A SG CYS 216 A CYS 235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 A SG CYS 212 A CYS 231 1_555 A SG CYS 224 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 A SG CYS 227 A CYS 246 1_555 A SG CYS 236 A CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf10 A SG CYS 240 A CYS 259 1_555 A SG CYS 267 A CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf11 A SG CYS 271 A CYS 290 1_555 A SG CYS 282 A CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf12 A SG CYS 286 A CYS 305 1_555 A SG CYS 301 A CYS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf13 A SG CYS 304 A CYS 323 1_555 A SG CYS 308 A CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf14 A SG CYS 312 A CYS 331 1_555 A SG CYS 335 A CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf15 A SG CYS 444 A CYS 463 1_555 A SG CYS 474 A CYS 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf16 A SG CYS 481 A CYS 500 1_555 A SG CYS 490 A CYS 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 A SG CYS 485 A CYS 504 1_555 A SG CYS 498 A CYS 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf18 A SG CYS 501 A CYS 520 1_555 A SG CYS 510 A CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf19 A SG CYS 514 A CYS 533 1_555 A SG CYS 530 A CYS 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf20 A SG CYS 533 A CYS 552 1_555 A SG CYS 546 A CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf21 A SG CYS 537 A CYS 556 1_555 A SG CYS 554 A CYS 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf22 A SG CYS 557 A CYS 576 1_555 A SG CYS 566 A CYS 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf23 A SG CYS 570 A CYS 589 1_555 A SG CYS 591 A CYS 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf24 A SG CYS 594 A CYS 613 1_555 A SG CYS 602 A CYS 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf25 A SG CYS 598 A CYS 617 1_555 A SG CYS 610 A CYS 629 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf26 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf27 B SG CYS 144 H CYS 144 1_555 B SG CYS 200 H CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf28 C SG CYS 23 L CYS 23 1_555 C SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf29 C SG CYS 134 L CYS 134 1_555 C SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A ND2 ASN 231 A ASN 250 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 A ND2 ASN 334 A ASN 353 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 A ND2 ASN 389 A ASN 408 1_555 F C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A ND2 ASN 395 A ASN 414 1_555 H C1 NAG . A NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 A ND2 ASN 418 A ASN 437 1_555 G C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 E O4 NAG . C NAG 1 1_555 E 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 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 4P59 _atom_sites.fract_transf_matrix[1][1] 0.00805 _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] 0.007095 _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] 0.005548 _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 F 5 NAG A 1 701 751 NAG NAG . G 5 NAG A 1 702 801 NAG NAG . H 5 NAG A 1 707 951 NAG NAG . I 6 HOH H 1 301 1 HOH HOH . I 6 HOH H 2 302 3 HOH HOH . J 6 HOH L 1 301 2 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 . . . H 5 -25.316 -35.827 -5.968 1 171.38 ? C1 NAG 707 A 1 HETATM 2 C C2 NAG . . . H 5 -24.771 -34.515 -6.526 1 173.23 ? C2 NAG 707 A 1 HETATM 3 C C3 NAG . . . H 5 -24.062 -34.917 -7.819 1 173.11 ? C3 NAG 707 A 1 HETATM 4 C C4 NAG . . . H 5 -22.968 -35.948 -7.549 1 171.72 ? C4 NAG 707 A 1 HETATM 5 C C5 NAG . . . H 5 -23.499 -37.155 -6.776 1 170.51 ? C5 NAG 707 A 1 HETATM 6 C C6 NAG . . . H 5 -22.393 -38.027 -6.23 1 168.94 ? C6 NAG 707 A 1 HETATM 7 C C7 NAG . . . H 5 -26.198 -32.565 -6.073 1 173.66 ? C7 NAG 707 A 1 HETATM 8 C C8 NAG . . . H 5 -27.271 -31.674 -6.625 1 172.68 ? C8 NAG 707 A 1 HETATM 9 N N2 NAG . . . H 5 -25.875 -33.618 -6.822 1 174.08 ? N2 NAG 707 A 1 HETATM 10 O O3 NAG . . . H 5 -23.466 -33.753 -8.385 1 173.53 ? O3 NAG 707 A 1 HETATM 11 O O4 NAG . . . H 5 -22.48 -36.402 -8.805 1 171.87 ? O4 NAG 707 A 1 HETATM 12 O O5 NAG . . . H 5 -24.248 -36.714 -5.634 1 171.31 ? O5 NAG 707 A 1 HETATM 13 O O6 NAG . . . H 5 -21.747 -37.396 -5.133 1 168.28 ? O6 NAG 707 A 1 HETATM 14 O O7 NAG . . . H 5 -25.655 -32.341 -4.996 1 174.02 ? O7 NAG 707 A 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #