data_4IRZ # _model_server_result.job_id qBiyyE6k2ir2cUDKV2Vt9Q _model_server_result.datetime_utc '2024-11-24 14:43:51' _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 4irz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":3105}' # _entry.id 4IRZ # _exptl.entry_id 4IRZ _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 4 _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 4IRZ _cell.length_a 73.61 _cell.length_b 77.89 _cell.length_c 217.74 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IRZ _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 ? 6 H N N ? 6 I N N ? 6 J N N ? 6 K 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 # 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 3196 NAG 4 n D NAG 2 B 2 NAG A 3197 NAG 4 n D BMA 3 B 3 BMA A 3198 BMA # 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 58 A CYS 58 1_555 A SG CYS 68 A CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 81 A CYS 81 1_555 A SG CYS 85 A CYS 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 111 A CYS 111 1_555 A SG CYS 132 A CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 150 A CYS 150 1_555 A SG CYS 165 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 453 A CYS 453 1_555 A SG CYS 462 A CYS 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 468 A CYS 468 1_555 A SG CYS 524 A CYS 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 133 L CYS 133 1_555 B SG CYS 193 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 C SG CYS 150 H CYS 150 1_555 C SG CYS 206 H CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 46 A ASN 46 1_555 H C1 NAG . A NAG 3046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 105 A ASN 105 1_555 I C1 NAG . A NAG 3105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 196 A ASN 196 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 485 A ASN 485 1_555 J C1 NAG . A NAG 3485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 505 A ASN 505 1_555 K C1 NAG . A NAG 3505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 D O4 NAG . B NAG 2 1_555 D C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? metalc ? metalc1 A OD1 ASP 281 A ASP 281 1_555 E CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc2 A OD1 ASN 283 A ASN 283 1_555 E CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc3 A OD1 ASP 285 A ASP 285 1_555 E CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc4 A O PHE 287 A PHE 287 1_555 E CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc5 A OD2 ASP 289 A ASP 289 1_555 E CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc6 A OD1 ASP 289 A ASP 289 1_555 E CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc7 A OD1 ASP 344 A ASP 344 1_555 F CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc8 A OD1 ASP 346 A ASP 346 1_555 F CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc9 A OD1 ASP 348 A ASP 348 1_555 F CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc10 A O PHE 350 A PHE 350 1_555 F CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc11 A OD1 ASP 352 A ASP 352 1_555 F CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc12 A OD2 ASP 352 A ASP 352 1_555 F CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc13 A OD1 ASP 406 A ASP 406 1_555 G CA CA . A CA 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc14 A OD1 ASP 408 A ASP 408 1_555 G CA CA . A CA 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc15 A OD1 ASN 410 A ASN 410 1_555 G CA CA . A CA 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc16 A O TYR 412 A TYR 412 1_555 G CA CA . A CA 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc17 A OD1 ASP 414 A ASP 414 1_555 G CA CA . A CA 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc18 A OD2 ASP 414 A ASP 414 1_555 G CA CA . A CA 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc19 O O HOH . A HOH 701 1_555 E CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc20 O O HOH . A HOH 702 1_555 F CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc21 O O HOH . A HOH 703 1_555 G CA CA . A CA 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc22 C O PHE 64 H PHE 64 1_555 N NA NA . H NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc23 C O GLN 65 H GLN 65 1_555 N NA NA . H NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 4IRZ _atom_sites.fract_transf_matrix[1][1] 0.013585 _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] 0.012839 _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 CA A 1 2005 2005 CA CA . F 5 CA A 1 2006 2006 CA CA . G 5 CA A 1 2007 2007 CA CA . H 6 NAG A 1 3046 3046 NAG NAG . I 6 NAG A 1 3105 3105 NAG NAG . J 6 NAG A 1 3485 3485 NAG NAG . K 6 NAG A 1 3505 3505 NAG NAG . L 7 PEG A 1 611 9 PEG PEG . M 8 NDS A 1 612 20 NDS NDS . N 9 NA H 1 301 27 NA NA . O 10 HOH A 1 701 1 HOH HOH . O 10 HOH A 2 702 2 HOH HOH . O 10 HOH A 3 703 19 HOH HOH . O 10 HOH A 4 704 10 HOH HOH . O 10 HOH A 5 705 12 HOH HOH . O 10 HOH A 6 706 22 HOH HOH . O 10 HOH A 7 707 24 HOH HOH . O 10 HOH A 8 708 25 HOH HOH . O 10 HOH A 9 709 26 HOH HOH . P 10 HOH L 1 301 14 HOH HOH . P 10 HOH L 2 302 15 HOH HOH . P 10 HOH L 3 303 17 HOH HOH . P 10 HOH L 4 304 21 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 6 22.914 -8.615 89.378 1 85.95 ? C1 NAG 3105 A 1 HETATM 2 C C2 NAG . . . I 6 23.48 -7.361 90.037 1 90.09 ? C2 NAG 3105 A 1 HETATM 3 C C3 NAG . . . I 6 25.001 -7.405 90.087 1 89.07 ? C3 NAG 3105 A 1 HETATM 4 C C4 NAG . . . I 6 25.487 -8.741 90.636 1 89.55 ? C4 NAG 3105 A 1 HETATM 5 C C5 NAG . . . I 6 24.813 -9.906 89.919 1 88.13 ? C5 NAG 3105 A 1 HETATM 6 C C6 NAG . . . I 6 25.237 -11.247 90.508 1 80.83 ? C6 NAG 3105 A 1 HETATM 7 C C7 NAG . . . I 6 22.169 -5.314 89.864 1 93.44 ? C7 NAG 3105 A 1 HETATM 8 C C8 NAG . . . I 6 21.991 -4.005 89.155 1 92.51 ? C8 NAG 3105 A 1 HETATM 9 N N2 NAG . . . I 6 23.036 -6.173 89.328 1 93.47 ? N2 NAG 3105 A 1 HETATM 10 O O3 NAG . . . I 6 25.469 -6.355 90.903 1 87.35 ? O3 NAG 3105 A 1 HETATM 11 O O4 NAG . . . I 6 26.885 -8.837 90.479 1 90.23 ? O4 NAG 3105 A 1 HETATM 12 O O5 NAG . . . I 6 23.41 -9.782 89.999 1 90.49 ? O5 NAG 3105 A 1 HETATM 13 O O6 NAG . . . I 6 24.433 -12.269 89.963 1 75.77 ? O6 NAG 3105 A 1 HETATM 14 O O7 NAG . . . I 6 21.53 -5.556 90.887 1 93.11 ? O7 NAG 3105 A 1 HETATM 15 H H2 NAG . . . I 6 23.108 -7.314 91.061 1 108.11 ? H2 NAG 3105 A 1 HETATM 16 H H3 NAG . . . I 6 25.381 -7.275 89.074 1 106.88 ? H3 NAG 3105 A 1 HETATM 17 H H4 NAG . . . I 6 25.237 -8.787 91.696 1 107.46 ? H4 NAG 3105 A 1 HETATM 18 H H5 NAG . . . I 6 25.112 -9.882 88.871 1 105.75 ? H5 NAG 3105 A 1 HETATM 19 H H61 NAG . . . I 6 25.149 -11.211 91.594 1 96.99 ? H61 NAG 3105 A 1 HETATM 20 H H62 NAG . . . I 6 26.282 -11.437 90.263 1 96.99 ? H62 NAG 3105 A 1 HETATM 21 H H81 NAG . . . I 6 22.259 -3.189 89.826 1 111.01 ? H81 NAG 3105 A 1 HETATM 22 H H82 NAG . . . I 6 20.951 -3.897 88.847 1 111.01 ? H82 NAG 3105 A 1 HETATM 23 H H83 NAG . . . I 6 22.635 -3.978 88.275 1 111.01 ? H83 NAG 3105 A 1 HETATM 24 H HN2 NAG . . . I 6 23.402 -6.003 88.402 1 112.16 ? HN2 NAG 3105 A 1 HETATM 25 H HO3 NAG . . . I 6 24.707 -5.844 91.247 1 104.82 ? HO3 NAG 3105 A 1 HETATM 26 H HO4 NAG . . . I 6 27.223 -8.022 90.052 1 108.27 ? HO4 NAG 3105 A 1 HETATM 27 H HO6 NAG . . . I 6 23.791 -11.878 89.334 1 90.92 ? HO6 NAG 3105 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #