data_4RET # _model_server_result.job_id IjkBItAFy-NWkHCmrMv3rA _model_server_result.datetime_utc '2024-11-27 18:57:38' _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 4ret # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":1003}' # _entry.id 4RET # _exptl.entry_id 4RET _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 10 _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 4RET _cell.length_a 118.24 _cell.length_b 118.35 _cell.length_c 494.09 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RET _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,I,J,K,L,M,N,O,P,Q,R,S,CA 1 1 D,E,F,T,U,V,W,X,Y,Z,AA,BA,DA 2 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 ? 10 Q N N ? 10 Z N N ? 10 AA N N ? 10 BA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 ? 5 1 2 GLC FRU C1 O1 . O2 HO2 . 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 G NAG 1 F 1 NAG B 1001 NAG 4 n G NAG 2 F 2 NAG B 1002 NAG 5 n H GLC 1 H 1 GLC A 1106 SUC 5 n H FRU 2 H 2 FRU A 1106 SUC 5 n I GLC 1 I 1 GLC A 1107 SUC 5 n I FRU 2 I 2 FRU A 1107 SUC # 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 B SG CYS 126 B CYS 126 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 159 B CYS 159 1_555 B SG CYS 175 B CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 213 B CYS 213 1_555 B SG CYS 276 B CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 E SG CYS 126 D CYS 126 1_555 E SG CYS 149 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 E SG CYS 159 D CYS 159 1_555 E SG CYS 175 D CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf6 E SG CYS 213 D CYS 213 1_555 E SG CYS 276 D CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A C SER 373 A SER 368 1_555 A N PHD 374 A PHD 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C PHD 374 A PHD 369 1_555 A N LYS 375 A LYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 B ND2 ASN 158 B ASN 158 1_555 G C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 B ND2 ASN 265 B ASN 265 1_555 Q C1 NAG . B NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 D C SER 373 C SER 368 1_555 D N PHD 374 C PHD 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 D C PHD 374 C PHD 369 1_555 D N LYS 375 C LYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 E ND2 ASN 158 D ASN 158 1_555 Z C1 NAG . D NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale8 E ND2 ASN 193 D ASN 193 1_555 AA C1 NAG . D NAG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 E ND2 ASN 265 D ASN 265 1_555 BA C1 NAG . D NAG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale10 G O4 NAG . F NAG 1 1_555 G C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale11 H C1 GLC . H GLC 1 1_555 H O2 FRU . H FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 sing covale ? covale12 I C1 GLC . I GLC 1 1_555 I O2 FRU . I FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 sing metalc ? metalc1 A OD2 PHD 374 A PHD 369 1_555 J MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc2 A OP3 PHD 374 A PHD 369 1_555 J MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc3 A OP1 PHD 374 A PHD 369 1_555 J MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc4 A O THR 376 A THR 371 1_555 J MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc5 A OG1 THR 376 A THR 371 1_555 J MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc6 A OD2 ASP 715 A ASP 710 1_555 J MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc7 A OD1 ASP 715 A ASP 710 1_555 J MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc8 A OD2 ASP 745 A ASP 740 1_555 K MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc9 A OD1 ASP 745 A ASP 740 1_555 K MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc10 A OD1 ASN 781 A ASN 776 1_555 L MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc11 A OE2 GLU 784 A GLU 779 1_555 L MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc12 A OD1 ASP 809 A ASP 804 1_555 L MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc13 A OD2 ASP 809 A ASP 804 1_555 L MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc14 L MG MG . A MG 1103 1_555 CA O HOH . A HOH 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc15 L MG MG . A MG 1103 1_555 CA O HOH . A HOH 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc16 L MG MG . A MG 1103 1_555 CA O HOH . A HOH 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc17 D OD2 PHD 374 C PHD 369 1_555 T MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc18 D OP3 PHD 374 C PHD 369 1_555 T MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc19 D OP1 PHD 374 C PHD 369 1_555 T MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc20 D O THR 376 C THR 371 1_555 T MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc21 D OG1 THR 376 C THR 371 1_555 T MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc22 D OD2 ASP 715 C ASP 710 1_555 T MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc23 D OD1 ASP 715 C ASP 710 1_555 T MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc24 D OD2 ASP 745 C ASP 740 1_555 U MG MG . C MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc25 D OD1 ASP 745 C ASP 740 1_555 U MG MG . C MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc26 D OD1 ASN 781 C ASN 776 1_555 V MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc27 D OE2 GLU 784 C GLU 779 1_555 V MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc28 D OD2 ASP 809 C ASP 804 1_555 V MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc29 D OD1 ASP 809 C ASP 804 1_555 V MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc30 V MG MG . C MG 2003 1_555 DA O HOH . C HOH 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc31 V MG MG . C MG 2003 1_555 DA O HOH . C HOH 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc32 V MG MG . C MG 2003 1_555 DA O HOH . C HOH 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? # _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 619 n n C1 O1 NAG sing 620 n n C1 O5 NAG sing 621 n n C1 H1 NAG sing 622 n n C2 C3 NAG sing 623 n n C2 N2 NAG sing 624 n n C2 H2 NAG sing 625 n n C3 C4 NAG sing 626 n n C3 O3 NAG sing 627 n n C3 H3 NAG sing 628 n n C4 C5 NAG sing 629 n n C4 O4 NAG sing 630 n n C4 H4 NAG sing 631 n n C5 C6 NAG sing 632 n n C5 O5 NAG sing 633 n n C5 H5 NAG sing 634 n n C6 O6 NAG sing 635 n n C6 H61 NAG sing 636 n n C6 H62 NAG sing 637 n n C7 C8 NAG sing 638 n n C7 N2 NAG sing 639 n n C7 O7 NAG doub 640 n n C8 H81 NAG sing 641 n n C8 H82 NAG sing 642 n n C8 H83 NAG sing 643 n n N2 HN2 NAG sing 644 n n O1 HO1 NAG sing 645 n n O3 HO3 NAG sing 646 n n O4 HO4 NAG sing 647 n n O6 HO6 NAG sing 648 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 4RET _atom_sites.fract_transf_matrix[1][1] 0.008457 _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] 0.00845 _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] 0.002024 _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 J 6 MG A 1 1101 1101 MG MG . K 6 MG A 1 1102 1102 MG MG . L 6 MG A 1 1103 1103 MG MG . M 7 CLR A 1 1104 1105 CLR CLR . N 8 DGX A 1 1107 1104 DGX DGX . O 9 17F A 1 1108 1108 17F 17F . P 9 17F A 1 1109 1109 17F 17F . Q 10 NAG B 1 1003 1004 NAG NAG . R 9 17F B 1 1004 1005 17F 17F . S 7 CLR G 1 1001 1001 CLR CLR . T 6 MG C 1 2001 2001 MG MG . U 6 MG C 1 2002 2002 MG MG . V 6 MG C 1 2003 2003 MG MG . W 7 CLR C 1 2004 2005 CLR CLR . X 8 DGX C 1 2005 2004 DGX DGX . Y 7 CLR C 1 2006 2001 CLR CLR . Z 10 NAG D 1 2001 2001 NAG NAG . AA 10 NAG D 1 2002 2002 NAG NAG . BA 10 NAG D 1 2003 2003 NAG NAG . CA 11 HOH A 1 1201 1201 HOH HOH . CA 11 HOH A 2 1202 1202 HOH HOH . CA 11 HOH A 3 1203 1203 HOH HOH . DA 11 HOH C 1 2101 2101 HOH HOH . DA 11 HOH C 2 2102 2102 HOH HOH . DA 11 HOH C 3 2103 2103 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 . . . Q 10 -12.821 -17.686 118.809 1 217.57 ? C1 NAG 1003 B 1 HETATM 2 C C2 NAG . . . Q 10 -12.267 -18.434 120.033 1 222.03 ? C2 NAG 1003 B 1 HETATM 3 C C3 NAG . . . Q 10 -11.198 -17.589 120.728 1 225.17 ? C3 NAG 1003 B 1 HETATM 4 C C4 NAG . . . Q 10 -10.133 -17.155 119.731 1 221.96 ? C4 NAG 1003 B 1 HETATM 5 C C5 NAG . . . Q 10 -10.792 -16.44 118.557 1 217.66 ? C5 NAG 1003 B 1 HETATM 6 C C6 NAG . . . Q 10 -9.812 -16.031 117.484 1 214.4 ? C6 NAG 1003 B 1 HETATM 7 C C7 NAG . . . Q 10 -13.415 -19.948 121.607 1 227.4 ? C7 NAG 1003 B 1 HETATM 8 C C8 NAG . . . Q 10 -12.344 -20.951 121.296 1 226.41 ? C8 NAG 1003 B 1 HETATM 9 N N2 NAG . . . Q 10 -13.33 -18.773 120.97 1 225.2 ? N2 NAG 1003 B 1 HETATM 10 O O3 NAG . . . Q 10 -10.604 -18.336 121.782 1 229.24 ? O3 NAG 1003 B 1 HETATM 11 O O4 NAG . . . Q 10 -9.197 -16.283 120.356 1 224.9 ? O4 NAG 1003 B 1 HETATM 12 O O5 NAG . . . Q 10 -11.742 -17.319 117.94 1 214.9 ? O5 NAG 1003 B 1 HETATM 13 O O6 NAG . . . Q 10 -10.096 -16.68 116.252 1 209.92 ? O6 NAG 1003 B 1 HETATM 14 O O7 NAG . . . Q 10 -14.323 -20.192 122.397 1 230.26 ? O7 NAG 1003 B 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #