data_5YDH # _model_server_result.job_id QBhK_nCKWuZf6V2zHGxqdw _model_server_result.datetime_utc '2025-02-20 02:46:16' _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 5ydh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":813}' # _entry.id 5YDH # _exptl.entry_id 5YDH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 238.305 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID' _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 120 _cell.entry_id 5YDH _cell.length_a 148.659 _cell.length_b 148.659 _cell.length_c 226.021 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YDH _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,D,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,PA 1 1 A,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,OA 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_445 x-y-1,x-1,z+1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 -74.3295 -128.742471 37.670167 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 P N N ? 6 Q N N ? 6 LA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . 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 2 n C NAG 1 C 1 NAG A 812 NAG 2 n C NAG 2 C 2 NAG A 813 NAG 2 n C BMA 3 C 3 BMA A 814 BMA 2 n C MAN 4 C 4 MAN A 815 MAN 3 n D NAG 1 D 1 NAG B 818 NAG 3 n D NAG 2 D 2 NAG B 819 NAG 3 n D BMA 3 D 3 BMA B 820 BMA 3 n D MAN 4 D 4 MAN B 822 MAN 3 n D MAN 5 D 5 MAN B 821 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 67 A CYS 228 1_555 A SG CYS 94 A CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 253 A CYS 414 1_555 A SG CYS 266 A CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 401 A CYS 562 1_555 A SG CYS 522 A CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 B SG CYS 67 B CYS 228 1_555 B SG CYS 94 B CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 253 B CYS 414 1_555 B SG CYS 266 B CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 B SG CYS 401 B CYS 562 1_555 B SG CYS 522 B CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 59 A ASN 220 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 A ND2 ASN 509 A ASN 670 1_555 O C1 NAG . A NAG 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 B ND2 ASN 59 B ASN 220 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 B ND2 ASN 509 B ASN 670 1_555 KA C1 NAG . B NAG 817 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale9 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale10 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale11 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? metalc ? metalc1 A NE2 HIS 255 A HIS 416 1_555 T CO CO . A CO 816 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc2 B NE2 HIS 255 B HIS 416 1_555 NA CO CO . B CO 820 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? # _chem_comp.formula 'C8 H18 N2 O4 S' _chem_comp.formula_weight 238.305 _chem_comp.id EPE _chem_comp.mon_nstd_flag . _chem_comp.name '4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEPES # 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 N1 C2 EPE sing 107 n n N1 C6 EPE sing 108 n n N1 C9 EPE sing 109 n n C2 C3 EPE sing 110 n n C2 H21 EPE sing 111 n n C2 H22 EPE sing 112 n n C3 N4 EPE sing 113 n n C3 H31 EPE sing 114 n n C3 H32 EPE sing 115 n n N4 C5 EPE sing 116 n n N4 C7 EPE sing 117 n n C5 C6 EPE sing 118 n n C5 H51 EPE sing 119 n n C5 H52 EPE sing 120 n n C6 H61 EPE sing 121 n n C6 H62 EPE sing 122 n n C7 C8 EPE sing 123 n n C7 H71 EPE sing 124 n n C7 H72 EPE sing 125 n n C8 O8 EPE sing 126 n n C8 H81 EPE sing 127 n n C8 H82 EPE sing 128 n n O8 HO8 EPE sing 129 n n C9 C10 EPE sing 130 n n C9 H91 EPE sing 131 n n C9 H92 EPE sing 132 n n C10 S EPE sing 133 n n C10 H101 EPE sing 134 n n C10 H102 EPE sing 135 n n S O1S EPE doub 136 n n S O2S EPE doub 137 n n S O3S EPE sing 138 n n O3S HOS3 EPE sing 139 n n # _atom_sites.entry_id 5YDH _atom_sites.fract_transf_matrix[1][1] 0.006727 _atom_sites.fract_transf_matrix[1][2] 0.003884 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007767 _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] 0.004424 _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 4 SO4 A 1 801 801 SO4 SO4 . F 4 SO4 A 1 802 802 SO4 SO4 . G 4 SO4 A 1 803 803 SO4 SO4 . H 4 SO4 A 1 804 804 SO4 SO4 . I 4 SO4 A 1 805 805 SO4 SO4 . J 4 SO4 A 1 806 806 SO4 SO4 . K 4 SO4 A 1 807 807 SO4 SO4 . L 4 SO4 A 1 808 808 SO4 SO4 . M 4 SO4 A 1 809 809 SO4 SO4 . N 4 SO4 A 1 810 810 SO4 SO4 . O 5 NAG A 1 811 811 NAG NAG . P 6 EPE A 1 812 816 EPE EPE . Q 6 EPE A 1 813 817 EPE EPE . R 7 GOL A 1 814 818 GOL GOL . S 7 GOL A 1 815 819 GOL GOL . T 8 CO A 1 816 820 CO CO . U 4 SO4 B 1 801 801 SO4 SO4 . V 4 SO4 B 1 802 802 SO4 SO4 . W 4 SO4 B 1 803 803 SO4 SO4 . X 4 SO4 B 1 804 804 SO4 SO4 . Y 4 SO4 B 1 805 805 SO4 SO4 . Z 4 SO4 B 1 806 806 SO4 SO4 . AA 4 SO4 B 1 807 807 SO4 SO4 . BA 4 SO4 B 1 808 808 SO4 SO4 . CA 4 SO4 B 1 809 809 SO4 SO4 . DA 4 SO4 B 1 810 810 SO4 SO4 . EA 4 SO4 B 1 811 811 SO4 SO4 . FA 4 SO4 B 1 812 812 SO4 SO4 . GA 4 SO4 B 1 813 813 SO4 SO4 . HA 4 SO4 B 1 814 814 SO4 SO4 . IA 4 SO4 B 1 815 815 SO4 SO4 . JA 4 SO4 B 1 816 816 SO4 SO4 . KA 5 NAG B 1 817 817 NAG NAG . LA 6 EPE B 1 818 823 EPE EPE . MA 7 GOL B 1 819 824 GOL GOL . NA 8 CO B 1 820 825 CO CO . OA 9 HOH A 1 901 901 HOH HOH . OA 9 HOH A 2 902 903 HOH HOH . OA 9 HOH A 3 903 907 HOH HOH . OA 9 HOH A 4 904 904 HOH HOH . OA 9 HOH A 5 905 905 HOH HOH . OA 9 HOH A 6 906 906 HOH HOH . OA 9 HOH A 7 907 902 HOH HOH . PA 9 HOH B 1 901 901 HOH HOH . PA 9 HOH B 2 902 902 HOH HOH . PA 9 HOH B 3 903 903 HOH HOH . PA 9 HOH B 4 904 905 HOH HOH . PA 9 HOH B 5 905 904 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 N N1 EPE . . . Q 6 65.313 -62.674 9.528 1 148.16 ? N1 EPE 813 A 1 HETATM 2 C C2 EPE . . . Q 6 65.281 -64.128 9.713 1 147.47 ? C2 EPE 813 A 1 HETATM 3 C C3 EPE . . . Q 6 66.45 -64.725 8.927 1 146.51 ? C3 EPE 813 A 1 HETATM 4 N N4 EPE . . . Q 6 66.452 -64.095 7.606 1 146.8 ? N4 EPE 813 A 1 HETATM 5 C C5 EPE . . . Q 6 66.524 -62.639 7.459 1 146.79 ? C5 EPE 813 A 1 HETATM 6 C C6 EPE . . . Q 6 66.437 -62.024 8.857 1 146.82 ? C6 EPE 813 A 1 HETATM 7 C C7 EPE . . . Q 6 66.404 -64.936 6.412 1 143.42 ? C7 EPE 813 A 1 HETATM 8 C C8 EPE . . . Q 6 64.938 -65.084 6.005 1 139.49 ? C8 EPE 813 A 1 HETATM 9 O O8 EPE . . . Q 6 64.836 -65.1 4.576 1 133.42 ? O8 EPE 813 A 1 HETATM 10 C C9 EPE . . . Q 6 64.216 -61.852 10.035 1 147.93 ? C9 EPE 813 A 1 HETATM 11 C C10 EPE . . . Q 6 63.046 -62.006 9.061 1 146.73 ? C10 EPE 813 A 1 HETATM 12 S S EPE . . . Q 6 61.689 -61.176 9.56 1 145.85 ? S EPE 813 A 1 HETATM 13 O O1S EPE . . . Q 6 60.485 -61.945 9.174 1 145.37 ? O1S EPE 813 A 1 HETATM 14 O O2S EPE . . . Q 6 61.65 -59.851 8.898 1 145.72 ? O2S EPE 813 A 1 HETATM 15 O O3S EPE . . . Q 6 61.682 -60.989 11.029 1 144.06 ? O3S EPE 813 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 425 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #