data_6D5K # _model_server_result.job_id spdvFiVgJGByJCFlkNPEHg _model_server_result.datetime_utc '2024-11-22 21:29:48' _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 6d5k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":303}' # _entry.id 6D5K # _exptl.entry_id 6D5K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 238.305 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID' _entity.pdbx_number_of_molecules 1 _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 6D5K _cell.length_a 112.252 _cell.length_b 112.252 _cell.length_c 117.993 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D5K _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # 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 hexameric 6 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,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 2 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_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -78.662 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id N _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 metalc ? metalc1 D C5' 5AD . A 5AD 301 1_555 E CO B12 . A B12 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc2 F CO B12 . A B12 303 1_555 I C5' 5AD . B 5AD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc3 C OD1 ASN 160 C ASN 214 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc4 L O1A ATP . C ATP 301 1_555 M MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc5 L O3G ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc6 L O2B ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? metalc ? metalc7 L O2A ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc8 M MG MG . C MG 302 1_555 T O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc9 M MG MG . C MG 302 1_555 T O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc10 M MG MG . C MG 302 1_555 T O HOH . C HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc11 M MG MG . C MG 302 1_555 T O HOH . C HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc12 Q MG MG . C MG 306 1_555 T O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc13 Q MG MG . C MG 306 1_555 T O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? # _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 355 n n N1 C6 EPE sing 356 n n N1 C9 EPE sing 357 n n C2 C3 EPE sing 358 n n C2 H21 EPE sing 359 n n C2 H22 EPE sing 360 n n C3 N4 EPE sing 361 n n C3 H31 EPE sing 362 n n C3 H32 EPE sing 363 n n N4 C5 EPE sing 364 n n N4 C7 EPE sing 365 n n C5 C6 EPE sing 366 n n C5 H51 EPE sing 367 n n C5 H52 EPE sing 368 n n C6 H61 EPE sing 369 n n C6 H62 EPE sing 370 n n C7 C8 EPE sing 371 n n C7 H71 EPE sing 372 n n C7 H72 EPE sing 373 n n C8 O8 EPE sing 374 n n C8 H81 EPE sing 375 n n C8 H82 EPE sing 376 n n O8 HO8 EPE sing 377 n n C9 C10 EPE sing 378 n n C9 H91 EPE sing 379 n n C9 H92 EPE sing 380 n n C10 S EPE sing 381 n n C10 H101 EPE sing 382 n n C10 H102 EPE sing 383 n n S O1S EPE doub 384 n n S O2S EPE doub 385 n n S O3S EPE sing 386 n n O3S HOS3 EPE sing 387 n n # _atom_sites.entry_id 6D5K _atom_sites.fract_transf_matrix[1][1] 0.008909 _atom_sites.fract_transf_matrix[1][2] 0.005143 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010287 _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] 0.008475 _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 D 2 5AD A 1 301 1 5AD 5AD . E 3 B12 A 1 302 2 B12 B12 . F 3 B12 A 1 303 4 B12 B12 . G 4 SO4 A 1 304 3 SO4 SO4 . H 4 SO4 A 1 305 6 SO4 SO4 . I 2 5AD B 1 301 3 5AD 5AD . J 4 SO4 B 1 302 1 SO4 SO4 . K 4 SO4 B 1 303 5 SO4 SO4 . L 5 ATP C 1 301 1 ATP ATP . M 6 MG C 1 302 1 MG MG . N 7 EPE C 1 303 1 EPE EPE . O 4 SO4 C 1 304 2 SO4 SO4 . P 4 SO4 C 1 305 4 SO4 SO4 . Q 6 MG C 1 306 2 MG MG . R 8 HOH A 1 401 7 HOH HOH . R 8 HOH A 2 402 64 HOH HOH . R 8 HOH A 3 403 58 HOH HOH . R 8 HOH A 4 404 70 HOH HOH . S 8 HOH B 1 401 71 HOH HOH . S 8 HOH B 2 402 54 HOH HOH . S 8 HOH B 3 403 19 HOH HOH . S 8 HOH B 4 404 63 HOH HOH . S 8 HOH B 5 405 44 HOH HOH . S 8 HOH B 6 406 40 HOH HOH . T 8 HOH C 1 401 1 HOH HOH . T 8 HOH C 2 402 5 HOH HOH . T 8 HOH C 3 403 2 HOH HOH . T 8 HOH C 4 404 3 HOH HOH . T 8 HOH C 5 405 6 HOH HOH . T 8 HOH C 6 406 16 HOH HOH . T 8 HOH C 7 407 4 HOH HOH . T 8 HOH C 8 408 13 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 . . . N 7 -19.005 57.904 -15.191 1 132.51 ? N1 EPE 303 C 1 HETATM 2 C C2 EPE . . . N 7 -17.827 58.758 -14.948 1 126.48 ? C2 EPE 303 C 1 HETATM 3 C C3 EPE . . . N 7 -17.177 59.125 -16.279 1 124.75 ? C3 EPE 303 C 1 HETATM 4 N N4 EPE . . . N 7 -17.063 57.998 -17.193 1 114.97 ? N4 EPE 303 C 1 HETATM 5 C C5 EPE . . . N 7 -17.432 56.674 -16.739 1 116.09 ? C5 EPE 303 C 1 HETATM 6 C C6 EPE . . . N 7 -18.644 56.614 -15.814 1 122.49 ? C6 EPE 303 C 1 HETATM 7 C C7 EPE . . . N 7 -16.027 58.042 -18.2 1 106.97 ? C7 EPE 303 C 1 HETATM 8 C C8 EPE . . . N 7 -14.869 57.11 -17.858 1 106.24 ? C8 EPE 303 C 1 HETATM 9 O O8 EPE . . . N 7 -14.205 56.682 -19.027 1 113.22 ? O8 EPE 303 C 1 HETATM 10 C C9 EPE . . . N 7 -19.744 57.647 -13.933 1 133.1 ? C9 EPE 303 C 1 HETATM 11 C C10 EPE . . . N 7 -19.001 56.649 -13.038 1 140.24 ? C10 EPE 303 C 1 HETATM 12 S S EPE . . . N 7 -19.807 55.029 -12.812 1 151.09 ? S EPE 303 C 1 HETATM 13 O O1S EPE . . . N 7 -18.815 53.959 -12.915 1 129.79 ? O1S EPE 303 C 1 HETATM 14 O O2S EPE . . . N 7 -20.815 54.813 -13.839 1 137.73 ? O2S EPE 303 C 1 HETATM 15 O O3S EPE . . . N 7 -20.46 54.973 -11.502 1 136.11 ? O3S EPE 303 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #