data_5KXI # _model_server_result.job_id eZsgzQXlBGM5Gw6OaUXJ_A _model_server_result.datetime_utc '2024-10-20 20:49:06' _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 5kxi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":402}' # _entry.id 5KXI # _exptl.entry_id 5KXI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 162.232 _entity.id 4 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE _entity.pdbx_number_of_molecules 2 _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 5KXI _cell.length_a 127.099 _cell.length_b 132.633 _cell.length_c 202.44 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KXI _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,Q,R _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 ? 4 G N N ? 4 L N 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 disulf ? disulf1 A SG CYS 135 A CYS 135 1_555 A SG CYS 149 A CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 199 A CYS 199 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 B SG CYS 130 B CYS 130 1_555 B SG CYS 144 B CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 C SG CYS 130 C CYS 130 1_555 C SG CYS 144 C CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 D SG CYS 135 D CYS 135 1_555 D SG CYS 149 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 D SG CYS 199 D CYS 199 1_555 D SG CYS 200 D CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf7 E SG CYS 130 E CYS 130 1_555 E SG CYS 144 E CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 148 A ASN 148 1_555 F C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 B ND2 ASN 143 B ASN 143 1_555 I C1 NAG . B NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 C ND2 ASN 143 C ASN 143 1_555 J C1 NAG . C NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 D ND2 ASN 148 D ASN 148 1_555 K C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 E ND2 ASN 143 E ASN 143 1_555 M C1 NAG . E NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 H NA NA . A NA 403 1_555 N O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc2 H NA NA . A NA 403 1_555 O O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc3 H NA NA . A NA 403 1_555 P O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc4 H NA NA . A NA 403 1_555 Q O HOH . D HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc5 H NA NA . A NA 403 1_555 R O HOH . E HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? # _chem_comp.formula 'C10 H14 N2' _chem_comp.formula_weight 162.232 _chem_comp.id NCT _chem_comp.mon_nstd_flag . _chem_comp.name (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(S)-(-)-NICOTINE;3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE' # 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 C1 NCT doub 267 n y N1 C5 NCT sing 268 n y C1 C2 NCT sing 269 n y C1 HC1 NCT sing 270 n n C2 C3 NCT doub 271 n y C2 C6 NCT sing 272 n n C3 C4 NCT sing 273 n y C3 HC3 NCT sing 274 n n C4 C5 NCT doub 275 n y C4 HC4 NCT sing 276 n n C5 HC5 NCT sing 277 n n N2 C6 NCT sing 278 n n N2 C9 NCT sing 279 n n N2 C10 NCT sing 280 n n C6 C7 NCT sing 281 n n C6 HC6 NCT sing 282 n n C7 C8 NCT sing 283 n n C7 HC71 NCT sing 284 n n C7 HC72 NCT sing 285 n n C8 C9 NCT sing 286 n n C8 HC81 NCT sing 287 n n C8 HC82 NCT sing 288 n n C9 HC91 NCT sing 289 n n C9 HC92 NCT sing 290 n n C10 H101 NCT sing 291 n n C10 H102 NCT sing 292 n n C10 H103 NCT sing 293 n n # _atom_sites.entry_id 5KXI _atom_sites.fract_transf_matrix[1][1] 0.007868 _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] 0.00754 _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] 0.00494 _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 3 NAG A 1 401 500 NAG NAG . G 4 NCT A 1 402 600 NCT NCT . H 5 NA A 1 403 1 NA NA . I 3 NAG B 1 500 500 NAG NAG . J 3 NAG C 1 500 500 NAG NAG . K 3 NAG D 1 401 500 NAG NAG . L 4 NCT D 1 402 600 NCT NCT . M 3 NAG E 1 500 500 NAG NAG . N 6 HOH A 1 501 2 HOH HOH . O 6 HOH B 1 601 3 HOH HOH . P 6 HOH C 1 601 4 HOH HOH . Q 6 HOH D 1 501 5 HOH HOH . R 6 HOH E 1 601 1 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 NCT . . . G 4 69.35 -25.734 -42.445 1 144.12 ? N1 NCT 402 A 1 HETATM 2 C C1 NCT . . . G 4 68.456 -26.235 -41.557 1 144.12 ? C1 NCT 402 A 1 HETATM 3 C C2 NCT . . . G 4 68.318 -27.612 -41.294 1 144.12 ? C2 NCT 402 A 1 HETATM 4 C C3 NCT . . . G 4 69.144 -28.479 -42.004 1 144.12 ? C3 NCT 402 A 1 HETATM 5 C C4 NCT . . . G 4 70.067 -27.989 -42.929 1 144.12 ? C4 NCT 402 A 1 HETATM 6 C C5 NCT . . . G 4 70.138 -26.605 -43.122 1 144.12 ? C5 NCT 402 A 1 HETATM 7 N N2 NCT . . . G 4 67.367 -27.202 -39.076 1 144.12 ? N2 NCT 402 A 1 HETATM 8 C C6 NCT . . . G 4 67.324 -28.11 -40.292 1 144.12 ? C6 NCT 402 A 1 HETATM 9 C C7 NCT . . . G 4 65.877 -28.032 -40.655 1 144.12 ? C7 NCT 402 A 1 HETATM 10 C C8 NCT . . . G 4 65.107 -27.914 -39.37 1 144.12 ? C8 NCT 402 A 1 HETATM 11 C C9 NCT . . . G 4 66 -27.095 -38.49 1 144.12 ? C9 NCT 402 A 1 HETATM 12 C C10 NCT . . . G 4 68.151 -28.017 -38.156 1 144.12 ? C10 NCT 402 A 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 12 #