data_6GOK # _model_server_result.job_id xh-xb9a8Yw0DN4NP8nXnRA _model_server_result.datetime_utc '2024-12-12 11:37:23' _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 6gok # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 6GOK # _exptl.entry_id 6GOK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 494.689 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N,N-pyridylbenzimidazole derivative-Pd complex' _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 90.61 _cell.angle_gamma 90 _cell.entry_id 6GOK _cell.length_a 100.282 _cell.length_b 32.805 _cell.length_c 72.661 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GOK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 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 ? 3 D N N ? 3 F 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 26 A CYS 26 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 40 A CYS 40 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 A SG CYS 58 A CYS 58 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 A SG CYS 65 A CYS 65 1_555 A SG CYS 72 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 B SG CYS 26 B CYS 26 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf6 B SG CYS 40 B CYS 40 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 58 B CYS 58 1_555 B SG CYS 110 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 B SG CYS 65 B CYS 65 1_555 B SG CYS 72 B CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc1 A NE2 HIS 105 A HIS 105 1_555 C PD PD . A PD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc2 A ND1 HIS 119 A HIS 119 1_555 D PD F6Q . A F6Q 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc3 C PD PD . A PD 201 1_555 G O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc4 C PD PD . A PD 201 1_555 G O HOH . A HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? metalc ? metalc5 D PD F6Q . A F6Q 202 1_555 G O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc6 B NE2 HIS 105 B HIS 105 1_555 E PD PD . B PD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc7 B ND1 HIS 119 B HIS 119 1_555 F PD F6Q . B F6Q 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? # _chem_comp.formula 'C15 H15 Cl2 N3 O3 Pd S 2' _chem_comp.formula_weight 494.689 _chem_comp.id F6Q _chem_comp.mon_nstd_flag . _chem_comp.name 'N,N-pyridylbenzimidazole derivative-Pd complex' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 OAU SAV F6Q doub 83 n n SAV OAS F6Q doub 84 n n SAV OAT F6Q sing 85 n n SAV CAP F6Q sing 86 n n CAP CAO F6Q sing 87 n n CAO CAN F6Q sing 88 n n CAN NAM F6Q sing 89 n n NAM CAB F6Q sing 90 n y NAM CAG F6Q sing 91 n y CAB CAC F6Q doub 92 n y CAB CAA F6Q sing 93 n y CAC CAD F6Q sing 94 n y CAD CAE F6Q doub 95 n y CAE CAF F6Q sing 96 n y CAF CAA F6Q doub 97 n y CAA NAL F6Q sing 98 n y NAL CAG F6Q doub 99 n y NAL PD F6Q sing 100 n n CAG CAH F6Q sing 101 n n CAH NAQ F6Q doub 102 n y CAH CAR F6Q sing 103 n y NAQ CAI F6Q sing 104 n y NAQ PD F6Q sing 105 n n CAI CAK F6Q doub 106 n y CAK CAJ F6Q sing 107 n y CAJ CAR F6Q doub 108 n y CL2 PD F6Q sing 109 n n CAP H1 F6Q sing 110 n n CAP H2 F6Q sing 111 n n CAO H3 F6Q sing 112 n n CAO H4 F6Q sing 113 n n CAN H5 F6Q sing 114 n n CAN H6 F6Q sing 115 n n CAC H7 F6Q sing 116 n n CAD H8 F6Q sing 117 n n CAE H9 F6Q sing 118 n n CAF H10 F6Q sing 119 n n CAI H11 F6Q sing 120 n n CAK H12 F6Q sing 121 n n CAJ H13 F6Q sing 122 n n CAR H14 F6Q sing 123 n n PD CL1 F6Q sing 124 n n OAT H16 F6Q sing 125 n n # _atom_sites.entry_id 6GOK _atom_sites.fract_transf_matrix[1][1] 0.009972 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000107 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.030483 _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] 0.013763 _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 C 2 PD A 1 201 1 PD PD . D 3 F6Q A 1 202 2 F6Q XXX . E 2 PD B 1 201 4 PD PD . F 3 F6Q B 1 202 3 F6Q XXX . G 4 HOH A 1 301 52 HOH HOH . G 4 HOH A 2 302 5 HOH HOH . G 4 HOH A 3 303 42 HOH HOH . G 4 HOH A 4 304 57 HOH HOH . G 4 HOH A 5 305 46 HOH HOH . G 4 HOH A 6 306 24 HOH HOH . G 4 HOH A 7 307 13 HOH HOH . G 4 HOH A 8 308 28 HOH HOH . G 4 HOH A 9 309 15 HOH HOH . G 4 HOH A 10 310 51 HOH HOH . G 4 HOH A 11 311 23 HOH HOH . G 4 HOH A 12 312 67 HOH HOH . G 4 HOH A 13 313 53 HOH HOH . G 4 HOH A 14 314 68 HOH HOH . G 4 HOH A 15 315 16 HOH HOH . G 4 HOH A 16 316 60 HOH HOH . G 4 HOH A 17 317 62 HOH HOH . G 4 HOH A 18 318 27 HOH HOH . G 4 HOH A 19 319 31 HOH HOH . G 4 HOH A 20 320 17 HOH HOH . G 4 HOH A 21 321 14 HOH HOH . G 4 HOH A 22 322 2 HOH HOH . G 4 HOH A 23 323 44 HOH HOH . G 4 HOH A 24 324 63 HOH HOH . G 4 HOH A 25 325 3 HOH HOH . G 4 HOH A 26 326 25 HOH HOH . G 4 HOH A 27 327 43 HOH HOH . G 4 HOH A 28 328 66 HOH HOH . H 4 HOH B 1 301 49 HOH HOH . H 4 HOH B 2 302 8 HOH HOH . H 4 HOH B 3 303 69 HOH HOH . H 4 HOH B 4 304 61 HOH HOH . H 4 HOH B 5 305 4 HOH HOH . H 4 HOH B 6 306 64 HOH HOH . H 4 HOH B 7 307 34 HOH HOH . H 4 HOH B 8 308 59 HOH HOH . H 4 HOH B 9 309 39 HOH HOH . H 4 HOH B 10 310 41 HOH HOH . H 4 HOH B 11 311 22 HOH HOH . H 4 HOH B 12 312 48 HOH HOH . H 4 HOH B 13 313 56 HOH HOH . H 4 HOH B 14 314 19 HOH HOH . H 4 HOH B 15 315 10 HOH HOH . H 4 HOH B 16 316 7 HOH HOH . H 4 HOH B 17 317 12 HOH HOH . H 4 HOH B 18 318 9 HOH HOH . H 4 HOH B 19 319 65 HOH HOH . H 4 HOH B 20 320 1 HOH HOH . H 4 HOH B 21 321 45 HOH HOH . H 4 HOH B 22 322 30 HOH HOH . H 4 HOH B 23 323 29 HOH HOH . H 4 HOH B 24 324 35 HOH HOH . H 4 HOH B 25 325 20 HOH HOH . H 4 HOH B 26 326 54 HOH HOH . H 4 HOH B 27 327 50 HOH HOH . H 4 HOH B 28 328 47 HOH HOH . H 4 HOH B 29 329 6 HOH HOH . H 4 HOH B 30 330 18 HOH HOH . H 4 HOH B 31 331 36 HOH HOH . H 4 HOH B 32 332 11 HOH HOH . H 4 HOH B 33 333 38 HOH HOH . H 4 HOH B 34 334 55 HOH HOH . H 4 HOH B 35 335 58 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 O OAU F6Q . . . D 3 9.794 -0.218 92.696 0.7 45.12 ? OAU F6Q 202 A 1 HETATM 2 S SAV F6Q . . . D 3 10.312 -1.29 93.655 0.7 46.74 ? SAV F6Q 202 A 1 HETATM 3 O OAS F6Q . . . D 3 9.147 -1.978 94.369 0.7 45.13 ? OAS F6Q 202 A 1 HETATM 4 O OAT F6Q . . . D 3 11.271 -0.663 94.656 0.7 52.36 ? OAT F6Q 202 A 1 HETATM 5 C CAP F6Q . . . D 3 11.284 -2.536 92.787 0.7 46.47 ? CAP F6Q 202 A 1 HETATM 6 C CAO F6Q . . . D 3 10.309 -2.802 91.687 0.7 42.51 ? CAO F6Q 202 A 1 HETATM 7 C CAN F6Q . . . D 3 10.059 -4.25 91.566 0.7 40.72 ? CAN F6Q 202 A 1 HETATM 8 N NAM F6Q . . . D 3 11.13 -5.328 91.668 0.7 40.01 ? NAM F6Q 202 A 1 HETATM 9 C CAB F6Q . . . D 3 11.608 -5.753 90.478 0.7 40.22 ? CAB F6Q 202 A 1 HETATM 10 C CAC F6Q . . . D 3 11.739 -5.11 89.287 0.7 40.96 ? CAC F6Q 202 A 1 HETATM 11 C CAD F6Q . . . D 3 12.387 -5.705 88.203 0.7 39.91 ? CAD F6Q 202 A 1 HETATM 12 C CAE F6Q . . . D 3 12.802 -7.02 88.347 0.7 38.21 ? CAE F6Q 202 A 1 HETATM 13 C CAF F6Q . . . D 3 12.527 -7.681 89.535 0.7 37.48 ? CAF F6Q 202 A 1 HETATM 14 C CAA F6Q . . . D 3 11.973 -7.046 90.584 0.7 37.88 ? CAA F6Q 202 A 1 HETATM 15 N NAL F6Q . . . D 3 11.728 -7.435 91.831 0.7 36.42 ? NAL F6Q 202 A 1 HETATM 16 C CAG F6Q . . . D 3 11.088 -6.433 92.455 0.7 38.64 ? CAG F6Q 202 A 1 HETATM 17 C CAH F6Q . . . D 3 10.681 -6.588 93.74 0.7 38.05 ? CAH F6Q 202 A 1 HETATM 18 N NAQ F6Q . . . D 3 10.896 -7.803 94.268 0.7 38.86 ? NAQ F6Q 202 A 1 HETATM 19 C CAI F6Q . . . D 3 10.524 -8.124 95.592 0.7 41.42 ? CAI F6Q 202 A 1 HETATM 20 C CAK F6Q . . . D 3 9.936 -7.154 96.406 0.7 39.52 ? CAK F6Q 202 A 1 HETATM 21 C CAJ F6Q . . . D 3 9.75 -5.878 95.902 0.7 37.85 ? CAJ F6Q 202 A 1 HETATM 22 C CAR F6Q . . . D 3 10.105 -5.614 94.581 0.7 38.49 ? CAR F6Q 202 A 1 HETATM 23 PD PD F6Q . . . D 3 11.807 -9.074 92.997 0.7 33.59 ? PD F6Q 202 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 373 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #