data_4YJ3 # _model_server_result.job_id vppxJYnRbxbalLRUO5ajOw _model_server_result.datetime_utc '2025-01-11 14:42:13' _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 4yj3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":504}' # _entry.id 4YJ3 # _exptl.entry_id 4YJ3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 69.085 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description IMIDAZOLE _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 90 _cell.entry_id 4YJ3 _cell.length_a 105.2 _cell.length_b 157.69 _cell.length_c 181.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YJ3 _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,S,T,U,V,W,X,Y _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 # _struct_asym.details ? _struct_asym.entity_id 11 _struct_asym.id R _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 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc2 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.129 ? metalc ? metalc3 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc5 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc6 A OE1 GLU 71 A GLU 71 1_555 G MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc7 G MG MG . A MG 501 1_555 H O2G GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.886 ? metalc ? metalc8 G MG MG . A MG 501 1_555 H O1B GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc9 G MG MG . A MG 501 1_555 V O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc10 G MG MG . A MG 501 1_555 V O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc11 G MG MG . A MG 501 1_555 V O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc12 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc13 B OE2 GLU 111 B GLU 113 1_555 M CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc14 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc15 K MG MG . B MG 502 1_555 W O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc16 K MG MG . B MG 502 1_555 W O HOH . B HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc17 K MG MG . B MG 502 1_555 W O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc18 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc19 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc20 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc21 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc22 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc23 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc24 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc25 O MG MG . C MG 501 1_555 P O3A GTP . C GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc26 O MG MG . C MG 501 1_555 X O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc27 O MG MG . C MG 501 1_555 X O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc28 O MG MG . C MG 501 1_555 X O HOH . C HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc29 O MG MG . C MG 501 1_555 X O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc30 Q CA CA . C CA 503 1_555 X O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc31 D OE1 GLN 11 D GLN 11 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc32 S O1A GDP . D GDP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc33 T MG MG . D MG 502 1_555 Y O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc34 T MG MG . D MG 502 1_555 Y O HOH . D HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? # _chem_comp.formula 'C3 H5 N2 1' _chem_comp.formula_weight 69.085 _chem_comp.id IMD _chem_comp.mon_nstd_flag . _chem_comp.name IMIDAZOLE _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 N1 C2 IMD sing 315 n y N1 C5 IMD sing 316 n y N1 HN1 IMD sing 317 n n C2 N3 IMD doub 318 n y C2 H2 IMD sing 319 n n N3 C4 IMD sing 320 n y N3 HN3 IMD sing 321 n n C4 C5 IMD doub 322 n y C4 H4 IMD sing 323 n n C5 H5 IMD sing 324 n n # _atom_sites.entry_id 4YJ3 _atom_sites.fract_transf_matrix[1][1] 0.009506 _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] 0.006342 _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] 0.005497 _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 G 5 MG A 1 501 439 MG MG . H 6 GTP A 1 502 440 GTP GTP . I 7 CA A 1 503 441 CA CA . J 8 GDP B 1 501 439 GDP GDP . K 5 MG B 1 502 440 MG MG . L 9 4EE B 1 503 441 4EE LIG . M 7 CA B 1 504 442 CA CA . N 10 MES B 1 505 443 MES MES . O 5 MG C 1 501 441 MG MG . P 6 GTP C 1 502 442 GTP GTP . Q 7 CA C 1 503 443 CA CA . R 11 IMD C 1 504 444 IMD IMD . S 8 GDP D 1 501 442 GDP GDP . T 5 MG D 1 502 443 MG MG . U 9 4EE D 1 503 444 4EE LIG . V 12 HOH A 1 601 444 HOH HOH . V 12 HOH A 2 602 443 HOH HOH . V 12 HOH A 3 603 442 HOH HOH . W 12 HOH B 1 601 447 HOH HOH . W 12 HOH B 2 602 446 HOH HOH . W 12 HOH B 3 603 444 HOH HOH . W 12 HOH B 4 604 445 HOH HOH . X 12 HOH C 1 601 451 HOH HOH . X 12 HOH C 2 602 447 HOH HOH . X 12 HOH C 3 603 450 HOH HOH . X 12 HOH C 4 604 445 HOH HOH . X 12 HOH C 5 605 449 HOH HOH . X 12 HOH C 6 606 446 HOH HOH . X 12 HOH C 7 607 448 HOH HOH . Y 12 HOH D 1 601 446 HOH HOH . Y 12 HOH D 2 602 445 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 IMD . . . R 11 23.687 180.752 15.328 1 72.09 ? N1 IMD 504 C 1 HETATM 2 C C2 IMD . . . R 11 24.106 179.778 14.491 1 72.09 ? C2 IMD 504 C 1 HETATM 3 N N3 IMD . . . R 11 23.734 178.584 15.004 1 72.09 ? N3 IMD 504 C 1 HETATM 4 C C4 IMD . . . R 11 23.08 178.801 16.164 1 72.09 ? C4 IMD 504 C 1 HETATM 5 C C5 IMD . . . R 11 23.049 180.173 16.37 1 72.09 ? C5 IMD 504 C 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 359 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 5 #