data_6AGG # _model_server_result.job_id QUo7LS76KnDeGHSREpKwFw _model_server_result.datetime_utc '2024-12-26 17:36:16' _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 6agg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 6AGG # _exptl.entry_id 6AGG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 130.191 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description AGMATINE _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 6AGG _cell.length_a 69.786 _cell.length_b 69.786 _cell.length_c 210.822 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6AGG _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 covale ? covale1 A C CYS 17 Z CYS 17 1_555 A N TPO 18 Z TPO 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C TPO 18 Z TPO 18 1_555 A N THR 19 Z THR 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? metalc ? metalc1 A OD2 ASP 8 Z ASP 8 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc2 A OD2 ASP 11 Z ASP 11 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc3 A O1P TPO 18 Z TPO 18 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc4 A O2P TPO 18 Z TPO 18 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc5 A O2P TPO 18 Z TPO 18 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc6 A O GLY 57 Z GLY 57 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc7 A SG CYS 352 Z CYS 352 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc8 A SG CYS 355 Z CYS 355 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc9 A SG CYS 370 Z CYS 370 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc10 A SG CYS 373 Z CYS 373 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc11 C O1A ACP . Z ACP 502 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc12 C O2A ACP . Z ACP 502 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? metalc ? metalc13 C O1B ACP . Z ACP 502 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc14 C O2A ACP . Z ACP 502 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? # _chem_comp.formula 'C5 H14 N4' _chem_comp.formula_weight 130.191 _chem_comp.id AG2 _chem_comp.mon_nstd_flag . _chem_comp.name AGMATINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (4-AMINOBUTYL)GUANIDINE # 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 N CA AG2 sing 58 n n N HN1 AG2 sing 59 n n N HN2 AG2 sing 60 n n CA CB AG2 sing 61 n n CA HA1 AG2 sing 62 n n CA HA2 AG2 sing 63 n n CB CG AG2 sing 64 n n CB HB1 AG2 sing 65 n n CB HB2 AG2 sing 66 n n CG CD AG2 sing 67 n n CG HG1 AG2 sing 68 n n CG HG2 AG2 sing 69 n n CD NE AG2 sing 70 n n CD HD1 AG2 sing 71 n n CD HD2 AG2 sing 72 n n NE CZ AG2 sing 73 n n NE HE1 AG2 sing 74 n n CZ NH1 AG2 doub 75 n n CZ NH2 AG2 sing 76 n n NH1 HH11 AG2 sing 77 n n NH2 HH21 AG2 sing 78 n n NH2 HH22 AG2 sing 79 n n # _atom_sites.entry_id 6AGG _atom_sites.fract_transf_matrix[1][1] 0.01433 _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] 0.01433 _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] 0.004743 _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 B 2 ZN Z 1 501 1 ZN ZN . C 3 ACP Z 1 502 1 ACP ACP . D 4 AG2 Z 1 503 1 AG2 AG2 . E 5 ACT Z 1 504 2 ACT ACT . F 5 ACT Z 1 505 3 ACT ACT . G 6 NH4 Z 1 506 1 NH4 NH4 . H 7 MG Z 1 507 1 MG MG . I 7 MG Z 1 508 2 MG MG . J 8 HOH Z 1 601 5 HOH HOH . J 8 HOH Z 2 602 7 HOH HOH . J 8 HOH Z 3 603 6 HOH HOH . J 8 HOH Z 4 604 1 HOH HOH . J 8 HOH Z 5 605 2 HOH HOH . J 8 HOH Z 6 606 8 HOH HOH . J 8 HOH Z 7 607 9 HOH HOH . J 8 HOH Z 8 608 10 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 N AG2 . . . D 4 28.842 11.477 45.99 1 76.36 ? N AG2 503 Z 1 HETATM 2 C CA AG2 . . . D 4 28.172 12.475 46.786 1 87.18 ? CA AG2 503 Z 1 HETATM 3 C CB AG2 . . . D 4 26.981 13.144 46.186 1 87.76 ? CB AG2 503 Z 1 HETATM 4 C CG AG2 . . . D 4 26.117 13.997 47.054 1 82.97 ? CG AG2 503 Z 1 HETATM 5 C CD AG2 . . . D 4 25.127 14.892 46.382 1 84.32 ? CD AG2 503 Z 1 HETATM 6 N NE AG2 . . . D 4 24.887 16.197 46.917 1 79.56 ? NE AG2 503 Z 1 HETATM 7 C CZ AG2 . . . D 4 23.921 17.062 46.299 1 80.75 ? CZ AG2 503 Z 1 HETATM 8 N NH1 AG2 . . . D 4 23.254 16.671 45.242 1 76.14 ? NH1 AG2 503 Z 1 HETATM 9 N NH2 AG2 . . . D 4 23.714 18.247 46.798 1 82.25 ? NH2 AG2 503 Z 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #