data_6HIZ # _model_server_result.job_id lUcgH01i6Wqr2muy102FvQ _model_server_result.datetime_utc '2024-11-22 01:15:38' _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 6hiz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":401}' # _entry.id 6HIZ # _exptl.entry_id 6HIZ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 145.246 _entity.id 29 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _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 6HIZ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HIZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 28-meric _pdbx_struct_assembly.oligomeric_count 28 _pdbx_struct_assembly.details author_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,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 ? _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 ? 29 CA N N ? 29 IA 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 metalc ? metalc1 W OG SER 156 Cg SER 156 1_555 FA MG MG . Cg MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc2 EA O3G GTP . Cg GTP 501 1_555 FA MG MG . Cg MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc3 EA O2B GTP . Cg GTP 501 1_555 FA MG MG . Cg MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc4 FA MG MG . Cg MG 502 1_555 JA O HOH . Cg HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc5 FA MG MG . Cg MG 502 1_555 JA O HOH . Cg HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 FA MG MG . Cg MG 502 1_555 JA O HOH . Cg HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? hydrog 'U-A PAIR' hydrog1 Z O2 U 398 CA U 398 1_555 Z N6 A 534 CA A 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 Z N3 U 402 CA U 402 1_555 Z N1 A 526 CA A 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 Z O4 U 402 CA U 402 1_555 Z N6 A 526 CA A 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 Z N3 U 403 CA U 403 1_555 Z N1 A 525 CA A 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 Z O4 U 403 CA U 403 1_555 Z N6 A 525 CA A 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 Z N3 U 404 CA U 404 1_555 Z N1 A 524 CA A 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 Z O4 U 404 CA U 404 1_555 Z N6 A 524 CA A 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 Z N1 A 405 CA A 405 1_555 Z N3 U 523 CA U 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 Z N6 A 405 CA A 405 1_555 Z O4 U 523 CA U 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 Z N3 U 406 CA U 406 1_555 Z N1 A 522 CA A 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 Z O4 U 406 CA U 406 1_555 Z N6 A 522 CA A 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-U MISPAIR' hydrog12 Z O2 U 440 CA U 440 1_555 Z N3 U 479 CA U 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog13 Z N2 G 441 CA G 441 1_555 Z N3 A 447 CA A 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-C MISPAIR' hydrog14 Z O4 U 443 CA U 443 1_555 Z N4 C 446 CA C 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog15 Z N4 C 446 CA C 446 1_555 Z N3 A 478 CA A 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-U MISPAIR' hydrog16 Z O4 U 451 CA U 451 1_555 Z N3 U 474 CA U 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-U MISPAIR' hydrog17 Z N2 G 455 CA G 455 1_555 Z O2 U 465 CA U 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C7 H19 N3' _chem_comp.formula_weight 145.246 _chem_comp.id SPD _chem_comp.mon_nstd_flag . _chem_comp.name SPERMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) # 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 SPD sing 455 n n N1 HN11 SPD sing 456 n n N1 HN12 SPD sing 457 n n C2 C3 SPD sing 458 n n C2 H21 SPD sing 459 n n C2 H22 SPD sing 460 n n C3 C4 SPD sing 461 n n C3 H31 SPD sing 462 n n C3 H32 SPD sing 463 n n C4 C5 SPD sing 464 n n C4 H41 SPD sing 465 n n C4 H42 SPD sing 466 n n C5 N6 SPD sing 467 n n C5 H51 SPD sing 468 n n C5 H52 SPD sing 469 n n N6 C7 SPD sing 470 n n N6 HN6 SPD sing 471 n n C7 C8 SPD sing 472 n n C7 H71 SPD sing 473 n n C7 H72 SPD sing 474 n n C8 C9 SPD sing 475 n n C8 H81 SPD sing 476 n n C8 H82 SPD sing 477 n n C9 N10 SPD sing 478 n n C9 H91 SPD sing 479 n n C9 H92 SPD sing 480 n n N10 H101 SPD sing 481 n n N10 H102 SPD sing 482 n n # _atom_sites.entry_id 6HIZ _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 CA 29 SPD DL 1 401 101 SPD SPD . DA 30 UTP DJ 1 401 200 UTP UTP . EA 31 GTP Cg 1 501 501 GTP GTP . FA 32 MG Cg 1 502 502 MG MG . GA 32 MG CA 1 701 1 MG MG . HA 32 MG CA 1 702 2 MG MG . IA 29 SPD CA 1 703 100 SPD SPD . JA 33 HOH Cg 1 601 503 HOH HOH . JA 33 HOH Cg 2 602 504 HOH HOH . JA 33 HOH Cg 3 603 505 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 SPD . . . CA 29 243.458 195.063 215.501 1 59.22 0 N1 SPD 401 DL 1 HETATM 2 C C2 SPD . . . CA 29 243.865 194.165 216.595 1 67.79 0 C2 SPD 401 DL 1 HETATM 3 C C3 SPD . . . CA 29 245.153 194.646 217.268 1 74.4 0 C3 SPD 401 DL 1 HETATM 4 C C4 SPD . . . CA 29 245.813 193.502 218.028 1 56.7 0 C4 SPD 401 DL 1 HETATM 5 C C5 SPD . . . CA 29 246.819 192.834 217.065 1 61.36 0 C5 SPD 401 DL 1 HETATM 6 N N6 SPD . . . CA 29 247.495 191.693 217.693 1 51.75 0 N6 SPD 401 DL 1 HETATM 7 C C7 SPD . . . CA 29 247.659 190.704 216.611 1 65.88 0 C7 SPD 401 DL 1 HETATM 8 C C8 SPD . . . CA 29 248.653 189.623 217.027 1 71.03 0 C8 SPD 401 DL 1 HETATM 9 C C9 SPD . . . CA 29 248.875 188.687 215.841 1 57.07 0 C9 SPD 401 DL 1 HETATM 10 N N10 SPD . . . CA 29 250.051 187.85 216.116 1 56.17 0 N10 SPD 401 DL 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 499 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 10 #