data_5GJP # _model_server_result.job_id CdVOJ_FYNxku4ldv166EjQ _model_server_result.datetime_utc '2024-12-14 04:06:25' _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 5gjp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5GJP # _exptl.entry_id 5GJP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 102.178 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PENTANE-1,5-DIAMINE _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 120 _cell.entry_id 5GJP _cell.length_a 111.734 _cell.length_b 111.734 _cell.length_c 112.976 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GJP _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C5 H14 N2' _chem_comp.formula_weight 102.178 _chem_comp.id N2P _chem_comp.mon_nstd_flag . _chem_comp.name PENTANE-1,5-DIAMINE _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 C1 C2 N2P sing 250 n n C1 NE2 N2P sing 251 n n C1 H1C1 N2P sing 252 n n C1 H1C2 N2P sing 253 n n C2 C3 N2P sing 254 n n C2 H2C1 N2P sing 255 n n C2 H2C2 N2P sing 256 n n C3 C4 N2P sing 257 n n C3 H3C1 N2P sing 258 n n C3 H3C2 N2P sing 259 n n C4 C5 N2P sing 260 n n C4 H4C1 N2P sing 261 n n C4 H4C2 N2P sing 262 n n NE2 HE21 N2P sing 263 n n NE2 HE22 N2P sing 264 n n C5 N1 N2P sing 265 n n C5 H5C1 N2P sing 266 n n C5 H5C2 N2P sing 267 n n N1 H1N1 N2P sing 268 n n N1 H1N2 N2P sing 269 n n # _atom_sites.entry_id 5GJP _atom_sites.fract_transf_matrix[1][1] 0.00895 _atom_sites.fract_transf_matrix[1][2] 0.005167 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010334 _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] 0.008851 _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 N2P A 1 401 1 N2P LYS . C 3 PLP A 1 402 1 PLP PLP . D 4 GOL A 1 403 1 GOL GOL . E 4 GOL A 1 404 2 GOL GOL . F 5 PGE A 1 405 1 PGE PGE . G 6 NA A 1 406 1 NA NA . H 6 NA A 1 407 2 NA NA . I 7 MG A 1 408 1 MG MG . J 8 HOH A 1 501 41 HOH HOH . J 8 HOH A 2 502 1 HOH HOH . J 8 HOH A 3 503 40 HOH HOH . J 8 HOH A 4 504 3 HOH HOH . J 8 HOH A 5 505 23 HOH HOH . J 8 HOH A 6 506 7 HOH HOH . J 8 HOH A 7 507 20 HOH HOH . J 8 HOH A 8 508 12 HOH HOH . J 8 HOH A 9 509 19 HOH HOH . J 8 HOH A 10 510 8 HOH HOH . J 8 HOH A 11 511 36 HOH HOH . J 8 HOH A 12 512 11 HOH HOH . J 8 HOH A 13 513 6 HOH HOH . J 8 HOH A 14 514 16 HOH HOH . J 8 HOH A 15 515 2 HOH HOH . J 8 HOH A 16 516 4 HOH HOH . J 8 HOH A 17 517 26 HOH HOH . J 8 HOH A 18 518 10 HOH HOH . J 8 HOH A 19 519 21 HOH HOH . J 8 HOH A 20 520 15 HOH HOH . J 8 HOH A 21 521 18 HOH HOH . J 8 HOH A 22 522 37 HOH HOH . J 8 HOH A 23 523 27 HOH HOH . J 8 HOH A 24 524 43 HOH HOH . J 8 HOH A 25 525 25 HOH HOH . J 8 HOH A 26 526 38 HOH HOH . J 8 HOH A 27 527 42 HOH HOH . J 8 HOH A 28 528 32 HOH HOH . J 8 HOH A 29 529 24 HOH HOH . J 8 HOH A 30 530 44 HOH HOH . J 8 HOH A 31 531 33 HOH HOH . J 8 HOH A 32 532 9 HOH HOH . J 8 HOH A 33 533 29 HOH HOH . J 8 HOH A 34 534 35 HOH HOH . J 8 HOH A 35 535 30 HOH HOH . J 8 HOH A 36 536 34 HOH HOH . J 8 HOH A 37 537 5 HOH HOH . J 8 HOH A 38 538 39 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 C C1 N2P . . . B 2 -24.124 -24.491 1.049 1 57.83 ? C1 N2P 401 A 1 HETATM 2 C C2 N2P . . . B 2 -24.491 -23.11 1.652 1 61.86 ? C2 N2P 401 A 1 HETATM 3 C C3 N2P . . . B 2 -25.382 -22.207 0.799 1 56.99 ? C3 N2P 401 A 1 HETATM 4 C C4 N2P . . . B 2 -26.382 -21.385 1.597 1 61.78 ? C4 N2P 401 A 1 HETATM 5 N NE2 N2P . . . B 2 -23.54 -25.432 2.07 1 56.45 ? NE2 N2P 401 A 1 HETATM 6 C C5 N2P . . . B 2 -27.711 -21.216 0.855 1 67.92 ? C5 N2P 401 A 1 HETATM 7 N N1 N2P . . . B 2 -27.633 -20.811 -0.581 1 66.1 ? N1 N2P 401 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 7 #