data_3L1R # _model_server_result.job_id xsy2Y8C7XSTeUw3ImBfotQ _model_server_result.datetime_utc '2024-11-18 17:54:50' _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 3l1r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":700}' # _entry.id 3L1R # _exptl.entry_id 3L1R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.246 _entity.id 5 _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 120 _cell.entry_id 3L1R _cell.length_a 137.676 _cell.length_b 137.676 _cell.length_c 189.148 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L1R _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 PISA monomeric 1 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,K 1 1 B,C,G,H,I,J,L 2 1 A,B,C,D,E,F,G,H,I,J,K,L 3 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 ? 5 F N N ? 5 H N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG B 600 NAG 2 n C NAG 2 C 2 NAG B 601 NAG # 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 457 A CYS 457 1_555 A SG CYS 463 A CYS 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf2 B SG CYS 457 B CYS 457 1_555 B SG CYS 463 B CYS 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? covale ? covale1 A ND2 ASN 77 A ASN 77 1_555 E C1 NAG . A NAG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 B ND2 ASN 77 B ASN 77 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? # _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 415 n n N1 HN11 SPD sing 416 n n N1 HN12 SPD sing 417 n n C2 C3 SPD sing 418 n n C2 H21 SPD sing 419 n n C2 H22 SPD sing 420 n n C3 C4 SPD sing 421 n n C3 H31 SPD sing 422 n n C3 H32 SPD sing 423 n n C4 C5 SPD sing 424 n n C4 H41 SPD sing 425 n n C4 H42 SPD sing 426 n n C5 N6 SPD sing 427 n n C5 H51 SPD sing 428 n n C5 H52 SPD sing 429 n n N6 C7 SPD sing 430 n n N6 HN6 SPD sing 431 n n C7 C8 SPD sing 432 n n C7 H71 SPD sing 433 n n C7 H72 SPD sing 434 n n C8 C9 SPD sing 435 n n C8 H81 SPD sing 436 n n C8 H82 SPD sing 437 n n C9 N10 SPD sing 438 n n C9 H91 SPD sing 439 n n C9 H92 SPD sing 440 n n N10 H101 SPD sing 441 n n N10 H102 SPD sing 442 n n # _atom_sites.entry_id 3L1R _atom_sites.fract_transf_matrix[1][1] 0.007263 _atom_sites.fract_transf_matrix[1][2] 0.004194 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008387 _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] 0.005287 _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 D 3 FAD A 1 500 500 FAD FAD . E 4 NAG A 1 600 600 NAG NAG . F 5 SPD A 1 700 700 SPD SPD . G 3 FAD B 1 500 500 FAD FAD . H 5 SPD B 1 700 700 SPD SPD . I 6 SO4 B 1 479 1 SO4 SO4 . J 7 CL B 1 480 2 CL CL . K 8 HOH A 1 479 1 HOH HOH . K 8 HOH A 2 480 3 HOH HOH . K 8 HOH A 3 481 5 HOH HOH . K 8 HOH A 4 482 7 HOH HOH . K 8 HOH A 5 483 8 HOH HOH . K 8 HOH A 6 484 11 HOH HOH . K 8 HOH A 7 485 12 HOH HOH . K 8 HOH A 8 486 13 HOH HOH . K 8 HOH A 9 487 14 HOH HOH . K 8 HOH A 10 488 17 HOH HOH . K 8 HOH A 11 489 18 HOH HOH . L 8 HOH B 1 481 2 HOH HOH . L 8 HOH B 2 482 4 HOH HOH . L 8 HOH B 3 483 6 HOH HOH . L 8 HOH B 4 484 9 HOH HOH . L 8 HOH B 5 485 10 HOH HOH . L 8 HOH B 6 486 15 HOH HOH . L 8 HOH B 7 487 16 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 . . . F 5 -80.141 34.519 2.454 1 43.14 ? N1 SPD 700 A 1 HETATM 2 C C2 SPD . . . F 5 -80.605 33.225 1.993 1 42.82 ? C2 SPD 700 A 1 HETATM 3 C C3 SPD . . . F 5 -79.72 32.127 2.577 1 41.77 ? C3 SPD 700 A 1 HETATM 4 C C4 SPD . . . F 5 -79.823 30.864 1.733 1 41.06 ? C4 SPD 700 A 1 HETATM 5 C C5 SPD . . . F 5 -78.71 30.818 0.69 1 40.38 ? C5 SPD 700 A 1 HETATM 6 N N6 SPD . . . F 5 -79.189 30.463 -0.635 1 39.1 ? N6 SPD 700 A 1 HETATM 7 C C7 SPD . . . F 5 -78.264 29.969 -1.638 1 37.43 ? C7 SPD 700 A 1 HETATM 8 C C8 SPD . . . F 5 -77.752 31.086 -2.536 1 35.93 ? C8 SPD 700 A 1 HETATM 9 C C9 SPD . . . F 5 -77.367 30.551 -3.904 1 34.66 ? C9 SPD 700 A 1 HETATM 10 N N10 SPD . . . F 5 -76.281 31.351 -4.427 1 33.26 ? N10 SPD 700 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 63 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 10 #