data_7RBN # _model_server_result.job_id KcQM4zM0VVPKOkzl9fGS3w _model_server_result.datetime_utc '2024-11-08 09:54:47' _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 7rbn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 7RBN # _exptl.entry_id 7RBN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 296.106 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol _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 108.38 _cell.angle_gamma 90 _cell.entry_id 7RBN _cell.length_a 55.526 _cell.length_b 81.711 _cell.length_c 56.068 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RBN _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 5 _struct_asym.id E _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 NZ LYS 72 A LYS 72 1_555 E C3' QPJ . A QPJ 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale2 E P2 QPJ . A QPJ 401 1_555 B O5' DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.494 ? metalc ? metalc1 A O LYS 60 A LYS 60 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc2 A O LEU 62 A LEU 62 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 D DG 1 1_555 D N3 DC 5 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 D DG 1 1_555 D O2 DC 5 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 D DG 1 1_555 D N4 DC 5 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 2 D DT 2 1_555 D N1 DA 4 T DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 2 D DT 2 1_555 D N6 DA 4 T DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 3 D DC 3 1_555 D N1 DG 3 T DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 3 D DC 3 1_555 D O6 DG 3 T DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 3 D DC 3 1_555 D N2 DG 3 T DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DG 4 D DG 4 1_555 D N3 DC 2 T DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N2 DG 4 D DG 4 1_555 D O2 DC 2 T DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O6 DG 4 D DG 4 1_555 D N4 DC 2 T DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DG 5 D DG 5 1_555 D N3 DC 1 T DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 DG 5 D DG 5 1_555 D O2 DC 1 T DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 DG 5 D DG 5 1_555 D N4 DC 1 T DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C N1 DG 1 P DG 1 1_555 D N3 DC 16 T DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N2 DG 1 P DG 1 1_555 D O2 DC 16 T DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C O6 DG 1 P DG 1 1_555 D N4 DC 16 T DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C N3 DC 2 P DC 2 1_555 D N1 DG 15 T DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N4 DC 2 P DC 2 1_555 D O6 DG 15 T DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C O2 DC 2 P DC 2 1_555 D N2 DG 15 T DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C N3 DT 3 P DT 3 1_555 D N1 DA 14 T DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C O4 DT 3 P DT 3 1_555 D N6 DA 14 T DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N1 DG 4 P DG 4 1_555 D N3 DC 13 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C N2 DG 4 P DG 4 1_555 D O2 DC 13 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C O6 DG 4 P DG 4 1_555 D N4 DC 13 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N1 DA 5 P DA 5 1_555 D N3 DT 12 T DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C N6 DA 5 P DA 5 1_555 D O4 DT 12 T DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C N3 DT 6 P DT 6 1_555 D N1 DA 11 T DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C O4 DT 6 P DT 6 1_555 D N6 DA 11 T DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C N1 DG 7 P DG 7 1_555 D N3 DC 10 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C N2 DG 7 P DG 7 1_555 D O2 DC 10 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C O6 DG 7 P DG 7 1_555 D N4 DC 10 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N3 DC 8 P DC 8 1_555 D N1 DG 9 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C N4 DC 8 P DC 8 1_555 D O6 DG 9 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C O2 DC 8 P DC 8 1_555 D N2 DG 9 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C N1 DG 9 P DG 9 1_555 D N3 DC 8 T DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C N2 DG 9 P DG 9 1_555 D O2 DC 8 T DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C O6 DG 9 P DG 9 1_555 D N4 DC 8 T DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C N3 DC 10 P DC 10 1_555 D N1 DG 7 T DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C N4 DC 10 P DC 10 1_555 D O6 DG 7 T DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C O2 DC 10 P DC 10 1_555 D N2 DG 7 T DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C5 H14 O10 P2' _chem_comp.formula_weight 296.106 _chem_comp.id QPJ _chem_comp.mon_nstd_flag . _chem_comp.name 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol _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 O22 P2 QPJ doub 426 n n O32 P2 QPJ sing 427 n n P2 OPP QPJ sing 428 n n OPP C1' QPJ sing 429 n n C3' C2' QPJ sing 430 n n C1' C2' QPJ sing 431 n n C1' C4' QPJ sing 432 n n C4' O4' QPJ sing 433 n n C4' C5' QPJ sing 434 n n C5' O5' QPJ sing 435 n n OP3 P QPJ doub 436 n n O5' P QPJ sing 437 n n P OP2 QPJ sing 438 n n P OP1 QPJ sing 439 n n C2' H1 QPJ sing 440 n n C2' H2 QPJ sing 441 n n C5' H3 QPJ sing 442 n n C5' H4 QPJ sing 443 n n C4' H5 QPJ sing 444 n n O4' H6 QPJ sing 445 n n C1' H7 QPJ sing 446 n n C3' H8 QPJ sing 447 n n C3' H9 QPJ sing 448 n n OP1 H11 QPJ sing 449 n n OP2 H12 QPJ sing 450 n n O32 H13 QPJ sing 451 n n C3' O2 QPJ sing 452 n n P2 O1 QPJ sing 453 n n O2 H10 QPJ sing 454 n n O1 H14 QPJ sing 455 n n # _atom_sites.entry_id 7RBN _atom_sites.fract_transf_matrix[1][1] 0.01801 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005985 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012238 _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] 0.018795 _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 E 5 QPJ A 1 401 401 QPJ DRP . F 6 MG A 1 402 1 MG MG . G 7 HOH A 1 501 3 HOH HOH . G 7 HOH A 2 502 12 HOH HOH . G 7 HOH A 3 503 9 HOH HOH . G 7 HOH A 4 504 4 HOH HOH . H 7 HOH P 1 101 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 P P QPJ . . . E 5 54.266 -1.21 43.249 1 124.11 ? P QPJ 401 A 1 HETATM 2 O O5' QPJ . . . E 5 52.683 -1.519 43.306 1 117.46 ? O5' QPJ 401 A 1 HETATM 3 C C2' QPJ . . . E 5 51.118 0.224 39.748 1 93.04 ? C2' QPJ 401 A 1 HETATM 4 C C5' QPJ . . . E 5 51.793 -0.925 42.362 1 108.13 ? C5' QPJ 401 A 1 HETATM 5 C C4' QPJ . . . E 5 51.512 -1.906 41.22 1 101.36 ? C4' QPJ 401 A 1 HETATM 6 O O4' QPJ . . . E 5 50.325 -2.638 41.554 1 101.46 ? O4' QPJ 401 A 1 HETATM 7 C C1' QPJ . . . E 5 51.364 -1.287 39.817 1 94.76 ? C1' QPJ 401 A 1 HETATM 8 C C3' QPJ . . . E 5 52.384 1.047 39.517 1 90.79 ? C3' QPJ 401 A 1 HETATM 9 O OP3 QPJ . . . E 5 54.363 0.29 43.402 1 123.75 ? OP3 QPJ 401 A 1 HETATM 10 O OP1 QPJ . . . E 5 54.84 -1.984 44.414 1 124.73 ? OP1 QPJ 401 A 1 HETATM 11 O OP2 QPJ . . . E 5 54.68 -1.727 41.892 1 123.31 ? OP2 QPJ 401 A 1 HETATM 12 O O32 QPJ . . . E 5 52.053 -3.851 37.6 1 85.09 ? O32 QPJ 401 A 1 HETATM 13 P P2 QPJ . . . E 5 50.412 -3.127 37.973 1 82.97 ? P2 QPJ 401 A 1 HETATM 14 O O22 QPJ . . . E 5 48.899 -3.721 37.128 1 86.84 ? O22 QPJ 401 A 1 HETATM 15 O OPP QPJ . . . E 5 50.245 -1.891 39.177 1 90.39 ? OPP QPJ 401 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #