data_7RBO # _model_server_result.job_id 25zWtgk7hbJNCOVo_VKI8w _model_server_result.datetime_utc '2024-11-27 20:00:50' _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 7rbo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 7RBO # _exptl.entry_id 7RBO _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 2.7.7.7,4.2.99.- # _cell.angle_alpha 90 _cell.angle_beta 109.08 _cell.angle_gamma 90 _cell.entry_id 7RBO _cell.length_a 55.416 _cell.length_b 81.772 _cell.length_c 55.736 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RBO _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale2 E P2 QPJ . A QPJ 401 1_555 B O5' DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? 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 7RBO _atom_sites.fract_transf_matrix[1][1] 0.018045 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006241 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012229 _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] 0.018985 _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 HOH A 1 501 30 HOH HOH . F 6 HOH A 2 502 27 HOH HOH . F 6 HOH A 3 503 7 HOH HOH . F 6 HOH A 4 504 5 HOH HOH . F 6 HOH A 5 505 13 HOH HOH . F 6 HOH A 6 506 1 HOH HOH . F 6 HOH A 7 507 26 HOH HOH . F 6 HOH A 8 508 4 HOH HOH . F 6 HOH A 9 509 28 HOH HOH . F 6 HOH A 10 510 18 HOH HOH . G 6 HOH T 1 101 24 HOH HOH . G 6 HOH T 2 102 2 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 54.217 -0.381 42.768 1 102.02 ? P QPJ 401 A 1 HETATM 2 O O5' QPJ . . . E 5 52.811 -0.812 42.108 1 95.34 ? O5' QPJ 401 A 1 HETATM 3 C C2' QPJ . . . E 5 51.252 0.231 39.797 1 79.3 ? C2' QPJ 401 A 1 HETATM 4 C C5' QPJ . . . E 5 52.644 -2.099 41.515 1 89.12 ? C5' QPJ 401 A 1 HETATM 5 C C4' QPJ . . . E 5 51.367 -2.191 40.676 1 84.9 ? C4' QPJ 401 A 1 HETATM 6 O O4' QPJ . . . E 5 50.239 -1.928 41.52 1 83.33 ? O4' QPJ 401 A 1 HETATM 7 C C1' QPJ . . . E 5 51.356 -1.26 39.453 1 80.9 ? C1' QPJ 401 A 1 HETATM 8 C C3' QPJ . . . E 5 52.576 0.988 39.681 1 77.64 ? C3' QPJ 401 A 1 HETATM 9 O OP3 QPJ . . . E 5 54.411 -1.356 43.908 1 102.23 ? OP3 QPJ 401 A 1 HETATM 10 O OP1 QPJ . . . E 5 55.215 -0.529 41.642 1 103.1 ? OP1 QPJ 401 A 1 HETATM 11 O OP2 QPJ . . . E 5 53.991 1.048 43.207 1 101.42 ? OP2 QPJ 401 A 1 HETATM 12 O O32 QPJ . . . E 5 51.529 -4.205 37.765 1 74.61 ? O32 QPJ 401 A 1 HETATM 13 P P2 QPJ . . . E 5 50.084 -3.086 37.791 1 70.95 ? P2 QPJ 401 A 1 HETATM 14 O O22 QPJ . . . E 5 48.519 -3.595 36.983 1 74.11 ? O22 QPJ 401 A 1 HETATM 15 O OPP QPJ . . . E 5 50.229 -1.572 38.629 1 76.75 ? OPP QPJ 401 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #