data_6LN5 # _model_server_result.job_id wEV_NzkP00XiENmXqHSuuw _model_server_result.datetime_utc '2024-11-27 05:45:33' _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 6ln5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2001}' # _entry.id 6LN5 # _exptl.entry_id 6LN5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 90 _cell.entry_id 6LN5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LN5 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # _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 # 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 903 A CYS 875 1_555 A SG CYS 915 A CYS 887 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc1 A O VAL 332 A VAL 304 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc2 A O ALA 333 A ALA 305 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? metalc ? metalc3 A O ILE 335 A ILE 307 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc4 A OE1 GLU 337 A GLU 309 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc5 A OE2 GLU 337 A GLU 309 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc6 A OD1 ASP 379 A ASP 351 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc7 A OD2 ASP 379 A ASP 351 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc8 A O THR 381 A THR 353 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc9 A OD1 ASP 730 A ASP 702 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc10 A OD1 ASN 795 A ASN 767 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc11 A OE2 GLU 798 A GLU 770 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc12 A OD1 ASN 823 A ASN 795 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc13 A OG1 THR 826 A THR 798 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc14 A OD2 ASP 827 A ASP 799 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc15 A OD1 ASP 827 A ASP 799 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc16 A OE2 GLU 935 A GLU 907 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc17 B O3G ACP . A ACP 2001 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 6LN5 _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 B 2 ACP A 1 2001 2001 ACP ACP . C 3 MG A 1 2002 3001 MG MG . D 4 CA A 1 2003 4001 CA CA . E 4 CA A 1 2004 4002 CA CA . # 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 PG ACP . . . B 2 95.647 112.24 143.383 1 36.21 ? PG ACP 2001 A 1 HETATM 2 O O1G ACP . . . B 2 96.743 111.249 143.095 1 36.21 ? O1G ACP 2001 A 1 HETATM 3 O O2G ACP . . . B 2 96.178 113.633 143.175 1 36.21 ? O2G ACP 2001 A 1 HETATM 4 O O3G ACP . . . B 2 94.488 112.007 142.448 1 36.21 ? O3G ACP 2001 A 1 HETATM 5 P PB ACP . . . B 2 93.459 112.839 145.427 1 36.21 ? PB ACP 2001 A 1 HETATM 6 O O1B ACP . . . B 2 92.422 111.775 145.673 1 36.21 ? O1B ACP 2001 A 1 HETATM 7 O O2B ACP . . . B 2 93.072 113.628 144.202 1 36.21 ? O2B ACP 2001 A 1 HETATM 8 C C3B ACP . . . B 2 95.117 112.049 145.156 1 36.21 ? C3B ACP 2001 A 1 HETATM 9 P PA ACP . . . B 2 93.62 115.486 146.582 1 36.21 ? PA ACP 2001 A 1 HETATM 10 O O1A ACP . . . B 2 94.881 115.857 145.851 1 36.21 ? O1A ACP 2001 A 1 HETATM 11 O O2A ACP . . . B 2 92.44 115.983 145.788 1 36.21 ? O2A ACP 2001 A 1 HETATM 12 O O3A ACP . . . B 2 93.523 113.85 146.72 1 36.21 ? O3A ACP 2001 A 1 HETATM 13 O O5' ACP . . . B 2 93.619 116.16 148.085 1 36.21 ? O5' ACP 2001 A 1 HETATM 14 C C5' ACP . . . B 2 94.619 115.785 148.987 1 36.21 ? C5' ACP 2001 A 1 HETATM 15 C C4' ACP . . . B 2 94.007 115.018 150.189 1 36.21 ? C4' ACP 2001 A 1 HETATM 16 O O4' ACP . . . B 2 92.787 115.415 150.408 1 36.21 ? O4' ACP 2001 A 1 HETATM 17 C C3' ACP . . . B 2 93.877 113.52 149.864 1 36.21 ? C3' ACP 2001 A 1 HETATM 18 O O3' ACP . . . B 2 94.972 112.856 150.304 1 36.21 ? O3' ACP 2001 A 1 HETATM 19 C C2' ACP . . . B 2 92.635 113.057 150.645 1 36.21 ? C2' ACP 2001 A 1 HETATM 20 O O2' ACP . . . B 2 93.06 112.372 151.902 1 36.21 ? O2' ACP 2001 A 1 HETATM 21 C C1' ACP . . . B 2 91.95 114.133 150.93 1 36.21 ? C1' ACP 2001 A 1 HETATM 22 N N9 ACP . . . B 2 90.678 114.09 150.261 1 36.21 ? N9 ACP 2001 A 1 HETATM 23 C C8 ACP . . . B 2 90.442 113.659 149.022 1 36.21 ? C8 ACP 2001 A 1 HETATM 24 N N7 ACP . . . B 2 89.136 113.787 148.784 1 36.21 ? N7 ACP 2001 A 1 HETATM 25 C C5 ACP . . . B 2 88.564 114.3 149.88 1 36.21 ? C5 ACP 2001 A 1 HETATM 26 C C6 ACP . . . B 2 87.261 114.628 150.175 1 36.21 ? C6 ACP 2001 A 1 HETATM 27 N N6 ACP . . . B 2 86.04 114.541 149.399 1 36.21 ? N6 ACP 2001 A 1 HETATM 28 N N1 ACP . . . B 2 86.96 115.129 151.359 1 36.21 ? N1 ACP 2001 A 1 HETATM 29 C C2 ACP . . . B 2 87.928 115.318 152.282 1 36.21 ? C2 ACP 2001 A 1 HETATM 30 N N3 ACP . . . B 2 89.204 114.994 151.994 1 36.21 ? N3 ACP 2001 A 1 HETATM 31 C C4 ACP . . . B 2 89.516 114.487 150.792 1 36.21 ? C4 ACP 2001 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 31 #