data_3NL5 # _model_server_result.job_id JrgUMH8XoQqQ-4C_jxRWiQ _model_server_result.datetime_utc '2024-11-15 09:43:43' _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 3nl5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":799}' # _entry.id 3NL5 # _exptl.entry_id 3NL5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 117.6 _cell.angle_gamma 90 _cell.entry_id 3NL5 _cell.length_a 161.327 _cell.length_b 153.926 _cell.length_c 108.581 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NL5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,K,L _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' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 161.327 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N ? 3 K N 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 metalc ? metalc1 D MG MG . A MG 541 1_555 E O2G ACP . A ACP 799 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? metalc ? metalc2 D MG MG . A MG 541 1_555 E O2B ACP . A ACP 799 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc3 F MG MG . B MG 541 1_555 G O1B ACP . B ACP 899 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc4 J MG MG . C MG 541 1_555 K O2B ACP . C ACP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? # _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 3NL5 _atom_sites.fract_transf_matrix[1][1] 0.006199 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003241 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006497 _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] 0.010392 _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 2 MG A 1 541 1 MG MG . E 3 ACP A 1 799 799 ACP ACP . F 2 MG B 1 541 1 MG MG . G 3 ACP B 1 899 899 ACP ACP . H 4 TZE B 1 542 301 TZE TZE . I 4 TZE B 1 543 303 TZE TZE . J 2 MG C 1 541 1 MG MG . K 3 ACP C 1 999 999 ACP ACP . L 4 TZE C 1 542 302 TZE TZE . # 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 . . . E 3 39.837 22.904 -29.744 1 107.56 ? PG ACP 799 A 1 HETATM 2 O O1G ACP . . . E 3 41.089 22.085 -30.433 1 101.31 ? O1G ACP 799 A 1 HETATM 3 O O2G ACP . . . E 3 40.327 23.559 -28.314 1 99.09 ? O2G ACP 799 A 1 HETATM 4 O O3G ACP . . . E 3 38.73 21.982 -29.501 1 99.3 ? O3G ACP 799 A 1 HETATM 5 P PB ACP . . . E 3 39.114 25.996 -30.187 1 104.12 ? PB ACP 799 A 1 HETATM 6 O O1B ACP . . . E 3 39.989 27.046 -31.099 1 90.09 ? O1B ACP 799 A 1 HETATM 7 O O2B ACP . . . E 3 39.614 26.009 -28.818 1 99.46 ? O2B ACP 799 A 1 HETATM 8 C C3B ACP . . . E 3 39.273 24.268 -30.895 1 95.47 ? C3B ACP 799 A 1 HETATM 9 P PA ACP . . . E 3 36.936 27.417 -31.435 1 103.21 ? PA ACP 799 A 1 HETATM 10 O O1A ACP . . . E 3 35.36 27.803 -31.14 1 93.87 ? O1A ACP 799 A 1 HETATM 11 O O2A ACP . . . E 3 37.731 28.643 -31.513 1 85.99 ? O2A ACP 799 A 1 HETATM 12 O O3A ACP . . . E 3 37.512 26.457 -30.195 1 103.97 ? O3A ACP 799 A 1 HETATM 13 O O5' ACP . . . E 3 37.046 26.589 -32.881 1 88.16 ? O5' ACP 799 A 1 HETATM 14 C C5' ACP . . . E 3 37.964 27.018 -33.874 1 85.47 ? C5' ACP 799 A 1 HETATM 15 C C4' ACP . . . E 3 37.579 26.785 -35.347 1 84.43 ? C4' ACP 799 A 1 HETATM 16 O O4' ACP . . . E 3 36.174 26.391 -35.613 1 87.06 ? O4' ACP 799 A 1 HETATM 17 C C3' ACP . . . E 3 37.822 27.949 -36.304 1 81.74 ? C3' ACP 799 A 1 HETATM 18 O O3' ACP . . . E 3 38.367 27.624 -37.555 1 76.9 ? O3' ACP 799 A 1 HETATM 19 C C2' ACP . . . E 3 36.495 28.669 -36.316 1 85.07 ? C2' ACP 799 A 1 HETATM 20 O O2' ACP . . . E 3 36.29 29.584 -37.358 1 85.44 ? O2' ACP 799 A 1 HETATM 21 C C1' ACP . . . E 3 35.484 27.545 -36.198 1 83.04 ? C1' ACP 799 A 1 HETATM 22 N N9 ACP . . . E 3 34.348 27.963 -35.339 1 81.73 ? N9 ACP 799 A 1 HETATM 23 C C8 ACP . . . E 3 34.233 27.813 -33.993 1 85.79 ? C8 ACP 799 A 1 HETATM 24 N N7 ACP . . . E 3 32.978 28.359 -33.594 1 83.86 ? N7 ACP 799 A 1 HETATM 25 C C5 ACP . . . E 3 32.328 28.85 -34.75 1 87.24 ? C5 ACP 799 A 1 HETATM 26 C C6 ACP . . . E 3 31.085 29.48 -34.935 1 92.19 ? C6 ACP 799 A 1 HETATM 27 N N6 ACP . . . E 3 30.207 29.73 -33.791 1 92.77 ? N6 ACP 799 A 1 HETATM 28 N N1 ACP . . . E 3 30.7 29.856 -36.17 1 92.64 ? N1 ACP 799 A 1 HETATM 29 C C2 ACP . . . E 3 31.521 29.623 -37.246 1 91.46 ? C2 ACP 799 A 1 HETATM 30 N N3 ACP . . . E 3 32.754 28.998 -37.062 1 85.4 ? N3 ACP 799 A 1 HETATM 31 C C4 ACP . . . E 3 33.143 28.62 -35.823 1 82.75 ? C4 ACP 799 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 53 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #