data_3NL6 # _model_server_result.job_id 9ztQI3YrNB4QTqmXZqphlw _model_server_result.datetime_utc '2024-11-15 09:39:10' _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 3nl6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":899}' # _entry.id 3NL6 # _exptl.entry_id 3NL6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _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 117.99 _cell.angle_gamma 90 _cell.entry_id 3NL6 _cell.length_a 163.173 _cell.length_b 153.528 _cell.length_c 109.618 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NL6 _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 -1 163.173 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 I N N ? 4 L 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 F O1B ACP . A ACP 799 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc2 G MG MG . B MG 541 1_555 I O2B ACP . B ACP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc3 G MG MG . B MG 541 1_555 I O2G ACP . B ACP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? metalc ? metalc4 J MG MG . C MG 541 1_555 L O1B ACP . C ACP 899 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.777 ? # _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 3NL6 _atom_sites.fract_transf_matrix[1][1] 0.006128 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003258 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006513 _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] 0.010331 _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 TPS A 1 2001 2001 TPS TPS . F 4 ACP A 1 799 799 ACP ACP . G 2 MG B 1 541 3 MG MG . H 3 TPS B 1 2006 2006 TPS TPS . I 4 ACP B 1 999 999 ACP ACP . J 2 MG C 1 541 2 MG MG . K 3 TPS C 1 2002 2002 TPS TPS . L 4 ACP C 1 899 899 ACP ACP . # 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 . . . L 4 52.603 5.956 -43.691 1 137.98 ? PG ACP 899 C 1 HETATM 2 O O1G ACP . . . L 4 54.073 6.694 -43.758 1 115.5 ? O1G ACP 899 C 1 HETATM 3 O O2G ACP . . . L 4 52.315 5.437 -42.155 1 174.03 ? O2G ACP 899 C 1 HETATM 4 O O3G ACP . . . L 4 51.565 6.906 -44.085 1 136.22 ? O3G ACP 899 C 1 HETATM 5 P PB ACP . . . L 4 54.184 4.05 -45.729 1 127.65 ? PB ACP 899 C 1 HETATM 6 O O1B ACP . . . L 4 55.195 3.3 -44.673 1 115.09 ? O1B ACP 899 C 1 HETATM 7 O O2B ACP . . . L 4 54.818 5.266 -46.227 1 102.35 ? O2B ACP 899 C 1 HETATM 8 C C3B ACP . . . L 4 52.584 4.492 -44.857 1 90.01 ? C3B ACP 899 C 1 HETATM 9 P PA ACP . . . L 4 53.206 3.654 -48.414 1 121.64 ? PA ACP 899 C 1 HETATM 10 O O1A ACP . . . L 4 54.021 3.048 -49.711 1 115.49 ? O1A ACP 899 C 1 HETATM 11 O O2A ACP . . . L 4 53.324 5.114 -48.402 1 128.28 ? O2A ACP 899 C 1 HETATM 12 O O3A ACP . . . L 4 53.861 3.032 -47.007 1 150.95 ? O3A ACP 899 C 1 HETATM 13 O O5' ACP . . . L 4 51.596 3.226 -48.517 1 80.04 ? O5' ACP 899 C 1 HETATM 14 C C5' ACP . . . L 4 51.203 1.883 -48.284 1 102.2 ? C5' ACP 899 C 1 HETATM 15 C C4' ACP . . . L 4 50.143 1.277 -49.224 1 87.48 ? C4' ACP 899 C 1 HETATM 16 O O4' ACP . . . L 4 49.227 2.23 -49.897 1 81.84 ? O4' ACP 899 C 1 HETATM 17 C C3' ACP . . . L 4 50.665 0.4 -50.358 1 94.18 ? C3' ACP 899 C 1 HETATM 18 O O3' ACP . . . L 4 51.292 -0.798 -49.982 1 108.33 ? O3' ACP 899 C 1 HETATM 19 C C2' ACP . . . L 4 49.472 0.275 -51.274 1 85.47 ? C2' ACP 899 C 1 HETATM 20 O O2' ACP . . . L 4 48.643 -0.838 -51.073 1 89.89 ? O2' ACP 899 C 1 HETATM 21 C C1' ACP . . . L 4 48.809 1.634 -51.169 1 91.73 ? C1' ACP 899 C 1 HETATM 22 N N9 ACP . . . L 4 49.218 2.495 -52.307 1 88.51 ? N9 ACP 899 C 1 HETATM 23 C C8 ACP . . . L 4 50.06 3.562 -52.273 1 92.11 ? C8 ACP 899 C 1 HETATM 24 N N7 ACP . . . L 4 50.163 4.086 -53.595 1 80.68 ? N7 ACP 899 C 1 HETATM 25 C C5 ACP . . . L 4 49.35 3.297 -54.442 1 95.24 ? C5 ACP 899 C 1 HETATM 26 C C6 ACP . . . L 4 49.082 3.363 -55.82 1 105.06 ? C6 ACP 899 C 1 HETATM 27 N N6 ACP . . . L 4 49.704 4.401 -56.643 1 96.88 ? N6 ACP 899 C 1 HETATM 28 N N1 ACP . . . L 4 48.249 2.467 -56.387 1 109.7 ? N1 ACP 899 C 1 HETATM 29 C C2 ACP . . . L 4 47.664 1.492 -55.618 1 108.02 ? C2 ACP 899 C 1 HETATM 30 N N3 ACP . . . L 4 47.93 1.426 -54.251 1 106.73 ? N3 ACP 899 C 1 HETATM 31 C C4 ACP . . . L 4 48.765 2.323 -53.679 1 92.35 ? C4 ACP 899 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #