data_6PH4 # _model_server_result.job_id QM7wsghk8W04-OVodJObTQ _model_server_result.datetime_utc '2025-02-20 15:12:09' _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 6ph4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":505}' # _entry.id 6PH4 # _exptl.entry_id 6PH4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 5 _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 6PH4 _cell.length_a 95.956 _cell.length_b 104.662 _cell.length_c 164.828 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PH4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 I _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 metalc ? metalc1 B OE1 GLU 371 B GLU 384 1_555 G MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc2 B OD1 ASN 375 B ASN 388 1_555 G MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc3 G MG MG . B MG 503 1_555 I O3G ACP . B ACP 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc4 G MG MG . B MG 503 1_555 I O2B ACP . B ACP 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc5 G MG MG . B MG 503 1_555 I O2A ACP . B ACP 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? # _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 6PH4 _atom_sites.fract_transf_matrix[1][1] 0.010421 _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] 0.009555 _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] 0.006067 _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 C 2 CL A 1 501 1 CL CL . D 3 FMN A 1 502 1 FMN FMN . E 2 CL B 1 501 2 CL CL . F 2 CL B 1 502 3 CL CL . G 4 MG B 1 503 1 MG MG . H 3 FMN B 1 504 1 FMN FMN . I 5 ACP B 1 505 1 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 . . . I 5 153.996 30.874 80.273 1 177.78 ? PG ACP 505 B 1 HETATM 2 O O1G ACP . . . I 5 153.834 30.721 78.786 1 175.94 ? O1G ACP 505 B 1 HETATM 3 O O2G ACP . . . I 5 154.027 29.528 80.916 1 178.6 ? O2G ACP 505 B 1 HETATM 4 O O3G ACP . . . I 5 152.84 31.677 80.829 1 182.96 ? O3G ACP 505 B 1 HETATM 5 P PB ACP . . . I 5 155.37 32.693 82.209 1 168.13 ? PB ACP 505 B 1 HETATM 6 O O1B ACP . . . I 5 156.733 33.119 82.761 1 171.53 ? O1B ACP 505 B 1 HETATM 7 O O2B ACP . . . I 5 154.708 31.828 83.182 1 167.12 ? O2B ACP 505 B 1 HETATM 8 C C3B ACP . . . I 5 155.601 31.776 80.65 1 173.56 ? C3B ACP 505 B 1 HETATM 9 P PA ACP . . . I 5 153.186 34.541 82.888 1 157.76 ? PA ACP 505 B 1 HETATM 10 O O1A ACP . . . I 5 152.171 35.286 82.036 1 176.29 ? O1A ACP 505 B 1 HETATM 11 O O2A ACP . . . I 5 152.502 33.386 83.582 1 163.24 ? O2A ACP 505 B 1 HETATM 12 O O3A ACP . . . I 5 154.451 33.99 81.906 1 170.53 ? O3A ACP 505 B 1 HETATM 13 O O5' ACP . . . I 5 153.835 35.591 84.066 1 165.44 ? O5' ACP 505 B 1 HETATM 14 C C5' ACP . . . I 5 155.145 36.121 83.827 1 168.14 ? C5' ACP 505 B 1 HETATM 15 C C4' ACP . . . I 5 155.788 36.453 85.143 1 169.67 ? C4' ACP 505 B 1 HETATM 16 O O4' ACP . . . I 5 154.871 36.851 86.003 1 171.4 ? O4' ACP 505 B 1 HETATM 17 C C3' ACP . . . I 5 156.412 35.17 85.784 1 163.88 ? C3' ACP 505 B 1 HETATM 18 O O3' ACP . . . I 5 157.676 34.981 85.375 1 169.53 ? O3' ACP 505 B 1 HETATM 19 C C2' ACP . . . I 5 156.365 35.501 87.281 1 159.64 ? C2' ACP 505 B 1 HETATM 20 O O2' ACP . . . I 5 157.502 36.35 87.627 1 160.99 ? O2' ACP 505 B 1 HETATM 21 C C1' ACP . . . I 5 155.228 36.188 87.44 1 161.96 ? C1' ACP 505 B 1 HETATM 22 N N9 ACP . . . I 5 154.178 35.336 87.855 1 162.79 ? N9 ACP 505 B 1 HETATM 23 C C8 ACP . . . I 5 153.402 34.595 87.044 1 165.7 ? C8 ACP 505 B 1 HETATM 24 N N7 ACP . . . I 5 152.512 33.915 87.808 1 159.81 ? N7 ACP 505 B 1 HETATM 25 C C5 ACP . . . I 5 152.739 34.243 89.097 1 159.07 ? C5 ACP 505 B 1 HETATM 26 C C6 ACP . . . I 5 152.135 33.852 90.266 1 154.77 ? C6 ACP 505 B 1 HETATM 27 N N6 ACP . . . I 5 150.997 32.902 90.464 1 156.63 ? N6 ACP 505 B 1 HETATM 28 N N1 ACP . . . I 5 152.565 34.34 91.437 1 148.63 ? N1 ACP 505 B 1 HETATM 29 C C2 ACP . . . I 5 153.586 35.213 91.467 1 150.21 ? C2 ACP 505 B 1 HETATM 30 N N3 ACP . . . I 5 154.19 35.604 90.302 1 155.85 ? N3 ACP 505 B 1 HETATM 31 C C4 ACP . . . I 5 153.765 35.12 89.129 1 159.78 ? C4 ACP 505 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 1014 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #