data_6CPF # _model_server_result.job_id rkcGjNDRBpqs1KZzcJBRww _model_server_result.datetime_utc '2024-11-24 21:33:34' _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 6cpf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6CPF # _exptl.entry_id 6CPF _exptl.method 'X-RAY DIFFRACTION' # _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 120 _cell.entry_id 6CPF _cell.length_a 81.75 _cell.length_b 81.75 _cell.length_c 172.871 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6CPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 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 metalc ? metalc1 A OD1 ASN 143 A ASN 261 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc2 A OD2 ASP 156 A ASP 274 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc3 B O1B ACP . A ACP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc4 B O1A ACP . A ACP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? # _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 6CPF _atom_sites.fract_transf_matrix[1][1] 0.012232 _atom_sites.fract_transf_matrix[1][2] 0.007062 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014125 _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] 0.005785 _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 1 501 1 ACP ACP . C 3 MG A 1 502 2 MG MG . D 4 HOH A 1 601 5 HOH HOH . D 4 HOH A 2 602 4 HOH HOH . D 4 HOH A 3 603 1 HOH HOH . D 4 HOH A 4 604 2 HOH HOH . D 4 HOH A 5 605 6 HOH HOH . D 4 HOH A 6 606 3 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 PG ACP . . . B 2 24.145 1.309 61.171 1 112.86 ? PG ACP 501 A 1 HETATM 2 O O1G ACP . . . B 2 23.726 1.169 59.736 1 102.82 ? O1G ACP 501 A 1 HETATM 3 O O2G ACP . . . B 2 22.914 1.539 62.058 1 92.48 ? O2G ACP 501 A 1 HETATM 4 O O3G ACP . . . B 2 24.869 0.034 61.606 1 109.12 ? O3G ACP 501 A 1 HETATM 5 P PB ACP . . . B 2 26.428 2.523 62.746 1 84.01 ? PB ACP 501 A 1 HETATM 6 O O1B ACP . . . B 2 27.8 2.29 62.203 1 84.59 ? O1B ACP 501 A 1 HETATM 7 O O2B ACP . . . B 2 26.007 1.355 63.561 1 96.75 ? O2B ACP 501 A 1 HETATM 8 C C3B ACP . . . B 2 25.266 2.759 61.321 1 97.78 ? C3B ACP 501 A 1 HETATM 9 P PA ACP . . . B 2 27.633 4.942 63.902 1 80.57 ? PA ACP 501 A 1 HETATM 10 O O1A ACP . . . B 2 28.877 4.431 63.29 1 81.37 ? O1A ACP 501 A 1 HETATM 11 O O2A ACP . . . B 2 27.851 5.172 65.349 1 83.34 ? O2A ACP 501 A 1 HETATM 12 O O3A ACP . . . B 2 26.4 3.885 63.703 1 96.72 ? O3A ACP 501 A 1 HETATM 13 O O5' ACP . . . B 2 27.188 6.366 63.148 1 77.42 ? O5' ACP 501 A 1 HETATM 14 C C5' ACP . . . B 2 27.176 6.406 61.732 1 77.1 ? C5' ACP 501 A 1 HETATM 15 C C4' ACP . . . B 2 27.858 7.708 61.251 1 76.9 ? C4' ACP 501 A 1 HETATM 16 O O4' ACP . . . B 2 27.292 8.743 61.794 1 74.08 ? O4' ACP 501 A 1 HETATM 17 C C3' ACP . . . B 2 29.345 7.762 61.723 1 73.63 ? C3' ACP 501 A 1 HETATM 18 O O3' ACP . . . B 2 30.176 7.2 60.81 1 61.18 ? O3' ACP 501 A 1 HETATM 19 C C2' ACP . . . B 2 29.589 9.256 61.855 1 71.36 ? C2' ACP 501 A 1 HETATM 20 O O2' ACP . . . B 2 29.877 9.873 60.501 1 70.57 ? O2' ACP 501 A 1 HETATM 21 C C1' ACP . . . B 2 28.452 9.746 62.314 1 67.19 ? C1' ACP 501 A 1 HETATM 22 N N9 ACP . . . B 2 28.443 9.807 63.769 1 66.95 ? N9 ACP 501 A 1 HETATM 23 C C8 ACP . . . B 2 28.053 8.829 64.622 1 69.25 ? C8 ACP 501 A 1 HETATM 24 N N7 ACP . . . B 2 28.194 9.289 65.883 1 66.36 ? N7 ACP 501 A 1 HETATM 25 C C5 ACP . . . B 2 28.665 10.539 65.814 1 58.33 ? C5 ACP 501 A 1 HETATM 26 C C6 ACP . . . B 2 28.985 11.452 66.795 1 52.67 ? C6 ACP 501 A 1 HETATM 27 N N6 ACP . . . B 2 28.951 11.452 68.312 1 54.05 ? N6 ACP 501 A 1 HETATM 28 N N1 ACP . . . B 2 29.447 12.662 66.471 1 49.71 ? N1 ACP 501 A 1 HETATM 29 C C2 ACP . . . B 2 29.603 12.994 65.157 1 57.55 ? C2 ACP 501 A 1 HETATM 30 N N3 ACP . . . B 2 29.283 12.087 64.176 1 61.51 ? N3 ACP 501 A 1 HETATM 31 C C4 ACP . . . B 2 28.818 10.866 64.503 1 59.37 ? C4 ACP 501 A 1 HETATM 32 H H3B1 ACP . . . B 2 25.78 2.854 60.503 1 117.41 ? H3B1 ACP 501 A 1 HETATM 33 H H3B2 ACP . . . B 2 24.739 3.559 61.468 1 117.41 ? H3B2 ACP 501 A 1 HETATM 34 H "H5'1" ACP . . . B 2 26.26 6.385 61.414 1 92.59 ? "H5'1" ACP 501 A 1 HETATM 35 H "H5'2" ACP . . . B 2 27.658 5.64 61.382 1 92.59 ? "H5'2" ACP 501 A 1 HETATM 36 H H4' ACP . . . B 2 27.815 7.764 60.284 1 92.36 ? H4' ACP 501 A 1 HETATM 37 H H3' ACP . . . B 2 29.478 7.303 62.568 1 88.44 ? H3' ACP 501 A 1 HETATM 38 H H2' ACP . . . B 2 30.321 9.415 62.471 1 85.7 ? H2' ACP 501 A 1 HETATM 39 H HO2' ACP . . . B 2 30.177 10.662 60.606 1 84.75 ? HO2' ACP 501 A 1 HETATM 40 H H1' ACP . . . B 2 28.325 10.636 61.949 1 80.7 ? H1' ACP 501 A 1 HETATM 41 H H8 ACP . . . B 2 27.742 7.987 64.38 1 83.17 ? H8 ACP 501 A 1 HETATM 42 H HN61 ACP . . . B 2 28.377 10.965 68.728 1 64.93 ? HN61 ACP 501 A 1 HETATM 43 H HN62 ACP . . . B 2 29.505 11.94 68.753 1 64.93 ? HN62 ACP 501 A 1 HETATM 44 H H2 ACP . . . B 2 29.925 13.835 64.925 1 69.13 ? H2 ACP 501 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 423 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 44 #