data_6HEF # _model_server_result.job_id 9_iUqi-pWpiF3IixZ1CgHA _model_server_result.datetime_utc '2024-11-23 20:27:47' _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 6hef # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 6HEF # _exptl.entry_id 6HEF _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 109.28 _cell.angle_gamma 90 _cell.entry_id 6HEF _cell.length_a 165.84 _cell.length_b 77.77 _cell.length_c 152.22 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HEF _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 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,E,F,G _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 O VAL 304 A VAL 304 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc2 A O ALA 305 A ALA 305 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc3 A O ILE 307 A ILE 307 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc4 A OE1 GLU 309 A GLU 309 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc5 A OD2 ASP 351 A ASP 351 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc6 A O THR 353 A THR 353 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc7 A OD1 ASP 703 A ASP 703 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc8 A O LYS 712 A LYS 712 1_555 F K K . A K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.147 ? metalc ? metalc9 A OD1 ASN 768 A ASN 768 1_555 E CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? metalc ? metalc10 A OE2 GLU 771 A GLU 771 1_555 E CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc11 A OD1 ASN 796 A ASN 796 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc12 A OG1 THR 799 A THR 799 1_555 E CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc13 A OD2 ASP 800 A ASP 800 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc14 A OD1 ASP 800 A ASP 800 1_555 E CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc15 A OD2 ASP 800 A ASP 800 1_555 E CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.168 ? metalc ? metalc16 A OE1 GLU 908 A GLU 908 1_555 E CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc17 B O2G ACP . A ACP 1001 1_555 C CA CA . A CA 1002 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 6HEF _atom_sites.fract_transf_matrix[1][1] 0.00603 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002109 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012858 _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] 0.00696 _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 1001 1001 ACP ACP . C 3 CA A 1 1002 1101 CA CA . D 3 CA A 1 1003 1201 CA CA . E 3 CA A 1 1004 1202 CA CA . F 4 K A 1 1005 1301 K K . G 5 PCW A 1 1006 1501 PCW PCW . # 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 -16.506 3.023 15.459 1 74.33 ? PG ACP 1001 A 1 HETATM 2 O O1G ACP . . . B 2 -16.521 4.559 15.275 1 77.49 ? O1G ACP 1001 A 1 HETATM 3 O O2G ACP . . . B 2 -17.19 2.629 16.77 1 73.84 ? O2G ACP 1001 A 1 HETATM 4 O O3G ACP . . . B 2 -15.1 2.513 15.455 1 74.08 ? O3G ACP 1001 A 1 HETATM 5 P PB ACP . . . B 2 -16.531 2.389 12.504 1 92.37 ? PB ACP 1001 A 1 HETATM 6 O O1B ACP . . . B 2 -15.27 3.102 12.898 1 113.23 ? O1B ACP 1001 A 1 HETATM 7 O O2B ACP . . . B 2 -17.287 3.154 11.49 1 98.08 ? O2B ACP 1001 A 1 HETATM 8 C C3B ACP . . . B 2 -17.46 2.21 14.101 1 83.26 ? C3B ACP 1001 A 1 HETATM 9 P PA ACP . . . B 2 -14.904 0.67 10.947 1 66.38 ? PA ACP 1001 A 1 HETATM 10 O O1A ACP . . . B 2 -13.826 -0.178 11.502 1 62.33 ? O1A ACP 1001 A 1 HETATM 11 O O2A ACP . . . B 2 -14.294 1.989 10.723 1 68.3 ? O2A ACP 1001 A 1 HETATM 12 O O3A ACP . . . B 2 -16.207 0.852 11.924 1 74.61 ? O3A ACP 1001 A 1 HETATM 13 O O5' ACP . . . B 2 -15.351 0.251 9.39 1 70.6 ? O5' ACP 1001 A 1 HETATM 14 C C5' ACP . . . B 2 -14.507 0.77 8.37 1 74.27 ? C5' ACP 1001 A 1 HETATM 15 C C4' ACP . . . B 2 -15.281 1.735 7.436 1 74.48 ? C4' ACP 1001 A 1 HETATM 16 O O4' ACP . . . B 2 -16.059 1.049 6.627 1 75.57 ? O4' ACP 1001 A 1 HETATM 17 C C3' ACP . . . B 2 -16.184 2.719 8.249 1 68.49 ? C3' ACP 1001 A 1 HETATM 18 O O3' ACP . . . B 2 -15.794 4.026 8.156 1 66.71 ? O3' ACP 1001 A 1 HETATM 19 C C2' ACP . . . B 2 -17.546 2.636 7.591 1 70.18 ? C2' ACP 1001 A 1 HETATM 20 O O2' ACP . . . B 2 -17.877 3.954 6.922 1 69.04 ? O2' ACP 1001 A 1 HETATM 21 C C1' ACP . . . B 2 -17.522 1.627 6.716 1 73.51 ? C1' ACP 1001 A 1 HETATM 22 N N9 ACP . . . B 2 -18.419 0.604 7.252 1 75.65 ? N9 ACP 1001 A 1 HETATM 23 C C8 ACP . . . B 2 -18.758 0.463 8.509 1 81.95 ? C8 ACP 1001 A 1 HETATM 24 N N7 ACP . . . B 2 -19.594 -0.605 8.657 1 80.1 ? N7 ACP 1001 A 1 HETATM 25 C C5 ACP . . . B 2 -19.741 -1.114 7.45 1 67.92 ? C5 ACP 1001 A 1 HETATM 26 C C6 ACP . . . B 2 -20.473 -2.203 6.965 1 86.2 ? C6 ACP 1001 A 1 HETATM 27 N N6 ACP . . . B 2 -21.379 -3.238 7.598 1 85.18 ? N6 ACP 1001 A 1 HETATM 28 N N1 ACP . . . B 2 -20.455 -2.512 5.682 1 86.89 ? N1 ACP 1001 A 1 HETATM 29 C C2 ACP . . . B 2 -19.726 -1.76 4.825 1 92.07 ? C2 ACP 1001 A 1 HETATM 30 N N3 ACP . . . B 2 -19.007 -0.692 5.294 1 87.83 ? N3 ACP 1001 A 1 HETATM 31 C C4 ACP . . . B 2 -19.019 -0.379 6.58 1 79.19 ? C4 ACP 1001 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #