data_6HXB # _model_server_result.job_id GIv8q3TkCoLyIq7WP-8bHQ _model_server_result.datetime_utc '2024-11-29 06:34:48' _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 6hxb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1004}' # _entry.id 6HXB # _exptl.entry_id 6HXB _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 106.13 _cell.angle_gamma 90 _cell.entry_id 6HXB _cell.length_a 116.995 _cell.length_b 51.776 _cell.length_c 125.604 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HXB _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 3 _struct_asym.id E _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 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.005 ? metalc ? metalc2 A O ALA 305 A ALA 305 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc3 A O ILE 307 A ILE 307 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc4 A OE1 GLU 309 A GLU 309 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc5 A OE2 GLU 309 A GLU 309 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc6 A OD2 ASP 351 A ASP 351 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc7 A O THR 353 A THR 353 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc8 A OD1 ASP 702 A ASP 702 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc9 A OD2 ASP 702 A ASP 702 1_555 D CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc10 A O LEU 710 A LEU 710 1_555 F K K . A K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc11 A O LYS 711 A LYS 711 1_555 F K K . A K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.977 ? metalc ? metalc12 A O SER 713 A SER 713 1_555 F K K . A K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? metalc ? metalc13 A OE1 GLU 731 A GLU 731 1_555 F K K . A K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? metalc ? metalc14 A OE2 GLU 731 A GLU 731 1_555 F K K . A K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc15 A OD1 ASN 767 A ASN 767 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc16 A OE2 GLU 770 A GLU 770 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc17 A OD1 ASN 795 A ASN 795 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc18 A OG1 THR 798 A THR 798 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc19 A OD1 ASP 799 A ASP 799 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc20 A OD2 ASP 799 A ASP 799 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc21 A OD2 ASP 799 A ASP 799 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc22 D CA CA . A CA 1003 1_555 E O3G ACP . A ACP 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc23 D CA CA . A CA 1003 1_555 E O2G ACP . A ACP 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc24 D CA CA . A CA 1003 1_555 G O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? # _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 6HXB _atom_sites.fract_transf_matrix[1][1] 0.008547 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002472 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019314 _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] 0.008288 _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 CA A 1 1001 1001 CA CA . C 2 CA A 1 1002 1002 CA CA . D 2 CA A 1 1003 1003 CA CA . E 3 ACP A 1 1004 1004 ACP ACP . F 4 K A 1 1005 1006 K K . G 5 HOH A 1 1101 1005 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 . . . E 3 170.746 -15.801 22.549 1 167.98 ? PG ACP 1004 A 1 HETATM 2 O O1G ACP . . . E 3 170.503 -16.369 21.171 1 148.43 ? O1G ACP 1004 A 1 HETATM 3 O O2G ACP . . . E 3 170.44 -16.844 23.597 1 173.7 ? O2G ACP 1004 A 1 HETATM 4 O O3G ACP . . . E 3 169.83 -14.619 22.772 1 148.87 ? O3G ACP 1004 A 1 HETATM 5 P PB ACP . . . E 3 173.666 -15.714 21.375 1 123.83 ? PB ACP 1004 A 1 HETATM 6 O O1B ACP . . . E 3 172.946 -16.344 20.209 1 161.29 ? O1B ACP 1004 A 1 HETATM 7 O O2B ACP . . . E 3 174.709 -16.673 21.898 1 146.3 ? O2B ACP 1004 A 1 HETATM 8 C C3B ACP . . . E 3 172.513 -15.251 22.765 1 135.17 ? C3B ACP 1004 A 1 HETATM 9 P PA ACP . . . E 3 175.971 -13.979 21.264 1 185.23 ? PA ACP 1004 A 1 HETATM 10 O O1A ACP . . . E 3 176.265 -12.541 20.911 1 180.69 ? O1A ACP 1004 A 1 HETATM 11 O O2A ACP . . . E 3 176.165 -14.197 22.745 1 165.63 ? O2A ACP 1004 A 1 HETATM 12 O O3A ACP . . . E 3 174.421 -14.35 20.851 1 149.95 ? O3A ACP 1004 A 1 HETATM 13 O O5' ACP . . . E 3 176.974 -14.984 20.435 1 182.17 ? O5' ACP 1004 A 1 HETATM 14 C C5' ACP . . . E 3 178.072 -14.437 19.769 1 166.05 ? C5' ACP 1004 A 1 HETATM 15 C C4' ACP . . . E 3 179.094 -15.574 19.5 1 158.66 ? C4' ACP 1004 A 1 HETATM 16 O O4' ACP . . . E 3 179.954 -15.632 20.479 1 154.26 ? O4' ACP 1004 A 1 HETATM 17 C C3' ACP . . . E 3 178.365 -16.934 19.452 1 155.8 ? C3' ACP 1004 A 1 HETATM 18 O O3' ACP . . . E 3 178.541 -17.514 18.238 1 157.83 ? O3' ACP 1004 A 1 HETATM 19 C C2' ACP . . . E 3 178.989 -17.813 20.555 1 155.02 ? C2' ACP 1004 A 1 HETATM 20 O O2' ACP . . . E 3 179.546 -19.055 19.938 1 161.68 ? O2' ACP 1004 A 1 HETATM 21 C C1' ACP . . . E 3 179.956 -17.124 21.103 1 153.53 ? C1' ACP 1004 A 1 HETATM 22 N N9 ACP . . . E 3 179.768 -17.039 22.53 1 156.56 ? N9 ACP 1004 A 1 HETATM 23 C C8 ACP . . . E 3 178.608 -16.867 23.169 1 183.52 ? C8 ACP 1004 A 1 HETATM 24 N N7 ACP . . . E 3 178.858 -16.839 24.482 1 191.91 ? N7 ACP 1004 A 1 HETATM 25 C C5 ACP . . . E 3 180.178 -16.993 24.657 1 173.47 ? C5 ACP 1004 A 1 HETATM 26 C C6 ACP . . . E 3 180.968 -17.038 25.79 1 179.01 ? C6 ACP 1004 A 1 HETATM 27 N N6 ACP . . . E 3 180.481 -16.919 27.152 1 168.07 ? N6 ACP 1004 A 1 HETATM 28 N N1 ACP . . . E 3 182.277 -17.202 25.682 1 187.2 ? N1 ACP 1004 A 1 HETATM 29 C C2 ACP . . . E 3 182.843 -17.325 24.46 1 180.33 ? C2 ACP 1004 A 1 HETATM 30 N N3 ACP . . . E 3 182.073 -17.28 23.349 1 179.34 ? N3 ACP 1004 A 1 HETATM 31 C C4 ACP . . . E 3 180.741 -17.114 23.451 1 167.04 ? C4 ACP 1004 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #