data_4XOU # _model_server_result.job_id Jc95ZWBdyrloc8KGi1vY7g _model_server_result.datetime_utc '2024-11-07 02:47:56' _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 4xou # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1004}' # _entry.id 4XOU # _exptl.entry_id 4XOU _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109 _cell.angle_gamma 90 _cell.entry_id 4XOU _cell.length_a 162 _cell.length_b 76.3 _cell.length_c 151.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XOU _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 _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 4 _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 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? metalc ? metalc2 A O ALA 305 A ALA 305 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc3 A O ILE 307 A ILE 307 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc4 A OE1 GLU 309 A GLU 309 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc5 A OE2 GLU 309 A GLU 309 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc6 A OD2 ASP 351 A ASP 351 1_555 F CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc7 A O THR 353 A THR 353 1_555 F CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc8 A OD1 ASP 703 A ASP 703 1_555 F CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc9 A O LEU 711 A LEU 711 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? metalc ? metalc10 A O LYS 712 A LYS 712 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.248 ? metalc ? metalc11 A O ALA 714 A ALA 714 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.448 ? metalc ? metalc12 A OE1 GLU 732 A GLU 732 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.002 ? metalc ? metalc13 A OE2 GLU 732 A GLU 732 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc14 A OD1 ASN 768 A ASN 768 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc15 A OE2 GLU 771 A GLU 771 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc16 A OD1 ASN 796 A ASN 796 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc17 A OG1 THR 799 A THR 799 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc18 A OD2 ASP 800 A ASP 800 1_555 B CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc19 A OD1 ASP 800 A ASP 800 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc20 A OE1 GLU 908 A GLU 908 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc21 A OE2 GLU 908 A GLU 908 1_555 C CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc22 E O3G ACP . A ACP 1004 1_555 F CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? # _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 4XOU _atom_sites.fract_transf_matrix[1][1] 0.006173 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002125 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013106 _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] 0.006999 _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 1003 CA CA . C 2 CA A 1 1002 1004 CA CA . D 3 K A 1 1003 1006 K K . E 4 ACP A 1 1004 1001 ACP ACP . F 2 CA A 1 1005 1005 CA CA . # 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 4 -15.683 39.954 15.298 1 84.04 ? PG ACP 1004 A 1 HETATM 2 O O1G ACP . . . E 4 -15.888 41.372 14.914 1 74.72 ? O1G ACP 1004 A 1 HETATM 3 O O2G ACP . . . E 4 -14.208 39.651 15.658 1 85.21 ? O2G ACP 1004 A 1 HETATM 4 O O3G ACP . . . E 4 -16.551 39.535 16.502 1 93.44 ? O3G ACP 1004 A 1 HETATM 5 P PB ACP . . . E 4 -16.146 39.578 12.31 1 89.43 ? PB ACP 1004 A 1 HETATM 6 O O1B ACP . . . E 4 -17.382 38.939 11.589 1 74.69 ? O1B ACP 1004 A 1 HETATM 7 O O2B ACP . . . E 4 -16.263 41.072 12.133 1 94.41 ? O2B ACP 1004 A 1 HETATM 8 C C3B ACP . . . E 4 -16.106 38.845 13.947 1 98.15 ? C3B ACP 1004 A 1 HETATM 9 P PA ACP . . . E 4 -14.456 37.588 10.974 1 98.82 ? PA ACP 1004 A 1 HETATM 10 O O1A ACP . . . E 4 -12.997 37.348 11.299 1 99.48 ? O1A ACP 1004 A 1 HETATM 11 O O2A ACP . . . E 4 -15.26 36.508 11.582 1 83.88 ? O2A ACP 1004 A 1 HETATM 12 O O3A ACP . . . E 4 -14.864 38.997 11.614 1 92.08 ? O3A ACP 1004 A 1 HETATM 13 O O5' ACP . . . E 4 -14.614 37.749 9.376 1 94.52 ? O5' ACP 1004 A 1 HETATM 14 C C5' ACP . . . E 4 -14.019 38.84 8.639 1 94.04 ? C5' ACP 1004 A 1 HETATM 15 C C4' ACP . . . E 4 -15.065 39.441 7.744 1 86.52 ? C4' ACP 1004 A 1 HETATM 16 O O4' ACP . . . E 4 -15.744 38.391 7.021 1 90.67 ? O4' ACP 1004 A 1 HETATM 17 C C3' ACP . . . E 4 -16.187 40.194 8.45 1 86.64 ? C3' ACP 1004 A 1 HETATM 18 O O3' ACP . . . E 4 -15.794 41.524 8.764 1 99.98 ? O3' ACP 1004 A 1 HETATM 19 C C2' ACP . . . E 4 -17.314 40.15 7.42 1 77.6 ? C2' ACP 1004 A 1 HETATM 20 O O2' ACP . . . E 4 -17.214 41.231 6.493 1 76.74 ? O2' ACP 1004 A 1 HETATM 21 C C1' ACP . . . E 4 -17.064 38.816 6.701 1 86.35 ? C1' ACP 1004 A 1 HETATM 22 N N9 ACP . . . E 4 -17.994 37.75 7.052 1 94.06 ? N9 ACP 1004 A 1 HETATM 23 C C8 ACP . . . E 4 -18.498 37.467 8.297 1 98.32 ? C8 ACP 1004 A 1 HETATM 24 N N7 ACP . . . E 4 -19.332 36.46 8.324 1 103.22 ? N7 ACP 1004 A 1 HETATM 25 C C5 ACP . . . E 4 -19.387 36.042 7.005 1 91.48 ? C5 ACP 1004 A 1 HETATM 26 C C6 ACP . . . E 4 -20.1 35.011 6.369 1 82.66 ? C6 ACP 1004 A 1 HETATM 27 N N6 ACP . . . E 4 -20.929 34.176 7 1 91.84 ? N6 ACP 1004 A 1 HETATM 28 N N1 ACP . . . E 4 -19.933 34.863 5.04 1 74.37 ? N1 ACP 1004 A 1 HETATM 29 C C2 ACP . . . E 4 -19.107 35.698 4.398 1 81.26 ? C2 ACP 1004 A 1 HETATM 30 N N3 ACP . . . E 4 -18.381 36.706 4.895 1 81.75 ? N3 ACP 1004 A 1 HETATM 31 C C4 ACP . . . E 4 -18.571 36.826 6.211 1 86.92 ? C4 ACP 1004 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #