data_4ZDK # _model_server_result.job_id KdDCtDIrs-oMP8x_u3I2CQ _model_server_result.datetime_utc '2024-10-28 14:25:58' _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 4zdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":602}' # _entry.id 4ZDK # _exptl.entry_id 4ZDK _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 2 _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 4ZDK _cell.length_a 121.732 _cell.length_b 194.724 _cell.length_c 207.457 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,G,H,I,J 1 1 A,C,D,E,F 1 2 B,G,H,I,J 1 4 A,C,D,E,F 1 6 A,C,D,E,F 2 1,5 B,G,H,I,J 2 3,6 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_545 x+1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 60.866 -97.362 0 3 'crystal symmetry operation' 4_445 x-1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 -60.866 -97.362 0 4 'crystal symmetry operation' 6_645 -x+1,-y-1/2,z -1 0 0 0 -1 0 0 0 1 121.732 -97.362 0 5 'crystal symmetry operation' 6_545 -x,-y-1/2,z -1 0 0 0 -1 0 0 0 1 0 -97.362 0 6 'crystal symmetry operation' 7_555 -x+1/2,y,-z -1 0 0 0 1 0 0 0 -1 60.866 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 H N 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 covale ? covale1 A SG CYS 393 A CYS 393 1_555 C CE ONL . A ONL 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale2 B SG CYS 393 B CYS 393 1_555 G CE ONL . B ONL 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? metalc ? metalc1 A OD1 ASP 78 A ASP 78 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc2 A OD2 ASP 78 A ASP 78 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc3 A OE1 GLU 152 A GLU 152 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? metalc ? metalc4 A OE2 GLU 152 A GLU 152 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc5 D O3G ACP . A ACP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc6 D O1B ACP . A ACP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc7 B OD2 ASP 78 B ASP 78 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc8 B OE2 GLU 152 B GLU 152 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc9 H O1B ACP . B ACP 602 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? # _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 4ZDK _atom_sites.fract_transf_matrix[1][1] 0.008215 _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] 0.005135 _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] 0.00482 _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 ONL A 1 601 601 ONL ONL . D 3 ACP A 1 602 1 ACP ACP . E 4 UTP A 1 603 3 UTP UTP . F 5 MG A 1 604 5 MG MG . G 2 ONL B 1 601 601 ONL ONL . H 3 ACP B 1 602 2 ACP ACP . I 4 UTP B 1 603 4 UTP UTP . J 5 MG B 1 604 6 MG MG . # 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 . . . H 3 60.62 -30.053 -9.662 1 184.82 ? PG ACP 602 B 1 HETATM 2 O O1G ACP . . . H 3 60.952 -28.984 -10.729 1 187.78 ? O1G ACP 602 B 1 HETATM 3 O O2G ACP . . . H 3 59.305 -30.724 -10.121 1 184.24 ? O2G ACP 602 B 1 HETATM 4 O O3G ACP . . . H 3 61.726 -31.042 -9.476 1 184.48 ? O3G ACP 602 B 1 HETATM 5 P PB ACP . . . H 3 61.584 -28.344 -7.273 1 179.74 ? PB ACP 602 B 1 HETATM 6 O O1B ACP . . . H 3 62.952 -28.969 -7.279 1 179.55 ? O1B ACP 602 B 1 HETATM 7 O O2B ACP . . . H 3 61.161 -28.225 -5.779 1 177.94 ? O2B ACP 602 B 1 HETATM 8 C C3B ACP . . . H 3 60.24 -29.18 -8.133 1 181.47 ? C3B ACP 602 B 1 HETATM 9 P PA ACP . . . H 3 61.836 -25.376 -7.367 1 180.63 ? PA ACP 602 B 1 HETATM 10 O O1A ACP . . . H 3 63.282 -25.226 -7.092 1 180.34 ? O1A ACP 602 B 1 HETATM 11 O O2A ACP . . . H 3 61.031 -25.281 -6.081 1 179.55 ? O2A ACP 602 B 1 HETATM 12 O O3A ACP . . . H 3 61.591 -26.855 -7.914 1 181.06 ? O3A ACP 602 B 1 HETATM 13 O O5' ACP . . . H 3 61.269 -24.15 -8.301 1 182.08 ? O5' ACP 602 B 1 HETATM 14 C C5' ACP . . . H 3 59.897 -23.68 -8.257 1 181.07 ? C5' ACP 602 B 1 HETATM 15 C C4' ACP . . . H 3 59.752 -22.319 -7.611 1 181.77 ? C4' ACP 602 B 1 HETATM 16 O O4' ACP . . . H 3 60.143 -22.367 -6.227 1 180.6 ? O4' ACP 602 B 1 HETATM 17 C C3' ACP . . . H 3 60.58 -21.182 -8.196 1 184.49 ? C3' ACP 602 B 1 HETATM 18 O O3' ACP . . . H 3 59.965 -20.632 -9.358 1 185.6 ? O3' ACP 602 B 1 HETATM 19 C C2' ACP . . . H 3 60.673 -20.182 -7.029 1 185.38 ? C2' ACP 602 B 1 HETATM 20 O O2' ACP . . . H 3 59.787 -19.073 -7.149 1 186.46 ? O2' ACP 602 B 1 HETATM 21 C C1' ACP . . . H 3 60.352 -21.037 -5.786 1 182.82 ? C1' ACP 602 B 1 HETATM 22 N N9 ACP . . . H 3 61.401 -21.032 -4.764 1 183.1 ? N9 ACP 602 B 1 HETATM 23 C C8 ACP . . . H 3 62.452 -21.906 -4.672 1 183.04 ? C8 ACP 602 B 1 HETATM 24 N N7 ACP . . . H 3 63.269 -21.662 -3.676 1 183.62 ? N7 ACP 602 B 1 HETATM 25 C C5 ACP . . . H 3 62.721 -20.544 -3.068 1 183.61 ? C5 ACP 602 B 1 HETATM 26 C C6 ACP . . . H 3 63.126 -19.773 -1.96 1 183.66 ? C6 ACP 602 B 1 HETATM 27 N N6 ACP . . . H 3 64.249 -19.997 -1.272 1 183.6 ? N6 ACP 602 B 1 HETATM 28 N N1 ACP . . . H 3 62.351 -18.72 -1.609 1 184.51 ? N1 ACP 602 B 1 HETATM 29 C C2 ACP . . . H 3 61.258 -18.453 -2.336 1 184.28 ? C2 ACP 602 B 1 HETATM 30 N N3 ACP . . . H 3 60.787 -19.098 -3.41 1 183.48 ? N3 ACP 602 B 1 HETATM 31 C C4 ACP . . . H 3 61.565 -20.145 -3.725 1 183.45 ? C4 ACP 602 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #