data_7KY8 # _model_server_result.job_id g56n3NJ9Yx8Ei4FU-7_7dw _model_server_result.datetime_utc '2024-12-26 14:40:08' _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 7ky8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1706}' # _entry.id 7KY8 # _exptl.entry_id 7KY8 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 505.208 _entity.id 7 _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 90 _cell.entry_id 7KY8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O _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 ? _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 7 _struct_asym.id L _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 MAN NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 MAN MAN C3 H3 . O3 HO3 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG B 1001 NAG 3 n C NAG 2 C 2 NAG B 1009 NAG 4 n D NAG 1 D 1 NAG B 1002 NAG 4 n D NAG 2 D 2 NAG B 1003 NAG 4 n D MAN 3 D 3 MAN B 1010 MAN 4 n D MAN 4 D 4 MAN B 1011 MAN 3 n E NAG 1 E 1 NAG B 1005 NAG 3 n E NAG 2 E 2 NAG B 1006 NAG 3 n F NAG 1 F 1 NAG B 1007 NAG 3 n F NAG 2 F 2 NAG B 1008 NAG # 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 disulf ? disulf1 B SG CYS 110 B CYS 110 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 B SG CYS 216 B CYS 216 1_555 B SG CYS 231 B CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 B ND2 ASN 113 B ASN 113 1_555 O C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B ND2 ASN 240 B ASN 240 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 B ND2 ASN 256 B ASN 256 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 B ND2 ASN 298 B ASN 298 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B ND2 ASN 332 B ASN 332 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 D O4 NAG . D NAG 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 D O3 MAN . D MAN 3 1_555 D C3 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A OG1 THR 714 A THR 714 1_555 K MG MG . A MG 1705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc2 A O ASP 1173 A ASP 1173 1_555 K MG MG . A MG 1705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? # _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 7KY8 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 G 5 CLR A 1 1701 2007 CLR CLR . H 5 CLR A 1 1702 2008 CLR CLR . I 5 CLR A 1 1703 2009 CLR CLR . J 5 CLR A 1 1704 2011 CLR CLR . K 6 MG A 1 1705 2012 MG MG . L 7 ACP A 1 1706 2013 ACP ACP . M 8 MAN A 1 1707 1012 MAN MAN . N 5 CLR B 1 501 2005 CLR CLR . O 9 NAG B 1 502 1004 NAG NAG . # 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 . . . L 7 157.801 151.3 146.809 1 73.62 ? PG ACP 1706 A 1 HETATM 2 O O1G ACP . . . L 7 157.013 150.047 146.782 1 73.62 ? O1G ACP 1706 A 1 HETATM 3 O O2G ACP . . . L 7 157.045 152.39 147.722 1 73.62 ? O2G ACP 1706 A 1 HETATM 4 O O3G ACP . . . L 7 157.955 151.869 145.311 1 73.62 ? O3G ACP 1706 A 1 HETATM 5 P PB ACP . . . L 7 160.369 149.897 146.37 1 73.62 ? PB ACP 1706 A 1 HETATM 6 O O1B ACP . . . L 7 159.477 148.836 145.852 1 73.62 ? O1B ACP 1706 A 1 HETATM 7 O O2B ACP . . . L 7 161.602 149.224 147.157 1 73.62 ? O2B ACP 1706 A 1 HETATM 8 C C3B ACP . . . L 7 159.442 150.967 147.501 1 73.62 ? C3B ACP 1706 A 1 HETATM 9 P PA ACP . . . L 7 161.794 152.104 145.413 1 73.62 ? PA ACP 1706 A 1 HETATM 10 O O1A ACP . . . L 7 160.961 153.045 146.251 1 73.62 ? O1A ACP 1706 A 1 HETATM 11 O O2A ACP . . . L 7 162.365 152.574 144.096 1 73.62 ? O2A ACP 1706 A 1 HETATM 12 O O3A ACP . . . L 7 160.93 150.773 145.141 1 73.62 ? O3A ACP 1706 A 1 HETATM 13 O O5' ACP . . . L 7 163.006 151.559 146.321 1 73.62 ? O5' ACP 1706 A 1 HETATM 14 C C5' ACP . . . L 7 163.936 152.467 146.907 1 73.62 ? C5' ACP 1706 A 1 HETATM 15 C C4' ACP . . . L 7 163.727 152.506 148.415 1 73.62 ? C4' ACP 1706 A 1 HETATM 16 O O4' ACP . . . L 7 164.073 153.8 148.917 1 73.62 ? O4' ACP 1706 A 1 HETATM 17 C C3' ACP . . . L 7 162.274 152.237 148.778 1 73.62 ? C3' ACP 1706 A 1 HETATM 18 O O3' ACP . . . L 7 162.185 151.036 149.555 1 73.62 ? O3' ACP 1706 A 1 HETATM 19 C C2' ACP . . . L 7 161.791 153.467 149.534 1 73.62 ? C2' ACP 1706 A 1 HETATM 20 O O2' ACP . . . L 7 161.348 153.163 150.864 1 73.62 ? O2' ACP 1706 A 1 HETATM 21 C C1' ACP . . . L 7 162.976 154.419 149.594 1 73.62 ? C1' ACP 1706 A 1 HETATM 22 N N9 ACP . . . L 7 162.627 155.695 148.919 1 73.62 ? N9 ACP 1706 A 1 HETATM 23 C C8 ACP . . . L 7 161.385 156.096 148.587 1 73.62 ? C8 ACP 1706 A 1 HETATM 24 N N7 ACP . . . L 7 161.408 157.311 147.982 1 73.62 ? N7 ACP 1706 A 1 HETATM 25 C C5 ACP . . . L 7 162.693 157.706 147.919 1 73.62 ? C5 ACP 1706 A 1 HETATM 26 C C6 ACP . . . L 7 163.422 158.889 147.404 1 73.62 ? C6 ACP 1706 A 1 HETATM 27 N N6 ACP . . . L 7 162.764 159.919 146.82 1 73.62 ? N6 ACP 1706 A 1 HETATM 28 N N1 ACP . . . L 7 164.767 158.906 147.538 1 73.62 ? N1 ACP 1706 A 1 HETATM 29 C C2 ACP . . . L 7 165.434 157.89 148.117 1 73.62 ? C2 ACP 1706 A 1 HETATM 30 N N3 ACP . . . L 7 164.837 156.788 148.605 1 73.62 ? N3 ACP 1706 A 1 HETATM 31 C C4 ACP . . . L 7 163.492 156.638 148.538 1 73.62 ? C4 ACP 1706 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #