data_5Z4U # _model_server_result.job_id 7o43PEParGGUvJkdjeIn9A _model_server_result.datetime_utc '2025-07-07 02:56:56' _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 5z4u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":401}' # _entry.id 5Z4U # _exptl.entry_id 5Z4U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 11 _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 5Z4U _cell.length_a 105.491 _cell.length_b 158.233 _cell.length_c 182.099 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z4U _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,P,Q,R,S,T,U,V _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 11 _struct_asym.id V _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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc2 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc3 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc5 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc6 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc7 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc8 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc9 B OE1 GLU 111 B GLU 111 1_555 M CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc10 B OD2 ASP 177 B ASP 177 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc11 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc12 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc13 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc14 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.087 ? metalc ? metalc15 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc16 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc18 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc19 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc20 S O1G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc21 S O2G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? # _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 54 n n PG O2G ACP sing 55 n n PG O3G ACP sing 56 n n PG C3B ACP sing 57 n n O2G HOG2 ACP sing 58 n n O3G HOG3 ACP sing 59 n n PB O1B ACP doub 60 n n PB O2B ACP sing 61 n n PB C3B ACP sing 62 n n PB O3A ACP sing 63 n n O2B HOB2 ACP sing 64 n n C3B H3B1 ACP sing 65 n n C3B H3B2 ACP sing 66 n n PA O1A ACP doub 67 n n PA O2A ACP sing 68 n n PA O3A ACP sing 69 n n PA O5' ACP sing 70 n n O2A HOA2 ACP sing 71 n n O5' C5' ACP sing 72 n n C5' C4' ACP sing 73 n n C5' "H5'1" ACP sing 74 n n C5' "H5'2" ACP sing 75 n n C4' O4' ACP sing 76 n n C4' C3' ACP sing 77 n n C4' H4' ACP sing 78 n n O4' C1' ACP sing 79 n n C3' O3' ACP sing 80 n n C3' C2' ACP sing 81 n n C3' H3' ACP sing 82 n n O3' HO3' ACP sing 83 n n C2' O2' ACP sing 84 n n C2' C1' ACP sing 85 n n C2' H2' ACP sing 86 n n O2' HO2' ACP sing 87 n n C1' N9 ACP sing 88 n n C1' H1' ACP sing 89 n n N9 C8 ACP sing 90 n y N9 C4 ACP sing 91 n y C8 N7 ACP doub 92 n y C8 H8 ACP sing 93 n n N7 C5 ACP sing 94 n y C5 C6 ACP sing 95 n y C5 C4 ACP doub 96 n y C6 N6 ACP sing 97 n n C6 N1 ACP doub 98 n y N6 HN61 ACP sing 99 n n N6 HN62 ACP sing 100 n n N1 C2 ACP sing 101 n y C2 N3 ACP doub 102 n y C2 H2 ACP sing 103 n n N3 C4 ACP sing 104 n y # _atom_sites.entry_id 5Z4U _atom_sites.fract_transf_matrix[1][1] 0.009479 _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] 0.00632 _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] 0.005492 _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 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GDP B 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 9 MES B 1 503 505 MES MES . M 7 CA B 1 504 2 CA CA . N 9 MES B 1 505 505 MES MES . O 10 96C B 1 506 1 96C 7A3 . P 5 GTP C 1 501 501 GTP GTP . Q 6 MG C 1 502 502 MG MG . R 7 CA C 1 503 1 CA CA . S 5 GTP D 1 501 501 GTP GTP . T 6 MG D 1 502 502 MG MG . U 10 96C D 1 503 2 96C 7A3 . V 11 ACP F 1 401 401 ACP ACP . # 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 . . . V 11 -7.669 -50.379 93.831 1 267.02 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . V 11 -7.913 -51.651 93.113 1 260.97 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . V 11 -8.636 -49.237 93.237 1 272.08 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . V 11 -6.138 -49.933 93.623 1 266.7 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . V 11 -9.597 -49.994 96.108 1 276.24 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . V 11 -10.522 -50.114 94.958 1 282.78 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . V 11 -9.5 -48.438 96.499 1 281.13 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . V 11 -7.965 -50.614 95.607 1 271.06 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . V 11 -9.49 -51.337 98.685 1 248.94 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . V 11 -7.995 -51.404 98.483 1 246.84 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . V 11 -10.239 -52.57 99.131 1 243.76 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . V 11 -10.234 -50.829 97.34 1 264.64 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . V 11 -9.812 -50.201 99.787 1 237.15 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . V 11 -9.229 -48.897 99.777 1 221.69 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . V 11 -8.447 -48.611 101.063 1 209.39 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . V 11 -9.071 -49.218 102.202 1 198.77 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . V 11 -7.004 -49.112 101.007 1 201.54 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . V 11 -6.092 -48.007 101.037 1 203.14 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . V 11 -6.831 -50.033 102.203 1 193.83 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . V 11 -5.681 -49.701 102.992 1 190.14 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . V 11 -8.109 -49.89 103.02 1 190.2 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . V 11 -8.602 -51.228 103.436 1 182.85 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . V 11 -9.447 -52.023 102.75 1 181.43 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . V 11 -9.682 -53.179 103.423 1 177.88 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . V 11 -8.975 -53.135 104.564 1 173.45 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . V 11 -8.765 -54.026 105.733 1 170.4 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . V 11 -9.382 -55.228 105.809 1 170.13 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . V 11 -7.937 -53.592 106.717 1 168.95 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . V 11 -7.314 -52.393 106.653 1 169.41 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . V 11 -7.462 -51.541 105.618 1 172.79 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . V 11 -8.262 -51.846 104.565 1 175.97 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 123 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #