data_5Z4P # _model_server_result.job_id 0J4ZAj8it4Y9NshNhV5tGg _model_server_result.datetime_utc '2024-12-22 06:06:04' _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 5z4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HA","auth_seq_id":401}' # _entry.id 5Z4P # _exptl.entry_id 5Z4P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 13 _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 5Z4P _cell.length_a 103.832 _cell.length_b 154.843 _cell.length_c 181.024 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z4P _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,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA _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 13 _struct_asym.id HA _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 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? metalc ? metalc8 G O3G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc9 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc11 B OE2 GLU 108 B GLU 110 1_555 P CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? metalc ? metalc12 B OE1 GLU 111 B GLU 113 1_555 P CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc13 B OE1 GLU 111 B GLU 113 1_555 Z CA CA . C CA 508 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc14 B OD2 ASP 177 B ASP 179 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc15 M O2A GDP . B GDP 501 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc16 N MG MG . B MG 502 1_555 JA O HOH . B HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc17 C OE1 GLU 71 C GLU 71 1_555 V MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.938 ? metalc ? metalc18 U O3G GTP . C GTP 503 1_555 V MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc19 U O2B GTP . C GTP 503 1_555 V MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc20 V MG MG . C MG 504 1_555 KA O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc21 DA O2B GDP . D GDP 501 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? # _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 53 n n PG O2G ACP sing 54 n n PG O3G ACP sing 55 n n PG C3B ACP sing 56 n n O2G HOG2 ACP sing 57 n n O3G HOG3 ACP sing 58 n n PB O1B ACP doub 59 n n PB O2B ACP sing 60 n n PB C3B ACP sing 61 n n PB O3A ACP sing 62 n n O2B HOB2 ACP sing 63 n n C3B H3B1 ACP sing 64 n n C3B H3B2 ACP sing 65 n n PA O1A ACP doub 66 n n PA O2A ACP sing 67 n n PA O3A ACP sing 68 n n PA O5' ACP sing 69 n n O2A HOA2 ACP sing 70 n n O5' C5' ACP sing 71 n n C5' C4' ACP sing 72 n n C5' "H5'1" ACP sing 73 n n C5' "H5'2" ACP sing 74 n n C4' O4' ACP sing 75 n n C4' C3' ACP sing 76 n n C4' H4' ACP sing 77 n n O4' C1' ACP sing 78 n n C3' O3' ACP sing 79 n n C3' C2' ACP sing 80 n n C3' H3' ACP sing 81 n n O3' HO3' ACP sing 82 n n C2' O2' ACP sing 83 n n C2' C1' ACP sing 84 n n C2' H2' ACP sing 85 n n O2' HO2' ACP sing 86 n n C1' N9 ACP sing 87 n n C1' H1' ACP sing 88 n n N9 C8 ACP sing 89 n y N9 C4 ACP sing 90 n y C8 N7 ACP doub 91 n y C8 H8 ACP sing 92 n n N7 C5 ACP sing 93 n y C5 C6 ACP sing 94 n y C5 C4 ACP doub 95 n y C6 N6 ACP sing 96 n n C6 N1 ACP doub 97 n y N6 HN61 ACP sing 98 n n N6 HN62 ACP sing 99 n n N1 C2 ACP sing 100 n y C2 N3 ACP doub 101 n y C2 H2 ACP sing 102 n n N3 C4 ACP sing 103 n y # _atom_sites.entry_id 5Z4P _atom_sites.fract_transf_matrix[1][1] 0.009631 _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] 0.006458 _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] 0.005524 _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 GOL A 1 503 504 GOL GOL . J 7 GOL A 1 504 505 GOL GOL . K 8 CA A 1 505 506 CA CA . L 7 GOL A 1 506 201 GOL GOL . M 9 GDP B 1 501 501 GDP GDP . N 6 MG B 1 502 502 MG MG . O 7 GOL B 1 503 506 GOL GOL . P 8 CA B 1 504 508 CA CA . Q 10 MES B 1 505 509 MES MES . R 11 97O B 1 506 999 97O UNK . S 7 GOL C 1 501 504 GOL GOL . T 7 GOL C 1 502 505 GOL GOL . U 5 GTP C 1 503 501 GTP GTP . V 6 MG C 1 504 502 MG MG . W 7 GOL C 1 505 503 GOL GOL . X 7 GOL C 1 506 504 GOL GOL . Y 7 GOL C 1 507 505 GOL GOL . Z 8 CA C 1 508 508 CA CA . AA 12 IMD C 1 509 509 IMD IMD . BA 12 IMD C 1 510 510 IMD IMD . CA 12 IMD C 1 511 511 IMD IMD . DA 9 GDP D 1 501 501 GDP GDP . EA 6 MG D 1 502 502 MG MG . FA 7 GOL D 1 503 504 GOL GOL . GA 7 GOL D 1 504 505 GOL GOL . HA 13 ACP F 1 401 402 ACP ACP . IA 14 HOH A 1 601 32 HOH HOH . IA 14 HOH A 2 602 46 HOH HOH . IA 14 HOH A 3 603 34 HOH HOH . IA 14 HOH A 4 604 28 HOH HOH . IA 14 HOH A 5 605 16 HOH HOH . IA 14 HOH A 6 606 30 HOH HOH . IA 14 HOH A 7 607 36 HOH HOH . IA 14 HOH A 8 608 31 HOH HOH . IA 14 HOH A 9 609 10 HOH HOH . IA 14 HOH A 10 610 6 HOH HOH . IA 14 HOH A 11 611 21 HOH HOH . JA 14 HOH B 1 601 17 HOH HOH . JA 14 HOH B 2 602 37 HOH HOH . JA 14 HOH B 3 603 41 HOH HOH . JA 14 HOH B 4 604 40 HOH HOH . JA 14 HOH B 5 605 19 HOH HOH . JA 14 HOH B 6 606 38 HOH HOH . JA 14 HOH B 7 607 42 HOH HOH . JA 14 HOH B 8 608 39 HOH HOH . JA 14 HOH B 9 609 3 HOH HOH . JA 14 HOH B 10 610 7 HOH HOH . JA 14 HOH B 11 611 20 HOH HOH . JA 14 HOH B 12 612 18 HOH HOH . JA 14 HOH B 13 613 44 HOH HOH . KA 14 HOH C 1 601 8 HOH HOH . KA 14 HOH C 2 602 49 HOH HOH . KA 14 HOH C 3 603 14 HOH HOH . KA 14 HOH C 4 604 50 HOH HOH . KA 14 HOH C 5 605 11 HOH HOH . KA 14 HOH C 6 606 45 HOH HOH . KA 14 HOH C 7 607 48 HOH HOH . KA 14 HOH C 8 608 47 HOH HOH . KA 14 HOH C 9 609 4 HOH HOH . KA 14 HOH C 10 610 51 HOH HOH . KA 14 HOH C 11 611 15 HOH HOH . KA 14 HOH C 12 612 1 HOH HOH . KA 14 HOH C 13 613 2 HOH HOH . KA 14 HOH C 14 614 9 HOH HOH . KA 14 HOH C 15 615 5 HOH HOH . KA 14 HOH C 16 616 12 HOH HOH . KA 14 HOH C 17 617 43 HOH HOH . LA 14 HOH D 1 601 52 HOH HOH . LA 14 HOH D 2 602 23 HOH HOH . LA 14 HOH D 3 603 22 HOH HOH . LA 14 HOH D 4 604 25 HOH HOH . MA 14 HOH F 1 501 13 HOH HOH . MA 14 HOH F 2 502 26 HOH HOH . MA 14 HOH F 3 503 27 HOH HOH . MA 14 HOH F 4 504 35 HOH HOH . MA 14 HOH F 5 505 33 HOH HOH . MA 14 HOH F 6 506 24 HOH HOH . MA 14 HOH F 7 507 29 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 . . . HA 13 12.339 -48.324 -91.984 1 218.53 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . HA 13 10.875 -47.956 -91.902 1 198.1 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . HA 13 12.627 -49.394 -90.943 1 221.06 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . HA 13 13.19 -47.113 -91.695 1 231.56 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . HA 13 12.721 -47.698 -95.023 1 217.79 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . HA 13 13.672 -48.132 -96.085 1 209.53 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . HA 13 13.266 -46.422 -94.445 1 227.47 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . HA 13 12.728 -48.996 -93.674 1 205.9 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . HA 13 10.35 -48.121 -96.93 1 207.36 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . HA 13 11.138 -49.278 -97.474 1 197.21 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . HA 13 9.023 -48.635 -96.435 1 180.52 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . HA 13 11.185 -47.44 -95.644 1 217.06 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . HA 13 10.078 -47.013 -98.162 1 214.96 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . HA 13 8.887 -46.879 -98.939 1 211.11 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . HA 13 9.241 -46.083 -100.193 1 214.06 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . HA 13 9.994 -46.979 -101.121 1 210.2 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . HA 13 7.786 -46.229 -100.8 1 211.17 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . HA 13 6.557 -45.017 -101.295 1 86.91 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . HA 13 7.702 -46.845 -101.803 1 207.21 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . HA 13 6.865 -46.55 -102.972 1 209.91 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . HA 13 9.054 -47.26 -102.256 1 205.38 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . HA 13 9.228 -48.619 -102.668 1 190.48 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . HA 13 9.713 -49.524 -101.813 1 184.74 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . HA 13 9.813 -50.715 -102.459 1 177.84 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . HA 13 9.35 -50.47 -103.839 1 178.88 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . HA 13 9.214 -51.256 -104.95 1 172.05 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . HA 13 9.571 -52.678 -104.905 1 161.98 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . HA 13 8.753 -50.718 -106.083 1 171.25 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . HA 13 8.441 -49.429 -106.121 1 178.91 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . HA 13 8.552 -48.629 -105.05 1 188.14 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . HA 13 8.999 -49.098 -103.91 1 186.68 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #