data_5ZXH # _model_server_result.job_id f116S2u9loYIFB9SmlFE0Q _model_server_result.datetime_utc '2024-10-19 09:22:02' _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 5zxh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":401}' # _entry.id 5ZXH # _exptl.entry_id 5ZXH _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 5ZXH _cell.length_a 104.91 _cell.length_b 157.06 _cell.length_c 182.838 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZXH _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc10 H MG MG . A MG 502 1_555 W O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc11 H MG MG . A MG 502 1_555 W O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.833 ? metalc ? metalc12 H MG MG . A MG 502 1_555 W O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc13 H MG MG . A MG 502 1_555 X O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc15 B OE1 GLU 111 B GLU 111 1_555 M CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc16 B OD2 ASP 177 B ASP 177 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc17 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc18 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc19 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc20 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc21 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc22 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc23 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc24 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc25 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc26 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc27 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc28 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc29 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc30 S O1G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc31 S O2G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? # _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 49 n n PG O2G ACP sing 50 n n PG O3G ACP sing 51 n n PG C3B ACP sing 52 n n O2G HOG2 ACP sing 53 n n O3G HOG3 ACP sing 54 n n PB O1B ACP doub 55 n n PB O2B ACP sing 56 n n PB C3B ACP sing 57 n n PB O3A ACP sing 58 n n O2B HOB2 ACP sing 59 n n C3B H3B1 ACP sing 60 n n C3B H3B2 ACP sing 61 n n PA O1A ACP doub 62 n n PA O2A ACP sing 63 n n PA O3A ACP sing 64 n n PA O5' ACP sing 65 n n O2A HOA2 ACP sing 66 n n O5' C5' ACP sing 67 n n C5' C4' ACP sing 68 n n C5' "H5'1" ACP sing 69 n n C5' "H5'2" ACP sing 70 n n C4' O4' ACP sing 71 n n C4' C3' ACP sing 72 n n C4' H4' ACP sing 73 n n O4' C1' ACP sing 74 n n C3' O3' ACP sing 75 n n C3' C2' ACP sing 76 n n C3' H3' ACP sing 77 n n O3' HO3' ACP sing 78 n n C2' O2' ACP sing 79 n n C2' C1' ACP sing 80 n n C2' H2' ACP sing 81 n n O2' HO2' ACP sing 82 n n C1' N9 ACP sing 83 n n C1' H1' ACP sing 84 n n N9 C8 ACP sing 85 n y N9 C4 ACP sing 86 n y C8 N7 ACP doub 87 n y C8 H8 ACP sing 88 n n N7 C5 ACP sing 89 n y C5 C6 ACP sing 90 n y C5 C4 ACP doub 91 n y C6 N6 ACP sing 92 n n C6 N1 ACP doub 93 n y N6 HN61 ACP sing 94 n n N6 HN62 ACP sing 95 n n N1 C2 ACP sing 96 n y C2 N3 ACP doub 97 n y C2 H2 ACP sing 98 n n N3 C4 ACP sing 99 n y # _atom_sites.entry_id 5ZXH _atom_sites.fract_transf_matrix[1][1] 0.009532 _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] 0.006367 _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] 0.005469 _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 9LX B 1 506 1 9LX LZP . 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 9LX D 1 503 2 9LX LZP . V 11 ACP F 1 401 401 ACP ACP . W 12 HOH A 1 601 7 HOH HOH . W 12 HOH A 2 602 4 HOH HOH . W 12 HOH A 3 603 8 HOH HOH . W 12 HOH A 4 604 2 HOH HOH . W 12 HOH A 5 605 5 HOH HOH . W 12 HOH A 6 606 1 HOH HOH . W 12 HOH A 7 607 10 HOH HOH . X 12 HOH B 1 601 3 HOH HOH . X 12 HOH B 2 602 9 HOH HOH . X 12 HOH B 3 603 11 HOH HOH . X 12 HOH B 4 604 6 HOH HOH . Y 12 HOH C 1 601 15 HOH HOH . Y 12 HOH C 2 602 13 HOH HOH . Y 12 HOH C 3 603 14 HOH HOH . Y 12 HOH C 4 604 12 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 . . . V 11 -8.16 -49.968 94.053 1 142.5 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . V 11 -9.172 -48.952 93.314 1 136.62 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . V 11 -8.254 -51.31 93.423 1 139.29 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . V 11 -6.64 -49.44 93.926 1 135.98 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . V 11 -10.199 -49.385 96.229 1 125.54 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . V 11 -11.152 -49.583 95.109 1 120.62 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . V 11 -10.014 -47.806 96.475 1 123.19 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . V 11 -8.564 -50.082 95.82 1 130.34 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . V 11 -10.124 -50.735 98.796 1 107.19 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . V 11 -8.635 -50.885 98.541 1 108.27 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . V 11 -10.948 -51.954 99.147 1 97.7 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . V 11 -10.874 -50.023 97.552 1 112.12 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . V 11 -10.299 -49.696 100.029 1 102.54 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . V 11 -9.681 -48.401 100.054 1 97.45 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . V 11 -8.824 -48.134 101.302 1 90.17 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . V 11 -9.436 -48.689 102.465 1 83.82 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . V 11 -7.407 -48.707 101.214 1 86.23 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . V 11 -6.438 -47.655 101.18 1 89.61 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . V 11 -7.225 -49.584 102.436 1 82.72 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . V 11 -6.043 -49.254 103.172 1 81.85 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . V 11 -8.475 -49.365 103.273 1 80.68 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . V 11 -9.037 -50.656 103.718 1 78.55 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . V 11 -9.971 -51.379 103.082 1 76.97 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . V 11 -10.253 -52.511 103.771 1 81.36 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . V 11 -9.489 -52.518 104.875 1 82.25 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . V 11 -9.287 -53.415 106.039 1 84.22 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . V 11 -9.989 -54.565 106.148 1 82.98 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . V 11 -8.38 -53.039 106.977 1 86.93 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . V 11 -7.67 -51.889 106.872 1 85.2 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . V 11 -7.809 -51.035 105.839 1 84.13 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . V 11 -8.686 -51.287 104.832 1 81.81 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #