data_3AR2 # _model_server_result.job_id Li-tpAlIBo1gx7h-bGDHnw _model_server_result.datetime_utc '2024-11-24 06:30:46' _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 3ar2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1002}' # _entry.id 3AR2 # _exptl.entry_id 3AR2 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.97 _cell.angle_gamma 90 _cell.entry_id 3AR2 _cell.length_a 161.995 _cell.length_b 75.306 _cell.length_c 151.541 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AR2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 3 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 877 A CYS 876 1_555 A SG CYS 889 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A O VAL 305 A VAL 304 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc2 A O ALA 306 A ALA 305 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc3 A O ILE 308 A ILE 307 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc4 A OE2 GLU 310 A GLU 309 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc5 A OE1 GLU 310 A GLU 309 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.103 ? metalc ? metalc6 A OD1 ASP 352 A ASP 351 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc7 A O THR 354 A THR 353 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc8 A OD1 ASP 704 A ASP 703 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc9 A OD2 ASP 704 A ASP 703 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc10 A O LYS 713 A LYS 712 1_555 F NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc11 A O ALA 715 A ALA 714 1_555 F NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc12 A OD1 ASN 769 A ASN 768 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? metalc ? metalc13 A OE2 GLU 772 A GLU 771 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc14 A OD1 ASN 797 A ASN 796 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc15 A OG1 THR 800 A THR 799 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc16 A OD1 ASP 801 A ASP 800 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc17 A OD2 ASP 801 A ASP 800 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? metalc ? metalc18 A OD2 ASP 801 A ASP 800 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc19 A OE2 GLU 909 A GLU 908 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? metalc ? metalc20 B CA CA . A CA 995 1_555 H O HOH . A HOH 3220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc21 B CA CA . A CA 995 1_555 H O HOH . A HOH 3401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.045 ? metalc ? metalc22 F NA NA . A NA 1000 1_555 H O HOH . A HOH 3101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc23 E CA CA . A CA 1001 1_555 D O3G ACP . A ACP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc24 E CA CA . A CA 1001 1_555 H O HOH . A HOH 3100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc25 E CA CA . A CA 1001 1_555 H O HOH . A HOH 3221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? # _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 7 n n PG O2G ACP sing 8 n n PG O3G ACP sing 9 n n PG C3B ACP sing 10 n n O2G HOG2 ACP sing 11 n n O3G HOG3 ACP sing 12 n n PB O1B ACP doub 13 n n PB O2B ACP sing 14 n n PB C3B ACP sing 15 n n PB O3A ACP sing 16 n n O2B HOB2 ACP sing 17 n n C3B H3B1 ACP sing 18 n n C3B H3B2 ACP sing 19 n n PA O1A ACP doub 20 n n PA O2A ACP sing 21 n n PA O3A ACP sing 22 n n PA O5' ACP sing 23 n n O2A HOA2 ACP sing 24 n n O5' C5' ACP sing 25 n n C5' C4' ACP sing 26 n n C5' "H5'1" ACP sing 27 n n C5' "H5'2" ACP sing 28 n n C4' O4' ACP sing 29 n n C4' C3' ACP sing 30 n n C4' H4' ACP sing 31 n n O4' C1' ACP sing 32 n n C3' O3' ACP sing 33 n n C3' C2' ACP sing 34 n n C3' H3' ACP sing 35 n n O3' HO3' ACP sing 36 n n C2' O2' ACP sing 37 n n C2' C1' ACP sing 38 n n C2' H2' ACP sing 39 n n O2' HO2' ACP sing 40 n n C1' N9 ACP sing 41 n n C1' H1' ACP sing 42 n n N9 C8 ACP sing 43 n y N9 C4 ACP sing 44 n y C8 N7 ACP doub 45 n y C8 H8 ACP sing 46 n n N7 C5 ACP sing 47 n y C5 C6 ACP sing 48 n y C5 C4 ACP doub 49 n y C6 N6 ACP sing 50 n n C6 N1 ACP doub 51 n y N6 HN61 ACP sing 52 n n N6 HN62 ACP sing 53 n n N1 C2 ACP sing 54 n y C2 N3 ACP doub 55 n y C2 H2 ACP sing 56 n n N3 C4 ACP sing 57 n y # _atom_sites.entry_id 3AR2 _atom_sites.fract_transf_matrix[1][1] 0.006173 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002122 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013279 _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] 0.006978 _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 B 2 CA A 1 995 995 CA CA . C 2 CA A 1 996 996 CA CA . D 3 ACP A 1 1002 1002 ACP ACP . E 2 CA A 1 1001 1001 CA CA . F 4 NA A 1 1000 1000 NA NA . G 5 PC1 A 1 1011 1011 PC1 PC1 . H 6 HOH A 1 1021 1021 HOH HOH . H 6 HOH A 2 1023 1023 HOH HOH . H 6 HOH A 3 3100 3100 HOH HOH . H 6 HOH A 4 3101 3101 HOH HOH . H 6 HOH A 5 3102 3102 HOH HOH . H 6 HOH A 6 3103 3103 HOH HOH . H 6 HOH A 7 3104 3104 HOH HOH . H 6 HOH A 8 3105 3105 HOH HOH . H 6 HOH A 9 3106 3106 HOH HOH . H 6 HOH A 10 3107 3107 HOH HOH . H 6 HOH A 11 3110 3110 HOH HOH . H 6 HOH A 12 3111 3111 HOH HOH . H 6 HOH A 13 3201 3201 HOH HOH . H 6 HOH A 14 3202 3202 HOH HOH . H 6 HOH A 15 3204 3204 HOH HOH . H 6 HOH A 16 3205 3205 HOH HOH . H 6 HOH A 17 3206 3206 HOH HOH . H 6 HOH A 18 3207 3207 HOH HOH . H 6 HOH A 19 3208 3208 HOH HOH . H 6 HOH A 20 3209 3209 HOH HOH . H 6 HOH A 21 3210 3210 HOH HOH . H 6 HOH A 22 3212 3212 HOH HOH . H 6 HOH A 23 3213 3213 HOH HOH . H 6 HOH A 24 3214 3214 HOH HOH . H 6 HOH A 25 3218 3218 HOH HOH . H 6 HOH A 26 3219 3219 HOH HOH . H 6 HOH A 27 3220 3220 HOH HOH . H 6 HOH A 28 3221 3221 HOH HOH . H 6 HOH A 29 3301 3301 HOH HOH . H 6 HOH A 30 3302 3302 HOH HOH . H 6 HOH A 31 3303 3303 HOH HOH . H 6 HOH A 32 3304 3304 HOH HOH . H 6 HOH A 33 3305 3305 HOH HOH . H 6 HOH A 34 3306 3306 HOH HOH . H 6 HOH A 35 3307 3307 HOH HOH . H 6 HOH A 36 3308 3308 HOH HOH . H 6 HOH A 37 3309 3309 HOH HOH . H 6 HOH A 38 3310 3310 HOH HOH . H 6 HOH A 39 3401 3401 HOH HOH . H 6 HOH A 40 3404 3404 HOH HOH . H 6 HOH A 41 3405 3405 HOH HOH . H 6 HOH A 42 3500 3500 HOH HOH . H 6 HOH A 43 4001 4001 HOH HOH . H 6 HOH A 44 4002 4002 HOH HOH . H 6 HOH A 45 4003 4003 HOH HOH . H 6 HOH A 46 4004 4004 HOH HOH . H 6 HOH A 47 4500 4500 HOH HOH . H 6 HOH A 48 4501 4501 HOH HOH . H 6 HOH A 49 4503 4503 HOH HOH . H 6 HOH A 50 4504 4504 HOH HOH . H 6 HOH A 51 4506 4506 HOH HOH . H 6 HOH A 52 4507 4507 HOH HOH . H 6 HOH A 53 4508 4508 HOH HOH . H 6 HOH A 54 4511 4511 HOH HOH . H 6 HOH A 55 5000 5000 HOH HOH . H 6 HOH A 56 5001 5001 HOH HOH . H 6 HOH A 57 5004 5004 HOH HOH . H 6 HOH A 58 5005 5005 HOH HOH . H 6 HOH A 59 5006 5006 HOH HOH . H 6 HOH A 60 5007 5007 HOH HOH . H 6 HOH A 61 5008 5008 HOH HOH . H 6 HOH A 62 5011 5011 HOH HOH . H 6 HOH A 63 5012 5012 HOH HOH . H 6 HOH A 64 5014 5014 HOH HOH . H 6 HOH A 65 5016 5016 HOH HOH . H 6 HOH A 66 5019 5019 HOH HOH . H 6 HOH A 67 5021 5021 HOH HOH . H 6 HOH A 68 5023 5023 HOH HOH . H 6 HOH A 69 5024 5024 HOH HOH . H 6 HOH A 70 5026 5026 HOH HOH . H 6 HOH A 71 5028 5028 HOH HOH . H 6 HOH A 72 5029 5029 HOH HOH . H 6 HOH A 73 5030 5030 HOH HOH . H 6 HOH A 74 5032 5032 HOH HOH . H 6 HOH A 75 5033 5033 HOH HOH . H 6 HOH A 76 5035 5035 HOH HOH . H 6 HOH A 77 5036 5036 HOH HOH . H 6 HOH A 78 5037 5037 HOH HOH . H 6 HOH A 79 5038 5038 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 . . . D 3 72.34 30.966 56.128 1 60.74 ? PG ACP 1002 A 1 HETATM 2 O O1G ACP . . . D 3 72.514 32.592 56.137 1 55.33 ? O1G ACP 1002 A 1 HETATM 3 O O2G ACP . . . D 3 70.839 30.699 56.241 1 51.02 ? O2G ACP 1002 A 1 HETATM 4 O O3G ACP . . . D 3 72.987 30.415 54.798 1 48.39 ? O3G ACP 1002 A 1 HETATM 5 P PB ACP . . . D 3 72.89 30.211 59.044 1 56.9 ? PB ACP 1002 A 1 HETATM 6 O O1B ACP . . . D 3 73.051 31.531 59.861 1 61.22 ? O1B ACP 1002 A 1 HETATM 7 O O2B ACP . . . D 3 74.024 29.346 59.522 1 53.95 ? O2B ACP 1002 A 1 HETATM 8 C C3B ACP . . . D 3 73.04 30.181 57.412 1 44.9 ? C3B ACP 1002 A 1 HETATM 9 P PA ACP . . . D 3 70.934 28.214 59.971 1 55.25 ? PA ACP 1002 A 1 HETATM 10 O O1A ACP . . . D 3 69.407 28.098 60.041 1 47.79 ? O1A ACP 1002 A 1 HETATM 11 O O2A ACP . . . D 3 71.816 27.307 59.146 1 46.33 ? O2A ACP 1002 A 1 HETATM 12 O O3A ACP . . . D 3 71.384 29.793 59.555 1 58 ? O3A ACP 1002 A 1 HETATM 13 O O5' ACP . . . D 3 71.337 28.248 61.53 1 54.02 ? O5' ACP 1002 A 1 HETATM 14 C C5' ACP . . . D 3 70.677 29.175 62.402 1 53.07 ? C5' ACP 1002 A 1 HETATM 15 C C4' ACP . . . D 3 71.618 29.649 63.508 1 57.47 ? C4' ACP 1002 A 1 HETATM 16 O O4' ACP . . . D 3 72.252 28.521 64.133 1 54.79 ? O4' ACP 1002 A 1 HETATM 17 C C3' ACP . . . D 3 72.746 30.566 63.043 1 59.88 ? C3' ACP 1002 A 1 HETATM 18 O O3' ACP . . . D 3 72.398 31.964 63.012 1 65.7 ? O3' ACP 1002 A 1 HETATM 19 C C2' ACP . . . D 3 73.859 30.284 64.025 1 60.24 ? C2' ACP 1002 A 1 HETATM 20 O O2' ACP . . . D 3 73.633 31.09 65.169 1 58.79 ? O2' ACP 1002 A 1 HETATM 21 C C1' ACP . . . D 3 73.585 28.875 64.533 1 58.96 ? C1' ACP 1002 A 1 HETATM 22 N N9 ACP . . . D 3 74.496 27.81 64.054 1 55.05 ? N9 ACP 1002 A 1 HETATM 23 C C8 ACP . . . D 3 74.902 27.6 62.791 1 56.68 ? C8 ACP 1002 A 1 HETATM 24 N N7 ACP . . . D 3 75.737 26.539 62.716 1 60.69 ? N7 ACP 1002 A 1 HETATM 25 C C5 ACP . . . D 3 75.857 26.049 63.966 1 56.03 ? C5 ACP 1002 A 1 HETATM 26 C C6 ACP . . . D 3 76.548 24.907 64.609 1 55.91 ? C6 ACP 1002 A 1 HETATM 27 N N6 ACP . . . D 3 77.314 24.077 63.859 1 58.66 ? N6 ACP 1002 A 1 HETATM 28 N N1 ACP . . . D 3 76.416 24.736 65.944 1 54.28 ? N1 ACP 1002 A 1 HETATM 29 C C2 ACP . . . D 3 75.65 25.557 66.693 1 56.89 ? C2 ACP 1002 A 1 HETATM 30 N N3 ACP . . . D 3 74.984 26.61 66.157 1 58.85 ? N3 ACP 1002 A 1 HETATM 31 C C4 ACP . . . D 3 75.038 26.893 64.835 1 55.78 ? C4 ACP 1002 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #