data_2PVF # _model_server_result.job_id Ei_MdGdAZkgvEfm18uXLmw _model_server_result.datetime_utc '2024-12-04 04:58:54' _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 2pvf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":300}' # _entry.id 2PVF # _exptl.entry_id 2PVF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _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 2PVF _cell.length_a 56.353 _cell.length_b 78.436 _cell.length_c 84.839 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PVF _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 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 _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 4 _struct_asym.id E _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 covale ? covale1 A C GLU 141 A GLU 585 1_555 A N PTR 142 A PTR 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C PTR 142 A PTR 586 1_555 A N SER 143 A SER 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C ASP 211 A ASP 655 1_555 A N PTR 212 A PTR 656 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C PTR 212 A PTR 656 1_555 A N PTR 213 A PTR 657 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale5 A C PTR 213 A PTR 657 1_555 A N LYS 214 A LYS 658 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 F O HOH . A HOH 2 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc2 F O HOH . A HOH 111 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 F O HOH . A HOH 112 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc4 F O HOH . A HOH 113 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc5 F O HOH . A HOH 114 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc6 E O2B ACP . A ACP 300 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc7 E O2A ACP . A ACP 300 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc8 E O1B ACP . A ACP 300 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc9 E O2G ACP . A ACP 300 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc10 C MG MG . A MG 301 1_555 A ND2 ASN 187 A ASN 631 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc11 C MG MG . A MG 301 1_555 A OD2 ASP 200 A ASP 644 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc12 C MG MG . A MG 301 1_555 G O HOH . B HOH 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? # _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 2PVF _atom_sites.fract_transf_matrix[1][1] 0.017745 _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] 0.012749 _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] 0.011787 _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 C 3 MG A 1 301 301 MG MG . D 3 MG A 1 302 302 MG MG . E 4 ACP A 1 300 300 ACP PCP . F 5 HOH A 1 2 2 HOH HOH . F 5 HOH A 2 3 3 HOH HOH . F 5 HOH A 3 4 4 HOH HOH . F 5 HOH A 4 5 5 HOH HOH . F 5 HOH A 5 6 6 HOH HOH . F 5 HOH A 6 7 7 HOH HOH . F 5 HOH A 7 8 8 HOH HOH . F 5 HOH A 8 9 9 HOH HOH . F 5 HOH A 9 10 10 HOH HOH . F 5 HOH A 10 11 11 HOH HOH . F 5 HOH A 11 12 12 HOH HOH . F 5 HOH A 12 13 13 HOH HOH . F 5 HOH A 13 14 14 HOH HOH . F 5 HOH A 14 15 15 HOH HOH . F 5 HOH A 15 16 16 HOH HOH . F 5 HOH A 16 17 17 HOH HOH . F 5 HOH A 17 18 18 HOH HOH . F 5 HOH A 18 19 19 HOH HOH . F 5 HOH A 19 20 20 HOH HOH . F 5 HOH A 20 21 21 HOH HOH . F 5 HOH A 21 22 22 HOH HOH . F 5 HOH A 22 23 23 HOH HOH . F 5 HOH A 23 24 24 HOH HOH . F 5 HOH A 24 25 25 HOH HOH . F 5 HOH A 25 26 26 HOH HOH . F 5 HOH A 26 27 27 HOH HOH . F 5 HOH A 27 28 28 HOH HOH . F 5 HOH A 28 29 29 HOH HOH . F 5 HOH A 29 30 30 HOH HOH . F 5 HOH A 30 31 31 HOH HOH . F 5 HOH A 31 32 32 HOH HOH . F 5 HOH A 32 33 33 HOH HOH . F 5 HOH A 33 34 34 HOH HOH . F 5 HOH A 34 35 35 HOH HOH . F 5 HOH A 35 36 36 HOH HOH . F 5 HOH A 36 37 37 HOH HOH . F 5 HOH A 37 38 38 HOH HOH . F 5 HOH A 38 39 39 HOH HOH . F 5 HOH A 39 40 40 HOH HOH . F 5 HOH A 40 41 41 HOH HOH . F 5 HOH A 41 42 42 HOH HOH . F 5 HOH A 42 43 43 HOH HOH . F 5 HOH A 43 44 44 HOH HOH . F 5 HOH A 44 45 45 HOH HOH . F 5 HOH A 45 46 46 HOH HOH . F 5 HOH A 46 47 47 HOH HOH . F 5 HOH A 47 48 48 HOH HOH . F 5 HOH A 48 49 49 HOH HOH . F 5 HOH A 49 50 50 HOH HOH . F 5 HOH A 50 51 51 HOH HOH . F 5 HOH A 51 52 52 HOH HOH . F 5 HOH A 52 53 53 HOH HOH . F 5 HOH A 53 54 54 HOH HOH . F 5 HOH A 54 55 55 HOH HOH . F 5 HOH A 55 56 56 HOH HOH . F 5 HOH A 56 57 57 HOH HOH . F 5 HOH A 57 58 58 HOH HOH . F 5 HOH A 58 59 59 HOH HOH . F 5 HOH A 59 60 60 HOH HOH . F 5 HOH A 60 61 61 HOH HOH . F 5 HOH A 61 62 62 HOH HOH . F 5 HOH A 62 63 63 HOH HOH . F 5 HOH A 63 64 64 HOH HOH . F 5 HOH A 64 65 65 HOH HOH . F 5 HOH A 65 66 66 HOH HOH . F 5 HOH A 66 67 67 HOH HOH . F 5 HOH A 67 68 68 HOH HOH . F 5 HOH A 68 69 69 HOH HOH . F 5 HOH A 69 70 70 HOH HOH . F 5 HOH A 70 71 71 HOH HOH . F 5 HOH A 71 72 72 HOH HOH . F 5 HOH A 72 73 73 HOH HOH . F 5 HOH A 73 74 74 HOH HOH . F 5 HOH A 74 75 75 HOH HOH . F 5 HOH A 75 76 76 HOH HOH . F 5 HOH A 76 77 77 HOH HOH . F 5 HOH A 77 78 78 HOH HOH . F 5 HOH A 78 79 79 HOH HOH . F 5 HOH A 79 80 80 HOH HOH . F 5 HOH A 80 81 81 HOH HOH . F 5 HOH A 81 82 82 HOH HOH . F 5 HOH A 82 83 83 HOH HOH . F 5 HOH A 83 84 84 HOH HOH . F 5 HOH A 84 85 85 HOH HOH . F 5 HOH A 85 86 86 HOH HOH . F 5 HOH A 86 87 87 HOH HOH . F 5 HOH A 87 88 88 HOH HOH . F 5 HOH A 88 89 89 HOH HOH . F 5 HOH A 89 90 90 HOH HOH . F 5 HOH A 90 91 91 HOH HOH . F 5 HOH A 91 92 92 HOH HOH . F 5 HOH A 92 93 93 HOH HOH . F 5 HOH A 93 94 94 HOH HOH . F 5 HOH A 94 95 95 HOH HOH . F 5 HOH A 95 96 96 HOH HOH . F 5 HOH A 96 97 97 HOH HOH . F 5 HOH A 97 98 98 HOH HOH . F 5 HOH A 98 99 99 HOH HOH . F 5 HOH A 99 100 100 HOH HOH . F 5 HOH A 100 101 101 HOH HOH . F 5 HOH A 101 102 102 HOH HOH . F 5 HOH A 102 103 103 HOH HOH . F 5 HOH A 103 104 104 HOH HOH . F 5 HOH A 104 105 105 HOH HOH . F 5 HOH A 105 106 106 HOH HOH . F 5 HOH A 106 107 107 HOH HOH . F 5 HOH A 107 108 108 HOH HOH . F 5 HOH A 108 109 109 HOH HOH . F 5 HOH A 109 110 110 HOH HOH . F 5 HOH A 110 111 111 HOH HOH . F 5 HOH A 111 112 112 HOH HOH . F 5 HOH A 112 113 113 HOH HOH . F 5 HOH A 113 114 114 HOH HOH . F 5 HOH A 114 115 115 HOH HOH . F 5 HOH A 115 116 116 HOH HOH . F 5 HOH A 116 117 117 HOH HOH . F 5 HOH A 117 119 119 HOH HOH . G 5 HOH B 1 1 1 HOH HOH . G 5 HOH B 2 118 118 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 . . . E 4 20.826 -4.739 -8.724 1 29.65 ? PG ACP 300 A 1 HETATM 2 O O1G ACP . . . E 4 21.444 -5.737 -9.634 1 31.3 ? O1G ACP 300 A 1 HETATM 3 O O2G ACP . . . E 4 21.096 -3.381 -9.18 1 29.6 ? O2G ACP 300 A 1 HETATM 4 O O3G ACP . . . E 4 19.425 -4.952 -8.354 1 30.67 ? O3G ACP 300 A 1 HETATM 5 P PB ACP . . . E 4 21.902 -3.886 -6.002 1 26.99 ? PB ACP 300 A 1 HETATM 6 O O1B ACP . . . E 4 22.823 -2.919 -6.517 1 27.14 ? O1B ACP 300 A 1 HETATM 7 O O2B ACP . . . E 4 20.545 -3.519 -5.609 1 26.41 ? O2B ACP 300 A 1 HETATM 8 C C3B ACP . . . E 4 21.645 -5.007 -7.252 1 28.92 ? C3B ACP 300 A 1 HETATM 9 P PA ACP . . . E 4 23.029 -4.046 -3.434 1 27.14 ? PA ACP 300 A 1 HETATM 10 O O1A ACP . . . E 4 24.464 -3.641 -3.402 1 28.02 ? O1A ACP 300 A 1 HETATM 11 O O2A ACP . . . E 4 22.04 -3.127 -2.841 1 27.45 ? O2A ACP 300 A 1 HETATM 12 O O3A ACP . . . E 4 22.622 -4.54 -4.825 1 27.26 ? O3A ACP 300 A 1 HETATM 13 O O5' ACP . . . E 4 22.902 -5.404 -2.583 1 27.49 ? O5' ACP 300 A 1 HETATM 14 C C5' ACP . . . E 4 21.779 -6.266 -2.78 1 27.33 ? C5' ACP 300 A 1 HETATM 15 C C4' ACP . . . E 4 21.537 -7.144 -1.575 1 27.83 ? C4' ACP 300 A 1 HETATM 16 O O4' ACP . . . E 4 22.695 -8.005 -1.366 1 27.82 ? O4' ACP 300 A 1 HETATM 17 C C3' ACP . . . E 4 21.368 -6.408 -0.253 1 27.92 ? C3' ACP 300 A 1 HETATM 18 O O3' ACP . . . E 4 20.027 -5.962 -0.071 1 27.81 ? O3' ACP 300 A 1 HETATM 19 C C2' ACP . . . E 4 21.773 -7.479 0.752 1 28.07 ? C2' ACP 300 A 1 HETATM 20 O O2' ACP . . . E 4 20.762 -8.442 0.989 1 28.86 ? O2' ACP 300 A 1 HETATM 21 C C1' ACP . . . E 4 22.951 -8.132 0.024 1 27.19 ? C1' ACP 300 A 1 HETATM 22 N N9 ACP . . . E 4 24.213 -7.451 0.317 1 26.27 ? N9 ACP 300 A 1 HETATM 23 C C8 ACP . . . E 4 24.825 -6.465 -0.42 1 26.01 ? C8 ACP 300 A 1 HETATM 24 N N7 ACP . . . E 4 25.93 -6.012 0.115 1 25.92 ? N7 ACP 300 A 1 HETATM 25 C C5 ACP . . . E 4 26.064 -6.757 1.277 1 25.61 ? C5 ACP 300 A 1 HETATM 26 C C6 ACP . . . E 4 27.036 -6.75 2.291 1 25.41 ? C6 ACP 300 A 1 HETATM 27 N N6 ACP . . . E 4 28.084 -5.928 2.3 1 24.84 ? N6 ACP 300 A 1 HETATM 28 N N1 ACP . . . E 4 26.886 -7.625 3.309 1 25.62 ? N1 ACP 300 A 1 HETATM 29 C C2 ACP . . . E 4 25.822 -8.438 3.303 1 25.89 ? C2 ACP 300 A 1 HETATM 30 N N3 ACP . . . E 4 24.835 -8.53 2.41 1 25.8 ? N3 ACP 300 A 1 HETATM 31 C C4 ACP . . . E 4 25.02 -7.653 1.41 1 25.86 ? C4 ACP 300 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #