data_3DVL # _model_server_result.job_id 66ktjYdSjuUDkRzFt4ZmgQ _model_server_result.datetime_utc '2024-11-27 14:07:44' _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 3dvl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":903}' # _entry.id 3DVL # _exptl.entry_id 3DVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 12 _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 3DVL _cell.length_a 132.873 _cell.length_b 135.576 _cell.length_c 204.951 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DVL _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 PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 I N N ? 3 K N N ? 3 L N N ? 3 N N N ? 3 O N N ? 3 Q N N ? 3 R N N ? 3 T N N ? 3 U N N ? 3 W N N ? 3 X N 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 ILE 430 A ILE 430 1_555 A N SEP 431 A SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C SEP 431 A SEP 431 1_555 A N TPO 432 A TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale3 A C TPO 432 A TPO 432 1_555 A N ILE 433 A ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 B C ILE 430 B ILE 430 1_555 B N SEP 431 B SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale5 B C SEP 431 B SEP 431 1_555 B N TPO 432 B TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 B C TPO 432 B TPO 432 1_555 B N ILE 433 B ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale7 C C ILE 430 C ILE 430 1_555 C N SEP 431 C SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale8 C C SEP 431 C SEP 431 1_555 C N TPO 432 C TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 C C TPO 432 C TPO 432 1_555 C N ILE 433 C ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 D C ILE 430 D ILE 430 1_555 D N SEP 431 D SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale11 D C SEP 431 D SEP 431 1_555 D N TPO 432 D TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale12 D C TPO 432 D TPO 432 1_555 D N ILE 433 D ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale13 E C ILE 430 E ILE 430 1_555 E N SEP 431 E SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale14 E C SEP 431 E SEP 431 1_555 E N TPO 432 E TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 E C TPO 432 E TPO 432 1_555 E N ILE 433 E ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale16 F C ILE 430 F ILE 430 1_555 F N SEP 431 F SEP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale17 F C SEP 431 F SEP 431 1_555 F N TPO 432 F TPO 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale18 F C TPO 432 F TPO 432 1_555 F N ILE 433 F ILE 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.245 ? metalc ? metalc1 B OE1 GLU 318 B GLU 318 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc2 C OG1 THR 295 C THR 295 1_555 M MG MG . C MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc3 D OG1 THR 295 D THR 295 1_555 P MG MG . D MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc4 E OG1 THR 295 E THR 295 1_555 S MG MG . E MG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 3DVL _atom_sites.fract_transf_matrix[1][1] 0.007526 _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] 0.007376 _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] 0.004879 _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 2 MG A 1 801 801 MG MG . H 3 ATP A 1 901 901 ATP ATP . I 3 ATP A 1 903 903 ATP ATP . J 2 MG B 1 802 802 MG MG . K 3 ATP B 1 901 901 ATP ATP . L 3 ATP B 1 903 903 ATP ATP . M 2 MG C 1 803 803 MG MG . N 3 ATP C 1 901 901 ATP ATP . O 3 ATP C 1 903 903 ATP ATP . P 2 MG D 1 804 804 MG MG . Q 3 ATP D 1 901 901 ATP ATP . R 3 ATP D 1 903 903 ATP ATP . S 2 MG E 1 805 805 MG MG . T 3 ATP E 1 901 901 ATP ATP . U 3 ATP E 1 903 903 ATP ATP . V 2 MG F 1 806 806 MG MG . W 3 ATP F 1 901 901 ATP ATP . X 3 ATP F 1 903 903 ATP ATP . Y 4 HOH A 1 520 4 HOH HOH . Y 4 HOH A 2 521 8 HOH HOH . Y 4 HOH A 3 522 11 HOH HOH . Y 4 HOH A 4 523 23 HOH HOH . Y 4 HOH A 5 524 30 HOH HOH . Y 4 HOH A 6 525 45 HOH HOH . Y 4 HOH A 7 526 63 HOH HOH . Z 4 HOH B 1 520 17 HOH HOH . Z 4 HOH B 2 521 21 HOH HOH . Z 4 HOH B 3 522 37 HOH HOH . Z 4 HOH B 4 523 38 HOH HOH . Z 4 HOH B 5 524 61 HOH HOH . AA 4 HOH C 1 520 16 HOH HOH . AA 4 HOH C 2 521 18 HOH HOH . AA 4 HOH C 3 522 32 HOH HOH . AA 4 HOH C 4 523 39 HOH HOH . AA 4 HOH C 5 524 43 HOH HOH . AA 4 HOH C 6 525 44 HOH HOH . AA 4 HOH C 7 526 46 HOH HOH . BA 4 HOH D 1 520 5 HOH HOH . BA 4 HOH D 2 521 7 HOH HOH . BA 4 HOH D 3 522 10 HOH HOH . BA 4 HOH D 4 523 12 HOH HOH . BA 4 HOH D 5 524 24 HOH HOH . BA 4 HOH D 6 525 29 HOH HOH . BA 4 HOH D 7 526 53 HOH HOH . BA 4 HOH D 8 527 57 HOH HOH . BA 4 HOH D 9 528 60 HOH HOH . BA 4 HOH D 10 529 64 HOH HOH . BA 4 HOH D 11 530 65 HOH HOH . BA 4 HOH D 12 531 72 HOH HOH . CA 4 HOH E 1 520 2 HOH HOH . CA 4 HOH E 2 521 3 HOH HOH . CA 4 HOH E 3 522 9 HOH HOH . CA 4 HOH E 4 523 19 HOH HOH . CA 4 HOH E 5 524 20 HOH HOH . CA 4 HOH E 6 525 36 HOH HOH . CA 4 HOH E 7 526 41 HOH HOH . CA 4 HOH E 8 527 51 HOH HOH . CA 4 HOH E 9 528 69 HOH HOH . CA 4 HOH E 10 529 73 HOH HOH . DA 4 HOH F 1 520 1 HOH HOH . DA 4 HOH F 2 521 6 HOH HOH . DA 4 HOH F 3 522 13 HOH HOH . DA 4 HOH F 4 523 14 HOH HOH . DA 4 HOH F 5 524 15 HOH HOH . DA 4 HOH F 6 525 22 HOH HOH . DA 4 HOH F 7 526 27 HOH HOH . DA 4 HOH F 8 527 31 HOH HOH . DA 4 HOH F 9 528 33 HOH HOH . DA 4 HOH F 10 529 35 HOH HOH . DA 4 HOH F 11 530 48 HOH HOH . DA 4 HOH F 12 531 49 HOH HOH . DA 4 HOH F 13 532 52 HOH HOH . DA 4 HOH F 14 533 54 HOH HOH . DA 4 HOH F 15 534 56 HOH HOH . DA 4 HOH F 16 535 58 HOH HOH . DA 4 HOH F 17 536 59 HOH HOH . DA 4 HOH F 18 537 62 HOH HOH . DA 4 HOH F 19 538 66 HOH HOH . DA 4 HOH F 20 539 67 HOH HOH . DA 4 HOH F 21 540 68 HOH HOH . DA 4 HOH F 22 541 70 HOH HOH . DA 4 HOH F 23 542 71 HOH HOH . DA 4 HOH F 24 543 74 HOH HOH . DA 4 HOH F 25 544 78 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 ATP . . . X 3 97.383 80.135 62.817 1 79.64 ? PG ATP 903 F 1 HETATM 2 O O1G ATP . . . X 3 97.756 78.723 62.474 1 66.9 ? O1G ATP 903 F 1 HETATM 3 O O2G ATP . . . X 3 96.937 80.452 64.287 1 76.24 ? O2G ATP 903 F 1 HETATM 4 O O3G ATP . . . X 3 98.549 81.012 62.416 1 78.01 ? O3G ATP 903 F 1 HETATM 5 P PB ATP . . . X 3 95.992 81.633 60.899 1 54.78 ? PB ATP 903 F 1 HETATM 6 O O1B ATP . . . X 3 94.715 81.386 60.35 1 57.02 ? O1B ATP 903 F 1 HETATM 7 O O2B ATP . . . X 3 97.02 81.707 59.854 1 67.44 ? O2B ATP 903 F 1 HETATM 8 O O3B ATP . . . X 3 96.153 80.51 61.913 1 67.05 ? O3B ATP 903 F 1 HETATM 9 P PA ATP . . . X 3 96.262 84.451 61.383 1 50.78 ? PA ATP 903 F 1 HETATM 10 O O1A ATP . . . X 3 95.082 85.222 61.061 1 55.07 ? O1A ATP 903 F 1 HETATM 11 O O2A ATP . . . X 3 96.952 84.881 62.623 1 53.28 ? O2A ATP 903 F 1 HETATM 12 O O3A ATP . . . X 3 95.738 82.97 61.585 1 55.26 ? O3A ATP 903 F 1 HETATM 13 O O5' ATP . . . X 3 97.193 84.725 60.182 1 42.34 ? O5' ATP 903 F 1 HETATM 14 C C5' ATP . . . X 3 97.866 85.998 60.2 1 53.93 ? C5' ATP 903 F 1 HETATM 15 C C4' ATP . . . X 3 98.596 86.295 58.897 1 56.41 ? C4' ATP 903 F 1 HETATM 16 O O4' ATP . . . X 3 98.248 87.536 58.333 1 45.12 ? O4' ATP 903 F 1 HETATM 17 C C3' ATP . . . X 3 100.129 86.263 58.968 1 55.07 ? C3' ATP 903 F 1 HETATM 18 O O3' ATP . . . X 3 100.535 84.988 58.531 1 57.91 ? O3' ATP 903 F 1 HETATM 19 C C2' ATP . . . X 3 100.594 87.34 58.05 1 51.25 ? C2' ATP 903 F 1 HETATM 20 O O2' ATP . . . X 3 101.032 86.911 56.786 1 58.57 ? O2' ATP 903 F 1 HETATM 21 C C1' ATP . . . X 3 99.404 88.217 57.891 1 49.39 ? C1' ATP 903 F 1 HETATM 22 N N9 ATP . . . X 3 99.362 89.538 58.491 1 50.15 ? N9 ATP 903 F 1 HETATM 23 C C8 ATP . . . X 3 99.281 89.827 59.819 1 53.8 ? C8 ATP 903 F 1 HETATM 24 N N7 ATP . . . X 3 99.279 91.138 59.938 1 51.26 ? N7 ATP 903 F 1 HETATM 25 C C5 ATP . . . X 3 99.351 91.734 58.725 1 50.75 ? C5 ATP 903 F 1 HETATM 26 C C6 ATP . . . X 3 99.379 93.04 58.207 1 52.79 ? C6 ATP 903 F 1 HETATM 27 N N6 ATP . . . X 3 99.29 94.116 58.873 1 48.1 ? N6 ATP 903 F 1 HETATM 28 N N1 ATP . . . X 3 99.454 93.242 56.857 1 52.6 ? N1 ATP 903 F 1 HETATM 29 C C2 ATP . . . X 3 99.514 92.164 55.989 1 55.66 ? C2 ATP 903 F 1 HETATM 30 N N3 ATP . . . X 3 99.491 90.864 56.47 1 58.91 ? N3 ATP 903 F 1 HETATM 31 C C4 ATP . . . X 3 99.413 90.671 57.808 1 51.24 ? C4 ATP 903 F 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 51 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #