data_4NDG # _model_server_result.job_id CMROq-rAP9bgj5otzYUFgw _model_server_result.datetime_utc '2024-10-19 11:46:44' _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 4ndg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 4NDG # _exptl.entry_id 4NDG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 350.182 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "adenosine-5'-vanadate" _entity.pdbx_number_of_molecules 2 _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 4NDG _cell.length_a 40.276 _cell.length_b 114.58 _cell.length_c 124.658 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NDG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G,H,K,M,N 1 1 B,E,F,I,J,L,O,P 2 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 ? 4 G N N ? 4 I 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 metalc ? metalc1 A NE2 HIS 100 A HIS 260 1_555 G V V5A . A V5A 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc2 A SG CYS 159 A CYS 319 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc3 A SG CYS 162 A CYS 322 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc4 A NE2 HIS 175 A HIS 335 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc5 A NE2 HIS 179 A HIS 339 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc6 G V V5A . A V5A 401 1_555 C OP3 G 1 D G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc7 B NE2 HIS 100 B HIS 260 1_555 I V V5A . B V5A 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc8 B SG CYS 159 B CYS 319 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc9 B SG CYS 162 B CYS 322 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc10 B NE2 HIS 175 B HIS 335 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc11 B NE2 HIS 179 B HIS 339 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc12 I V V5A . B V5A 401 1_555 E OP3 G 1 G G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? hydrog WATSON-CRICK hydrog1 C N3 DT 2 D DT 2 1_555 D N1 DA 9 E DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C O4 DT 2 D DT 2 1_555 D N6 DA 9 E DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C N3 DT 3 D DT 3 1_555 D N1 DA 8 E DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C O4 DT 3 D DT 3 1_555 D N6 DA 8 E DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N1 DA 4 D DA 4 1_555 D N3 DT 7 E DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N6 DA 4 D DA 4 1_555 D O4 DT 7 E DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N3 DT 5 D DT 5 1_555 D N1 DA 6 E DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C O4 DT 5 D DT 5 1_555 D N6 DA 6 E DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N1 DG 6 D DG 6 1_555 D N3 DC 5 E DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N2 DG 6 D DG 6 1_555 D O2 DC 5 E DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C O6 DG 6 D DG 6 1_555 D N4 DC 5 E DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N1 DA 7 D DA 7 1_555 D N3 DT 4 E DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N6 DA 7 D DA 7 1_555 D O4 DT 4 E DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N3 DT 8 D DT 8 1_555 D N1 DA 3 E DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O4 DT 8 D DT 8 1_555 D N6 DA 3 E DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N3 DT 9 D DT 9 1_555 D N1 DA 2 E DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C O4 DT 9 D DT 9 1_555 D N6 DA 2 E DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C N3 DC 10 D DC 10 1_555 D N1 DG 1 E DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N4 DC 10 D DC 10 1_555 D O6 DG 1 E DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C O2 DC 10 D DC 10 1_555 D N2 DG 1 E DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 E N3 DT 2 G DT 2 1_555 F N1 DA 9 H DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 E O4 DT 2 G DT 2 1_555 F N6 DA 9 H DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 E N3 DT 3 G DT 3 1_555 F N1 DA 8 H DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 E O4 DT 3 G DT 3 1_555 F N6 DA 8 H DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 E N1 DA 4 G DA 4 1_555 F N3 DT 7 H DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 E N6 DA 4 G DA 4 1_555 F O4 DT 7 H DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 E N3 DT 5 G DT 5 1_555 F N1 DA 6 H DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 E O4 DT 5 G DT 5 1_555 F N6 DA 6 H DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 E N1 DG 6 G DG 6 1_555 F N3 DC 5 H DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 E N2 DG 6 G DG 6 1_555 F O2 DC 5 H DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 E O6 DG 6 G DG 6 1_555 F N4 DC 5 H DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 E N1 DA 7 G DA 7 1_555 F N3 DT 4 H DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 E N6 DA 7 G DA 7 1_555 F O4 DT 4 H DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 E N3 DT 8 G DT 8 1_555 F N1 DA 3 H DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 E O4 DT 8 G DT 8 1_555 F N6 DA 3 H DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 E N3 DT 9 G DT 9 1_555 F N1 DA 2 H DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 E O4 DT 9 G DT 9 1_555 F N6 DA 2 H DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 E N3 DC 10 G DC 10 1_555 F N1 DG 1 H DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 E N4 DC 10 G DC 10 1_555 F O6 DG 1 H DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 E O2 DC 10 G DC 10 1_555 F N2 DG 1 H DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H13 N5 O6 V' _chem_comp.formula_weight 350.182 _chem_comp.id V5A _chem_comp.mon_nstd_flag . _chem_comp.name "adenosine-5'-vanadate" _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 O2' C2' V5A sing 547 n n O3' C3' V5A sing 548 n n C3' C2' V5A sing 549 n n C3' C4' V5A sing 550 n n C2' C1' V5A sing 551 n n C1' N9 V5A sing 552 n n C1' O4' V5A sing 553 n n C4' O4' V5A sing 554 n n C4' C5' V5A sing 555 n n N9 C8 V5A sing 556 n y N9 C4 V5A sing 557 n y C5' O5' V5A sing 558 n n O5' V V5A sing 559 n n C8 N7 V5A doub 560 n y OV2 V V5A sing 561 n n C4 N3 V5A doub 562 n y C4 C5 V5A sing 563 n y V OV1 V5A doub 564 n n N3 C2 V5A sing 565 n y N7 C5 V5A sing 566 n y C5 C6 V5A doub 567 n y C2 N1 V5A doub 568 n y C6 N1 V5A sing 569 n y C6 N6 V5A sing 570 n n OV2 H1 V5A sing 571 n n C5' H2 V5A sing 572 n n C5' H3 V5A sing 573 n n C4' H4 V5A sing 574 n n C3' H5 V5A sing 575 n n O3' H6 V5A sing 576 n n C2' H7 V5A sing 577 n n O2' H8 V5A sing 578 n n C1' H9 V5A sing 579 n n C8 H10 V5A sing 580 n n C2 H11 V5A sing 581 n n N6 H12 V5A sing 582 n n N6 H13 V5A sing 583 n n # _atom_sites.entry_id 4NDG _atom_sites.fract_transf_matrix[1][1] 0.024829 _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] 0.008728 _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] 0.008022 _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 4 V5A A 1 401 1 V5A V5A . H 5 ZN A 1 402 1 ZN ZN . I 4 V5A B 1 401 1 V5A V5A . J 5 ZN B 1 402 1 ZN ZN . K 6 HOH A 1 501 3 HOH HOH . K 6 HOH A 2 502 4 HOH HOH . K 6 HOH A 3 503 5 HOH HOH . K 6 HOH A 4 504 10 HOH HOH . K 6 HOH A 5 505 15 HOH HOH . K 6 HOH A 6 506 17 HOH HOH . K 6 HOH A 7 507 19 HOH HOH . K 6 HOH A 8 508 21 HOH HOH . K 6 HOH A 9 509 22 HOH HOH . K 6 HOH A 10 510 24 HOH HOH . L 6 HOH B 1 501 1 HOH HOH . L 6 HOH B 2 502 7 HOH HOH . L 6 HOH B 3 503 14 HOH HOH . L 6 HOH B 4 504 18 HOH HOH . L 6 HOH B 5 505 20 HOH HOH . L 6 HOH B 6 506 23 HOH HOH . M 6 HOH D 1 101 11 HOH HOH . M 6 HOH D 2 102 12 HOH HOH . M 6 HOH D 3 103 16 HOH HOH . N 6 HOH E 1 101 13 HOH HOH . O 6 HOH G 1 101 2 HOH HOH . O 6 HOH G 2 102 6 HOH HOH . O 6 HOH G 3 103 9 HOH HOH . P 6 HOH H 1 101 8 HOH HOH . P 6 HOH H 2 102 25 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 O OV2 V5A . . . G 4 2.559 -19.465 -16.051 1 37.62 ? OV2 V5A 401 A 1 HETATM 2 V V V5A . . . G 4 1.002 -19.475 -15.85 1 61.83 ? V V5A 401 A 1 HETATM 3 O OV1 V5A . . . G 4 0.286 -18.351 -15.029 1 38.47 ? OV1 V5A 401 A 1 HETATM 4 O O5' V5A . . . G 4 0.153 -20.783 -16.446 1 54.17 ? O5' V5A 401 A 1 HETATM 5 C C5' V5A . . . G 4 -1.257 -20.581 -16.474 1 44.29 ? C5' V5A 401 A 1 HETATM 6 C C4' V5A . . . G 4 -1.933 -21.665 -17.283 1 48.2 ? C4' V5A 401 A 1 HETATM 7 C C3' V5A . . . G 4 -2.527 -21.228 -18.627 1 48.62 ? C3' V5A 401 A 1 HETATM 8 O O3' V5A . . . G 4 -2.008 -22.061 -19.66 1 51.59 ? O3' V5A 401 A 1 HETATM 9 C C2' V5A . . . G 4 -4.034 -21.482 -18.476 1 53.88 ? C2' V5A 401 A 1 HETATM 10 O O2' V5A . . . G 4 -4.672 -21.917 -19.662 1 61.65 ? O2' V5A 401 A 1 HETATM 11 C C1' V5A . . . G 4 -4.083 -22.547 -17.386 1 43.38 ? C1' V5A 401 A 1 HETATM 12 O O4' V5A . . . G 4 -3.018 -22.243 -16.521 1 47.62 ? O4' V5A 401 A 1 HETATM 13 N N9 V5A . . . G 4 -5.303 -22.53 -16.578 1 45.83 ? N9 V5A 401 A 1 HETATM 14 C C4 V5A . . . G 4 -5.875 -23.601 -15.931 1 47.37 ? C4 V5A 401 A 1 HETATM 15 C C5 V5A . . . G 4 -6.999 -23.092 -15.259 1 46.65 ? C5 V5A 401 A 1 HETATM 16 N N7 V5A . . . G 4 -7.057 -21.763 -15.526 1 47.1 ? N7 V5A 401 A 1 HETATM 17 C C8 V5A . . . G 4 -6.055 -21.429 -16.293 1 46.62 ? C8 V5A 401 A 1 HETATM 18 N N3 V5A . . . G 4 -5.596 -24.9 -15.821 1 48.31 ? N3 V5A 401 A 1 HETATM 19 C C2 V5A . . . G 4 -6.367 -25.698 -15.104 1 46 ? C2 V5A 401 A 1 HETATM 20 N N1 V5A . . . G 4 -7.44 -25.262 -14.46 1 41.65 ? N1 V5A 401 A 1 HETATM 21 C C6 V5A . . . G 4 -7.788 -23.982 -14.506 1 46.36 ? C6 V5A 401 A 1 HETATM 22 N N6 V5A . . . G 4 -8.908 -23.53 -13.836 1 49.16 ? N6 V5A 401 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #