data_6LVX # _model_server_result.job_id 2nxVaDnUlakFKO-yugBRkg _model_server_result.datetime_utc '2024-11-25 00:51:06' _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 6lvx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 6LVX # _exptl.entry_id 6LVX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 313.354 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-azanyl-2-butoxy-9-(phenylmethyl)-7H-purin-8-one _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 6LVX _cell.length_a 98.754 _cell.length_b 138.504 _cell.length_c 148.462 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LVX _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 D N N ? 3 P N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG D 905 NAG 2 n C NAG 2 C 2 NAG D 909 NAG # 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 14 A CYS 36 1_555 A SG CYS 29 A CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 76 A CYS 98 1_555 A SG CYS 453 A CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 78 A CYS 100 1_555 A SG CYS 90 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 A SG CYS 161 A CYS 183 1_555 A SG CYS 167 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf5 A SG CYS 238 A CYS 260 1_555 A SG CYS 251 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 241 A CYS 263 1_555 A SG CYS 248 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf7 A SG CYS 469 A CYS 491 1_555 A SG CYS 499 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 A SG CYS 765 A CYS 787 1_555 A SG CYS 792 A CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? disulf ? disulf9 A SG CYS 767 A CYS 789 1_555 A SG CYS 811 A CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf10 B SG CYS 14 B CYS 36 1_555 B SG CYS 29 B CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf11 B SG CYS 76 B CYS 98 1_555 B SG CYS 453 B CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 B SG CYS 78 B CYS 100 1_555 B SG CYS 90 B CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 B SG CYS 161 B CYS 183 1_555 B SG CYS 167 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf14 B SG CYS 238 B CYS 260 1_555 B SG CYS 251 B CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf15 B SG CYS 241 B CYS 263 1_555 B SG CYS 248 B CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf16 B SG CYS 469 B CYS 491 1_555 B SG CYS 499 B CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf17 B SG CYS 765 B CYS 787 1_555 B SG CYS 792 B CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf18 B SG CYS 767 B CYS 789 1_555 B SG CYS 811 B CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? covale ? covale1 A ND2 ASN 47 A ASN 69 1_555 H C1 NAG . A NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale2 A ND2 ASN 193 A ASN 215 1_555 E C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale3 A ND2 ASN 391 A ASN 413 1_555 G C1 NAG . A NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale4 A ND2 ASN 501 A ASN 523 1_555 F C1 NAG . A NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 A ND2 ASN 568 A ASN 590 1_555 K C1 NAG . A NAG 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 A ND2 ASN 657 A ASN 679 1_555 J C1 NAG . A NAG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale7 A ND2 ASN 698 A ASN 720 1_555 I C1 NAG . A NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale8 B ND2 ASN 47 B ASN 69 1_555 R C1 NAG . B NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale9 B ND2 ASN 193 B ASN 215 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale10 B ND2 ASN 501 B ASN 523 1_555 Q C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale11 B ND2 ASN 512 B ASN 534 1_555 S C1 NAG . B NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale12 B ND2 ASN 568 B ASN 590 1_555 T C1 NAG . B NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale13 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? # _chem_comp.formula 'C16 H19 N5 O2' _chem_comp.formula_weight 313.354 _chem_comp.id EWL _chem_comp.mon_nstd_flag . _chem_comp.name 6-azanyl-2-butoxy-9-(phenylmethyl)-7H-purin-8-one _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 O1 C5 EWL sing 83 n n O1 C3 EWL sing 84 n n C5 C6 EWL sing 85 n n N1 C3 EWL doub 86 n y N1 C2 EWL sing 87 n y C3 N EWL sing 88 n y C15 C13 EWL doub 89 n y C15 C14 EWL sing 90 n y C13 C12 EWL sing 91 n y C7 C6 EWL sing 92 n n C7 C8 EWL sing 93 n n N4 C2 EWL sing 94 n n C2 C EWL doub 95 n y N C1 EWL doub 96 n y C14 C10 EWL doub 97 n y C12 C11 EWL doub 98 n y C C1 EWL sing 99 n y C N2 EWL sing 100 n n C1 N3 EWL sing 101 n n C10 C11 EWL sing 102 n y C10 C9 EWL sing 103 n n N2 C4 EWL sing 104 n n N3 C9 EWL sing 105 n n N3 C4 EWL sing 106 n n C4 O EWL doub 107 n n C9 H1 EWL sing 108 n n C9 H2 EWL sing 109 n n C11 H3 EWL sing 110 n n C12 H4 EWL sing 111 n n C13 H5 EWL sing 112 n n C15 H6 EWL sing 113 n n C14 H7 EWL sing 114 n n N4 H8 EWL sing 115 n n N4 H9 EWL sing 116 n n N2 H10 EWL sing 117 n n C5 H11 EWL sing 118 n n C5 H12 EWL sing 119 n n C6 H13 EWL sing 120 n n C6 H14 EWL sing 121 n n C7 H15 EWL sing 122 n n C7 H16 EWL sing 123 n n C8 H17 EWL sing 124 n n C8 H18 EWL sing 125 n n C8 H19 EWL sing 126 n n # _atom_sites.entry_id 6LVX _atom_sites.fract_transf_matrix[1][1] 0.010126 _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] 0.00722 _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] 0.006736 _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 D 3 EWL A 1 1001 1 EWL sdf . E 4 NAG A 1 1002 903 NAG NAG . F 4 NAG A 1 1003 904 NAG NAG . G 4 NAG A 1 1004 907 NAG NAG . H 4 NAG A 1 1005 910 NAG NAG . I 4 NAG A 1 1006 911 NAG NAG . J 4 NAG A 1 1007 914 NAG NAG . K 4 NAG A 1 1008 915 NAG NAG . L 5 SO4 A 1 1009 1 SO4 SO4 . M 5 SO4 A 1 1010 1 SO4 SO4 . N 5 SO4 A 1 1011 1 SO4 SO4 . O 5 SO4 A 1 1012 1 SO4 SO4 . P 3 EWL B 1 1001 2 EWL sdf . Q 4 NAG B 1 1002 906 NAG NAG . R 4 NAG B 1 1003 908 NAG NAG . S 4 NAG B 1 1004 912 NAG NAG . T 4 NAG B 1 1005 913 NAG NAG . U 5 SO4 B 1 1006 1 SO4 SO4 . V 5 SO4 B 1 1007 1 SO4 SO4 . W 6 HOH A 1 1101 29 HOH HOH . W 6 HOH A 2 1102 32 HOH HOH . W 6 HOH A 3 1103 24 HOH HOH . W 6 HOH A 4 1104 23 HOH HOH . W 6 HOH A 5 1105 12 HOH HOH . W 6 HOH A 6 1106 41 HOH HOH . W 6 HOH A 7 1107 17 HOH HOH . W 6 HOH A 8 1108 34 HOH HOH . W 6 HOH A 9 1109 22 HOH HOH . W 6 HOH A 10 1110 14 HOH HOH . W 6 HOH A 11 1111 31 HOH HOH . W 6 HOH A 12 1112 26 HOH HOH . W 6 HOH A 13 1113 9 HOH HOH . W 6 HOH A 14 1114 6 HOH HOH . W 6 HOH A 15 1115 21 HOH HOH . W 6 HOH A 16 1116 46 HOH HOH . W 6 HOH A 17 1117 1 HOH HOH . W 6 HOH A 18 1118 27 HOH HOH . W 6 HOH A 19 1119 7 HOH HOH . W 6 HOH A 20 1120 10 HOH HOH . W 6 HOH A 21 1121 8 HOH HOH . W 6 HOH A 22 1122 28 HOH HOH . W 6 HOH A 23 1123 13 HOH HOH . W 6 HOH A 24 1124 2 HOH HOH . W 6 HOH A 25 1125 43 HOH HOH . W 6 HOH A 26 1126 39 HOH HOH . W 6 HOH A 27 1127 30 HOH HOH . W 6 HOH A 28 1128 33 HOH HOH . W 6 HOH A 29 1129 11 HOH HOH . X 6 HOH B 1 1101 40 HOH HOH . X 6 HOH B 2 1102 5 HOH HOH . X 6 HOH B 3 1103 4 HOH HOH . X 6 HOH B 4 1104 37 HOH HOH . X 6 HOH B 5 1105 3 HOH HOH . X 6 HOH B 6 1106 25 HOH HOH . X 6 HOH B 7 1107 44 HOH HOH . X 6 HOH B 8 1108 38 HOH HOH . X 6 HOH B 9 1109 20 HOH HOH . X 6 HOH B 10 1110 15 HOH HOH . X 6 HOH B 11 1111 16 HOH HOH . X 6 HOH B 12 1112 19 HOH HOH . X 6 HOH B 13 1113 36 HOH HOH . X 6 HOH B 14 1114 18 HOH HOH . X 6 HOH B 15 1115 45 HOH HOH . X 6 HOH B 16 1116 42 HOH HOH . X 6 HOH B 17 1117 35 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 O EWL . . . D 3 11.316 -29.271 15.719 1 34.68 ? O EWL 1001 A 1 HETATM 2 C C4 EWL . . . D 3 11.9 -28.647 14.735 1 30.85 ? C4 EWL 1001 A 1 HETATM 3 N N3 EWL . . . D 3 13.096 -29.037 14.228 1 31.44 ? N3 EWL 1001 A 1 HETATM 4 C C9 EWL . . . D 3 13.958 -30.152 14.635 1 28.74 ? C9 EWL 1001 A 1 HETATM 5 C C10 EWL . . . D 3 13.891 -31.251 13.639 1 25.88 ? C10 EWL 1001 A 1 HETATM 6 C C11 EWL . . . D 3 12.815 -32.126 13.677 1 25.62 ? C11 EWL 1001 A 1 HETATM 7 C C12 EWL . . . D 3 12.713 -33.167 12.757 1 24.84 ? C12 EWL 1001 A 1 HETATM 8 C C13 EWL . . . D 3 13.719 -33.315 11.8 1 26.2 ? C13 EWL 1001 A 1 HETATM 9 C C15 EWL . . . D 3 14.812 -32.43 11.766 1 27.47 ? C15 EWL 1001 A 1 HETATM 10 C C14 EWL . . . D 3 14.895 -31.387 12.701 1 27.1 ? C14 EWL 1001 A 1 HETATM 11 C C1 EWL . . . D 3 13.394 -28.169 13.256 1 30.2 ? C1 EWL 1001 A 1 HETATM 12 N N EWL . . . D 3 14.434 -28.022 12.382 1 28.79 ? N EWL 1001 A 1 HETATM 13 C C3 EWL . . . D 3 14.455 -26.997 11.474 1 29.32 ? C3 EWL 1001 A 1 HETATM 14 N N1 EWL . . . D 3 13.458 -26.099 11.401 1 27.71 ? N1 EWL 1001 A 1 HETATM 15 C C2 EWL . . . D 3 12.374 -26.179 12.189 1 28.2 ? C2 EWL 1001 A 1 HETATM 16 N N4 EWL . . . D 3 11.408 -25.268 12.081 1 29.12 ? N4 EWL 1001 A 1 HETATM 17 C C EWL . . . D 3 12.251 -27.235 13.209 1 28.74 ? C EWL 1001 A 1 HETATM 18 N N2 EWL . . . D 3 11.353 -27.569 14.159 1 27.41 ? N2 EWL 1001 A 1 HETATM 19 O O1 EWL . . . D 3 15.486 -26.818 10.583 1 30.96 ? O1 EWL 1001 A 1 HETATM 20 C C5 EWL . . . D 3 16.671 -27.602 10.699 1 32.1 ? C5 EWL 1001 A 1 HETATM 21 C C6 EWL . . . D 3 17.384 -27.366 12.05 1 32.73 ? C6 EWL 1001 A 1 HETATM 22 C C7 EWL . . . D 3 18.421 -26.236 12.016 1 33.07 ? C7 EWL 1001 A 1 HETATM 23 C C8 EWL . . . D 3 18.383 -25.297 13.189 1 32.88 ? C8 EWL 1001 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 52 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 23 #