data_6QCN # _model_server_result.job_id uSY7F4u_9hbCKTLmHlKAYg _model_server_result.datetime_utc '2024-11-29 21:41:40' _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 6qcn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":402}' # _entry.id 6QCN # _exptl.entry_id 6QCN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _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 6QCN _cell.length_a 78.214 _cell.length_b 78.302 _cell.length_c 114.528 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QCN _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,E,H 1 1 B,F,G,I 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 ? 3 D N N ? 3 G 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 SG CYS 143 A CYS 195 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc2 A SG CYS 148 A CYS 200 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc3 A SG CYS 169 A CYS 221 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc4 A SG CYS 172 A CYS 224 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc5 B SG CYS 143 B CYS 195 1_555 F ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc6 B SG CYS 148 B CYS 200 1_555 F ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc7 B SG CYS 169 B CYS 221 1_555 F ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc8 B SG CYS 172 B CYS 224 1_555 F ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id AR6 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Adenosine-5-Diphosphoribose # 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 N1 C2 AR6 doub 13 n y N1 C6 AR6 sing 14 n y C2 N3 AR6 sing 15 n y N3 C4 AR6 doub 16 n y C4 C5 AR6 sing 17 n y C4 N9 AR6 sing 18 n y C5 C6 AR6 doub 19 n y C5 N7 AR6 sing 20 n y C6 N6 AR6 sing 21 n n N7 C8 AR6 doub 22 n y C8 N9 AR6 sing 23 n y N9 C1' AR6 sing 24 n n PA O1A AR6 sing 25 n n PA O2A AR6 doub 26 n n PA O3A AR6 sing 27 n n PA O5' AR6 sing 28 n n PB O1B AR6 sing 29 n n PB O2B AR6 doub 30 n n PB O3A AR6 sing 31 n n PB O5D AR6 sing 32 n n C1' C2' AR6 sing 33 n n C1' O4' AR6 sing 34 n n C1D O1D AR6 sing 35 n n C1D C2D AR6 sing 36 n n C1D O4D AR6 sing 37 n n C2' O2' AR6 sing 38 n n C2' C3' AR6 sing 39 n n C2D O2D AR6 sing 40 n n C2D C3D AR6 sing 41 n n C3' O3' AR6 sing 42 n n C3' C4' AR6 sing 43 n n C3D O3D AR6 sing 44 n n C3D C4D AR6 sing 45 n n C4' O4' AR6 sing 46 n n C4' C5' AR6 sing 47 n n C4D O4D AR6 sing 48 n n C4D C5D AR6 sing 49 n n C5' O5' AR6 sing 50 n n C5D O5D AR6 sing 51 n n C2 H2 AR6 sing 52 n n N6 HN6 AR6 sing 53 n n N6 HN6A AR6 sing 54 n n C8 H8 AR6 sing 55 n n C1' H1' AR6 sing 56 n n C1D H1D AR6 sing 57 n n C2' H2' AR6 sing 58 n n O2' HO2' AR6 sing 59 n n C2D H2D AR6 sing 60 n n O2D HO2D AR6 sing 61 n n C3' H3' AR6 sing 62 n n O3' HO3' AR6 sing 63 n n C3D H3D AR6 sing 64 n n O3D HO3D AR6 sing 65 n n C4' H4' AR6 sing 66 n n C4D H4D AR6 sing 67 n n C5' H5' AR6 sing 68 n n C5' "H5'A" AR6 sing 69 n n C5D H5D AR6 sing 70 n n C5D H5DA AR6 sing 71 n n O1A H1A AR6 sing 72 n n O1B H1B AR6 sing 73 n n O1D HD1 AR6 sing 74 n n # _atom_sites.entry_id 6QCN _atom_sites.fract_transf_matrix[1][1] 0.012785 _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] 0.012771 _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] 0.008731 _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 2 ZN A 1 401 401 ZN ZN . D 3 AR6 A 1 402 402 AR6 AR6 . E 4 QUE A 1 403 403 QUE QUE . F 2 ZN B 1 401 401 ZN ZN . G 3 AR6 B 1 402 402 AR6 AR6 . H 5 HOH A 1 501 501 HOH HOH . H 5 HOH A 2 502 502 HOH HOH . H 5 HOH A 3 503 503 HOH HOH . H 5 HOH A 4 504 504 HOH HOH . H 5 HOH A 5 505 506 HOH HOH . H 5 HOH A 6 506 505 HOH HOH . H 5 HOH A 7 507 507 HOH HOH . H 5 HOH A 8 508 509 HOH HOH . H 5 HOH A 9 509 508 HOH HOH . H 5 HOH A 10 510 510 HOH HOH . H 5 HOH A 11 511 511 HOH HOH . I 5 HOH B 1 501 501 HOH HOH . I 5 HOH B 2 502 504 HOH HOH . I 5 HOH B 3 503 502 HOH HOH . I 5 HOH B 4 504 503 HOH HOH . I 5 HOH B 5 505 508 HOH HOH . I 5 HOH B 6 506 505 HOH HOH . I 5 HOH B 7 507 506 HOH HOH . I 5 HOH B 8 508 507 HOH HOH . I 5 HOH B 9 509 509 HOH HOH . I 5 HOH B 10 510 512 HOH HOH . I 5 HOH B 11 511 511 HOH HOH . I 5 HOH B 12 512 510 HOH HOH . I 5 HOH B 13 513 516 HOH HOH . I 5 HOH B 14 514 513 HOH HOH . I 5 HOH B 15 515 514 HOH HOH . I 5 HOH B 16 516 515 HOH HOH . I 5 HOH B 17 517 517 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 N N1 AR6 . . . G 3 -1.757 -37.297 -34.747 1 36.51 ? N1 AR6 402 B 1 HETATM 2 C C2 AR6 . . . G 3 -2.339 -36.914 -33.604 1 41.9 ? C2 AR6 402 B 1 HETATM 3 N N3 AR6 . . . G 3 -1.802 -36.746 -32.4 1 46.14 ? N3 AR6 402 B 1 HETATM 4 C C4 AR6 . . . G 3 -0.475 -36.978 -32.451 1 40.56 ? C4 AR6 402 B 1 HETATM 5 C C5 AR6 . . . G 3 0.274 -37.369 -33.533 1 39.89 ? C5 AR6 402 B 1 HETATM 6 C C6 AR6 . . . G 3 -0.412 -37.518 -34.748 1 47.89 ? C6 AR6 402 B 1 HETATM 7 N N6 AR6 . . . G 3 0.209 -37.85 -35.882 1 37.34 ? N6 AR6 402 B 1 HETATM 8 N N7 AR6 . . . G 3 1.629 -37.518 -33.188 1 36.99 ? N7 AR6 402 B 1 HETATM 9 C C8 AR6 . . . G 3 1.678 -37.241 -31.922 1 31.7 ? C8 AR6 402 B 1 HETATM 10 N N9 AR6 . . . G 3 0.413 -36.946 -31.418 1 42.49 ? N9 AR6 402 B 1 HETATM 11 P PA AR6 . . . G 3 4.467 -34.006 -27.033 1 35.81 ? PA AR6 402 B 1 HETATM 12 P PB AR6 . . . G 3 4.316 -30.971 -27.26 1 28.16 ? PB AR6 402 B 1 HETATM 13 C C1' AR6 . . . G 3 0.141 -36.534 -30.103 1 41.99 ? C1' AR6 402 B 1 HETATM 14 O O1A AR6 . . . G 3 4.265 -33.838 -25.572 1 35.14 ? O1A AR6 402 B 1 HETATM 15 O O1B AR6 . . . G 3 4.284 -30.113 -28.439 1 23.17 ? O1B AR6 402 B 1 HETATM 16 C C1D AR6 . . . G 3 9.111 -29.963 -25.187 1 30.94 ? C1D AR6 402 B 1 HETATM 17 O O1D AR6 . . . G 3 9.766 -30.096 -23.938 1 38.88 ? O1D AR6 402 B 1 HETATM 18 C C2' AR6 . . . G 3 0.764 -37.367 -28.988 1 41.41 ? C2' AR6 402 B 1 HETATM 19 O O2' AR6 . . . G 3 -0.181 -38.312 -28.501 1 37.01 ? O2' AR6 402 B 1 HETATM 20 O O2A AR6 . . . G 3 5.542 -34.731 -27.779 1 33.01 ? O2A AR6 402 B 1 HETATM 21 O O2B AR6 . . . G 3 3.02 -30.823 -26.529 1 30.25 ? O2B AR6 402 B 1 HETATM 22 C C2D AR6 . . . G 3 9.33 -28.789 -26.156 1 30.24 ? C2D AR6 402 B 1 HETATM 23 O O2D AR6 . . . G 3 9.735 -27.545 -25.664 1 38.17 ? O2D AR6 402 B 1 HETATM 24 C C3' AR6 . . . G 3 1.011 -36.296 -27.912 1 32.84 ? C3' AR6 402 B 1 HETATM 25 O O3' AR6 . . . G 3 -0.125 -36.214 -27.06 1 38.6 ? O3' AR6 402 B 1 HETATM 26 O O3A AR6 . . . G 3 4.614 -32.519 -27.611 1 31.73 ? O3A AR6 402 B 1 HETATM 27 C C3D AR6 . . . G 3 7.989 -28.617 -26.88 1 34.22 ? C3D AR6 402 B 1 HETATM 28 O O3D AR6 . . . G 3 7.553 -27.32 -27.348 1 33.24 ? O3D AR6 402 B 1 HETATM 29 C C4' AR6 . . . G 3 1.174 -35.006 -28.701 1 29.05 ? C4' AR6 402 B 1 HETATM 30 O O4' AR6 . . . G 3 0.747 -35.265 -30.045 1 40.94 ? O4' AR6 402 B 1 HETATM 31 C C4D AR6 . . . G 3 7.08 -28.88 -25.708 1 29.85 ? C4D AR6 402 B 1 HETATM 32 O O4D AR6 . . . G 3 7.671 -29.952 -24.962 1 34.7 ? O4D AR6 402 B 1 HETATM 33 C C5' AR6 . . . G 3 2.537 -34.394 -28.773 1 30.66 ? C5' AR6 402 B 1 HETATM 34 O O5' AR6 . . . G 3 3.064 -34.6 -27.489 1 30.58 ? O5' AR6 402 B 1 HETATM 35 C C5D AR6 . . . G 3 5.664 -29.23 -26.066 1 30.12 ? C5D AR6 402 B 1 HETATM 36 O O5D AR6 . . . G 3 5.597 -30.641 -26.34 1 27.86 ? O5D AR6 402 B 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 887 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 36 #