data_6BYR # _model_server_result.job_id I7te5Gt4DaqrDN8yrWDFJQ _model_server_result.datetime_utc '2024-11-04 22:49:03' _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 6byr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 6BYR # _exptl.entry_id 6BYR _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 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 120 _cell.entry_id 6BYR _cell.length_a 166.504 _cell.length_b 166.504 _cell.length_c 332.701 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BYR _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,B,E,F,G 2 1 C,D,H,I,J 3 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 E N N ? 3 H 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 PHE 193 A PHE 193 1_555 A N SEP 194 A SEP 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C SEP 194 A SEP 194 1_555 A N GLU 195 A GLU 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C TRP 251 A TRP 251 1_555 A N TPO 252 A TPO 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C TPO 252 A TPO 252 1_555 A N LEU 253 A LEU 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C VAL 392 A VAL 392 1_555 A N SEP 393 A SEP 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C SEP 393 A SEP 393 1_555 A N ILE 394 A ILE 394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 C C PHE 193 C PHE 193 1_555 C N SEP 194 C SEP 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 C C SEP 194 C SEP 194 1_555 C N GLU 195 C GLU 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 C C TRP 251 C TRP 251 1_555 C N TPO 252 C TPO 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 C C TPO 252 C TPO 252 1_555 C N LEU 253 C LEU 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 C C VAL 392 C VAL 392 1_555 C N SEP 393 C SEP 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 C C SEP 393 C SEP 393 1_555 C N ILE 394 C ILE 394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD1 ASN 226 A ASN 226 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc2 A OD1 ASP 239 A ASP 239 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc3 A OD2 ASP 239 A ASP 239 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc4 A OD2 ASP 239 A ASP 239 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc5 E O1G ATP . A ATP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? metalc ? metalc6 E O1B ATP . A ATP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc7 E O2G ATP . A ATP 501 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc8 E O3B ATP . A ATP 501 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc9 E O1A ATP . A ATP 501 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc10 C OD1 ASN 226 C ASN 226 1_555 J MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc11 C OD1 ASP 239 C ASP 239 1_555 I MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc12 C OD2 ASP 239 C ASP 239 1_555 I MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc13 H O3G ATP . C ATP 501 1_555 I MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc14 H O2B ATP . C ATP 501 1_555 I MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc15 H O2G ATP . C ATP 501 1_555 J MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc16 H O3B ATP . C ATP 501 1_555 J MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc17 H O2A ATP . C ATP 501 1_555 J MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? # _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 6BYR _atom_sites.fract_transf_matrix[1][1] 0.006006 _atom_sites.fract_transf_matrix[1][2] 0.003467 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006935 _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] 0.003006 _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 E 3 ATP A 1 501 501 ATP ATP . F 4 MG A 1 502 502 MG MG . G 4 MG A 1 503 503 MG MG . H 3 ATP C 1 501 501 ATP ATP . I 4 MG C 1 502 502 MG MG . J 4 MG C 1 503 503 MG MG . # 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 . . . H 3 -8.503 -69.502 -46.216 0.82 116.2 ? PG ATP 501 C 1 HETATM 2 O O1G ATP . . . H 3 -7.239 -69.469 -47.044 0.82 105.37 ? O1G ATP 501 C 1 HETATM 3 O O2G ATP . . . H 3 -9.068 -68.145 -45.87 0.82 97.19 ? O2G ATP 501 C 1 HETATM 4 O O3G ATP . . . H 3 -8.432 -70.446 -45.04 0.82 111.98 ? O3G ATP 501 C 1 HETATM 5 P PB ATP . . . H 3 -9.999 -71.707 -47.234 0.82 115.28 ? PB ATP 501 C 1 HETATM 6 O O1B ATP . . . H 3 -8.874 -72.469 -47.896 0.82 107.74 ? O1B ATP 501 C 1 HETATM 7 O O2B ATP . . . H 3 -10.466 -72.132 -45.864 0.82 105.65 ? O2B ATP 501 C 1 HETATM 8 O O3B ATP . . . H 3 -9.62 -70.135 -47.201 0.82 113.36 ? O3B ATP 501 C 1 HETATM 9 P PA ATP . . . H 3 -12.68 -71.059 -47.83 0.82 97.65 ? PA ATP 501 C 1 HETATM 10 O O1A ATP . . . H 3 -13.587 -72.08 -47.179 0.82 85.76 ? O1A ATP 501 C 1 HETATM 11 O O2A ATP . . . H 3 -12.386 -69.758 -47.123 0.82 99.06 ? O2A ATP 501 C 1 HETATM 12 O O3A ATP . . . H 3 -11.278 -71.761 -48.22 0.82 101.37 ? O3A ATP 501 C 1 HETATM 13 O O5' ATP . . . H 3 -13.31 -70.692 -49.263 0.82 97.21 ? O5' ATP 501 C 1 HETATM 14 C C5' ATP . . . H 3 -12.515 -70.075 -50.242 0.82 94.73 ? C5' ATP 501 C 1 HETATM 15 C C4' ATP . . . H 3 -13.237 -69.01 -51.056 0.82 88.51 ? C4' ATP 501 C 1 HETATM 16 O O4' ATP . . . H 3 -14.312 -69.536 -51.781 0.82 81.7 ? O4' ATP 501 C 1 HETATM 17 C C3' ATP . . . H 3 -13.762 -67.899 -50.217 0.82 87.92 ? C3' ATP 501 C 1 HETATM 18 O O3' ATP . . . H 3 -12.809 -66.852 -50.373 0.82 94.27 ? O3' ATP 501 C 1 HETATM 19 C C2' ATP . . . H 3 -15.109 -67.583 -50.794 0.82 81.63 ? C2' ATP 501 C 1 HETATM 20 O O2' ATP . . . H 3 -15.058 -66.442 -51.635 0.82 80.22 ? O2' ATP 501 C 1 HETATM 21 C C1' ATP . . . H 3 -15.447 -68.721 -51.69 0.82 81 ? C1' ATP 501 C 1 HETATM 22 N N9 ATP . . . H 3 -16.453 -69.562 -51.076 0.82 83.24 ? N9 ATP 501 C 1 HETATM 23 C C8 ATP . . . H 3 -16.221 -70.648 -50.368 0.82 88.52 ? C8 ATP 501 C 1 HETATM 24 N N7 ATP . . . H 3 -17.368 -71.212 -49.968 0.82 90.47 ? N7 ATP 501 C 1 HETATM 25 C C5 ATP . . . H 3 -18.353 -70.475 -50.419 0.82 86.35 ? C5 ATP 501 C 1 HETATM 26 C C6 ATP . . . H 3 -19.79 -70.52 -50.341 0.82 84.32 ? C6 ATP 501 C 1 HETATM 27 N N6 ATP . . . H 3 -20.4 -71.48 -49.667 0.82 84.47 ? N6 ATP 501 C 1 HETATM 28 N N1 ATP . . . H 3 -20.49 -69.593 -50.934 0.82 87.92 ? N1 ATP 501 C 1 HETATM 29 C C2 ATP . . . H 3 -19.867 -68.639 -51.594 0.82 92.83 ? C2 ATP 501 C 1 HETATM 30 N N3 ATP . . . H 3 -18.545 -68.539 -51.7 0.82 91.6 ? N3 ATP 501 C 1 HETATM 31 C C4 ATP . . . H 3 -17.741 -69.412 -51.148 0.82 86.4 ? C4 ATP 501 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #