data_3RAA # _model_server_result.job_id VKyktF1Nbn1s_IkdnbFOgw _model_server_result.datetime_utc '2024-10-19 10:23:13' _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 3raa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2}' # _entry.id 3RAA # _exptl.entry_id 3RAA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _entity.pdbx_number_of_molecules 1 _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 3RAA _cell.length_a 256.4 _cell.length_b 256.4 _cell.length_c 447.43 _cell.Z_PDB 120 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RAA _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 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 ? 60-MERIC 60 'complete icosahedral assembly' 1 ? monomeric 1 'icosahedral asymmetric unit' 2 ? pentameric 5 'icosahedral pentamer' 3 ? hexameric 6 'icosahedral 23 hexamer' 4 ? monomeric 1 'icosahedral asymmetric unit, std point frame' 5 ? decameric 10 'crystal asymmetric unit, crystal frame' 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B 1 (1-60) A,B 2 1 A,B 3 (1-5) A,B 4 (1,2,6,10,23,24) A,B 5 P A,B 6 (X0)(1-5,21-25) # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] P 'transform to point frame' ? ? -0.467088 -0.809017 0.35682 -0.866024 0.500002 0.000002 -0.178412 -0.309014 -0.934173 -39.91249 148.03241 104.49428 X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.563661 0.75576 0.333337 -0.755762 0.309017 0.577349 0.33333 -0.577352 0.745356 74.59101 -18.83565 -56.98259 3 'point symmetry operation' ? ? -0.14235 0.467082 0.87268 -0.46709 -0.809017 0.356818 0.872676 -0.356827 0.333333 83.40547 -113.9281 -63.71665 4 'point symmetry operation' ? ? -0.14235 -0.46709 0.872676 0.467082 -0.809017 -0.356827 0.87268 0.356818 0.333333 14.2621 -153.86282 -10.89593 5 'point symmetry operation' ? ? 0.563661 -0.755762 0.33333 0.75576 0.309017 -0.577352 0.333337 0.577349 0.745356 -37.28532 -83.45138 28.48313 6 'point symmetry operation' ? ? -0.936338 0.110264 0.333336 0.110264 -0.80902 0.577346 0.333336 0.577346 0.745359 219.11405 -212.61273 28.48269 7 'point symmetry operation' ? ? -0.5 -0.866025 -0.000001 0.866025 -0.5 -0.000004 0.000003 -0.000003 1 128.20042 -222.04827 -0.00061 8 'point symmetry operation' ? ? 0.372678 -0.645496 -0.666668 0.866025 0.500001 0 0.333334 -0.577351 0.745355 107.21715 -148.03251 -56.98293 9 'point symmetry operation' ? ? 0.475685 0.467089 -0.745354 0.110263 0.809015 0.577353 0.872677 -0.356823 0.333334 185.1624 -92.85271 -63.71664 10 'point symmetry operation' ? ? -0.333332 0.934174 -0.127317 -0.356823 -0.000004 0.934172 0.872678 0.356819 0.333336 254.31849 -132.76548 -10.89598 11 'point symmetry operation' ? ? 0.499996 -0.866028 -0.000003 -0.866028 -0.499996 0.000002 -0.000003 0.000002 -1 0.00082 0.0007 223.71465 12 'point symmetry operation' ? ? 0.936339 0.110261 -0.333335 -0.110267 -0.809017 -0.57735 -0.333333 0.577351 -0.745356 53.60839 -55.17952 280.69701 13 'point symmetry operation' ? ? 0.333336 0.934171 0.127322 0.356823 -0.000001 -0.934172 -0.872677 0.356824 -0.333334 140.3683 -15.26724 287.43088 14 'point symmetry operation' ? ? -0.475683 0.467087 0.745356 -0.110259 0.809019 -0.577349 -0.872679 -0.356818 -0.333336 140.3813 64.58013 234.61029 15 'point symmetry operation' ? ? -0.372681 -0.645497 0.666665 -0.866023 0.500005 0.000002 -0.333337 -0.577346 -0.745358 53.62943 74.01623 195.2315 16 'point symmetry operation' ? ? -0.563658 0.755764 -0.333333 0.755764 0.309017 -0.577347 -0.333333 -0.577347 -0.745359 293.68543 -83.45253 195.231 17 'point symmetry operation' ? ? -1 0.000004 0 0.000004 1 0.000005 0 0.000005 -1 256.40048 -0.00112 223.71454 18 'point symmetry operation' ? ? -0.563665 -0.755758 -0.333334 -0.755758 0.309017 0.577354 -0.333334 0.577354 -0.745353 181.80939 -18.83672 280.69704 19 'point symmetry operation' ? ? 0.142347 -0.467086 -0.872679 -0.467086 -0.809017 0.356823 -0.872679 0.356823 -0.333331 172.9945 -113.92916 287.43062 20 'point symmetry operation' ? ? 0.142352 0.467086 -0.872678 0.467086 -0.809017 -0.356822 -0.872678 -0.356822 -0.333334 242.1377 -153.86393 234.6097 21 'point symmetry operation' ? ? 0.642353 0.755759 0.127326 0.178408 -0.30902 0.934172 0.745355 -0.577352 -0.333333 87.54648 -224.25422 10.85481 22 'point symmetry operation' ? ? -0.166663 0.645495 0.745359 0.645495 -0.500006 0.577348 0.745359 0.577348 -0.333331 113.96968 -258.35758 96.32055 23 'point symmetry operation' ? ? -0.333332 -0.356823 0.872678 0.934174 -0.000004 0.356819 -0.127317 0.934172 0.333336 46.90732 -233.69032 160.03697 24 'point symmetry operation' ? ? 0.372677 -0.866026 0.333333 0.645499 0.499999 0.577349 -0.666665 0.000001 0.745358 -20.96271 -184.34175 113.95014 25 'point symmetry operation' ? ? 0.975684 -0.178413 -0.127321 0.17841 0.309017 0.934173 -0.127324 -0.934172 0.333333 4.15368 -178.50992 21.7505 26 'point symmetry operation' ? ? -0.475685 -0.467085 0.745356 0.110269 0.809015 0.577351 -0.872677 0.356827 -0.333331 71.23767 -92.85332 287.43072 27 'point symmetry operation' ? ? 0.33333 -0.934174 0.127321 -0.35682 0.000001 0.934173 -0.87268 -0.356819 -0.333332 2.0814 -132.76553 234.60986 28 'point symmetry operation' ? ? 0.936339 -0.110267 -0.333333 0.110261 -0.809017 0.577351 -0.333335 -0.57735 -0.745356 37.28548 -212.61274 195.23079 29 'point symmetry operation' ? ? 0.500004 0.866023 0.000001 0.866023 -0.500004 0.000001 0.000001 0.000001 -1 128.19908 -222.04883 223.71405 30 'point symmetry operation' ? ? -0.372674 0.645498 0.666668 0.866028 0.499995 0.000001 -0.33333 0.577354 -0.745355 149.18268 -148.03344 280.69673 31 'point symmetry operation' ? ? -0.333334 -0.934171 -0.127326 0.35682 0.000004 -0.934173 0.872678 -0.356824 0.33333 116.03211 -15.26632 -63.71642 32 'point symmetry operation' ? ? 0.475682 -0.467083 -0.745358 -0.110266 0.809019 -0.577347 0.872678 0.356822 0.333333 116.01947 64.58079 -10.89543 33 'point symmetry operation' ? ? 0.372677 0.645499 -0.666665 -0.866026 0.499999 0.000001 0.333333 0.577349 0.745358 202.77138 74.01631 28.48341 34 'point symmetry operation' ? ? -0.5 0.866025 0.000003 -0.866025 -0.5 -0.000003 -0.000001 -0.000004 1 256.39966 0.00068 -0.00012 35 'point symmetry operation' ? ? -0.936339 -0.110265 0.333333 -0.110265 -0.809014 -0.577355 0.333333 -0.577355 0.745353 202.79184 -55.17902 -56.98274 36 'point symmetry operation' ? ? 0.166666 0.645498 -0.745356 -0.645497 -0.5 -0.57735 -0.745356 0.57735 0.333334 237.98405 36.3093 212.85923 37 'point symmetry operation' ? ? -0.642349 0.755762 -0.127322 -0.178409 -0.309015 -0.934174 -0.745357 -0.577351 0.33333 280.72976 30.47776 127.39336 38 'point symmetry operation' ? ? -0.975684 -0.178409 0.12732 -0.178409 0.309022 -0.934171 0.12732 -0.934171 -0.333338 225.83612 76.22219 63.67717 39 'point symmetry operation' ? ? -0.372681 -0.866023 -0.333337 -0.645497 0.500005 -0.577346 0.666665 0.000002 -0.745358 149.16428 110.32533 109.76427 40 'point symmetry operation' ? ? 0.33333 -0.35682 -0.87268 -0.934174 0.000001 -0.356819 0.127321 0.934173 -0.333332 156.67211 85.65781 201.96385 41 'point symmetry operation' ? ? 0.642353 0.178408 0.745355 0.755759 -0.30902 -0.577352 0.127326 0.934172 -0.333333 -24.31777 -129.19598 201.9634 42 'point symmetry operation' ? ? 0.475685 0.110263 0.872677 0.467089 0.809015 -0.356823 -0.745354 0.577353 0.333334 -22.23669 -34.10357 212.85917 43 'point symmetry operation' ? ? 0.475682 -0.110266 0.872678 -0.467083 0.809019 0.356822 -0.745358 -0.577347 0.333333 -38.55916 5.83142 127.39345 44 'point symmetry operation' ? ? 0.642349 -0.178415 0.745356 -0.755763 -0.309014 0.577349 0.127318 -0.934172 -0.333335 -50.72808 -64.57981 63.67695 45 'point symmetry operation' ? ? 0.745357 -0.000006 0.666666 -0.000006 -1 -0.000002 0.666666 -0.000002 -0.745357 -41.92642 -148.03134 109.76372 46 'point symmetry operation' ? ? -0.333334 0.35682 0.872678 -0.934171 0.000004 -0.356824 -0.127326 -0.934173 0.33333 99.72875 85.65838 21.75111 47 'point symmetry operation' ? ? -0.166669 -0.6455 0.745353 -0.6455 -0.499994 -0.577352 0.745353 -0.577352 -0.333337 18.41659 36.31029 10.85549 48 'point symmetry operation' ? ? 0.642349 -0.755763 0.127318 -0.178415 -0.309014 -0.934172 0.745356 0.577349 -0.333335 -24.32914 30.47852 96.32132 49 'point symmetry operation' ? ? 0.975684 0.17841 -0.127324 -0.178413 0.309017 -0.934172 -0.127321 0.934173 0.333333 30.5647 76.22238 160.03774 50 'point symmetry operation' ? ? 0.372678 0.866025 0.333334 -0.645496 0.500001 -0.577351 -0.666668 0 0.745355 107.23669 110.32541 113.95081 51 'point symmetry operation' ? ? 0.166666 -0.645497 -0.745356 0.645498 -0.5 0.57735 -0.745356 -0.57735 0.333334 142.42965 -258.35772 127.39271 52 'point symmetry operation' ? ? 0.333336 0.356823 -0.872677 0.934171 -0.000001 0.356824 0.127322 -0.934172 -0.333334 209.49213 -233.69044 63.67642 53 'point symmetry operation' ? ? -0.372674 0.866028 -0.33333 0.645498 0.499995 0.577354 0.666668 0.000001 -0.745355 277.36237 -184.3424 109.76348 54 'point symmetry operation' ? ? -0.975683 0.178414 0.127325 0.178414 0.309012 0.934174 0.127325 0.934174 -0.333329 252.24601 -178.51092 201.96315 55 'point symmetry operation' ? ? -0.642352 -0.75576 -0.127321 0.178414 -0.309019 0.934171 -0.745354 0.577351 0.333337 168.85301 -224.2549 212.85861 56 'point symmetry operation' ? ? -0.475685 0.110269 -0.872677 -0.467085 0.809015 0.356827 0.745356 0.577351 -0.333331 294.95967 5.83076 96.32112 57 'point symmetry operation' ? ? -0.642352 0.178414 -0.745354 -0.75576 -0.309019 0.577351 -0.127321 0.934171 0.333337 307.12828 -64.58084 160.03727 58 'point symmetry operation' ? ? -0.745357 0.000001 -0.666666 0.000001 -1 -0.000003 -0.666666 -0.000003 0.745357 298.32624 -148.0321 113.95009 59 'point symmetry operation' ? ? -0.642349 -0.178409 -0.745357 0.755762 -0.309015 -0.577351 -0.127322 -0.934174 0.33333 280.71768 -129.19621 21.7505 60 'point symmetry operation' ? ? -0.475683 -0.110259 -0.872679 0.467087 0.809019 -0.356818 0.745356 -0.577349 -0.333336 278.63702 -34.10373 10.8552 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 3RAA _atom_sites.fract_transf_matrix[1][1] 0.0039 _atom_sites.fract_transf_matrix[1][2] 0.002252 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004504 _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] 0.002235 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id AMP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 2 _pdbx_nonpoly_scheme.auth_seq_num 2 _pdbx_nonpoly_scheme.pdb_mon_id AMP _pdbx_nonpoly_scheme.auth_mon_id ADE _pdbx_nonpoly_scheme.pdb_ins_code . # 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 O5' AMP . . . B 2 99.717 -124.284 36.399 0.7 32.33 ? O5' AMP 2 A 1 HETATM 2 C C5' AMP . . . B 2 98.731 -125.06 35.763 0.7 36.99 ? C5' AMP 2 A 1 HETATM 3 C C4' AMP . . . B 2 97.354 -124.609 36.198 0.7 40.11 ? C4' AMP 2 A 1 HETATM 4 O O4' AMP . . . B 2 97.084 -123.276 35.679 0.7 40.3 ? O4' AMP 2 A 1 HETATM 5 C C3' AMP . . . B 2 96.18 -125.442 35.692 0.7 42.04 ? C3' AMP 2 A 1 HETATM 6 O O3' AMP . . . B 2 95.947 -126.563 36.586 0.7 43.62 ? O3' AMP 2 A 1 HETATM 7 C C2' AMP . . . B 2 95.025 -124.443 35.749 0.7 41.93 ? C2' AMP 2 A 1 HETATM 8 C C1' AMP . . . B 2 95.677 -123.071 35.627 0.7 40.3 ? C1' AMP 2 A 1 HETATM 9 N N9 AMP . . . B 2 95.321 -122.322 34.416 0.7 38.59 ? N9 AMP 2 A 1 HETATM 10 C C8 AMP . . . B 2 95.81 -122.433 33.129 0.7 38.25 ? C8 AMP 2 A 1 HETATM 11 N N7 AMP . . . B 2 95.321 -121.537 32.301 0.7 36.86 ? N7 AMP 2 A 1 HETATM 12 C C5 AMP . . . B 2 94.438 -120.801 33.089 0.7 36.72 ? C5 AMP 2 A 1 HETATM 13 C C6 AMP . . . B 2 93.621 -119.688 32.809 0.7 36.53 ? C6 AMP 2 A 1 HETATM 14 N N6 AMP . . . B 2 93.59 -119.086 31.618 0.7 36.36 ? N6 AMP 2 A 1 HETATM 15 N N1 AMP . . . B 2 92.853 -119.196 33.812 0.7 35.64 ? N1 AMP 2 A 1 HETATM 16 C C2 AMP . . . B 2 92.919 -119.78 35.011 0.7 35.4 ? C2 AMP 2 A 1 HETATM 17 N N3 AMP . . . B 2 93.658 -120.817 35.403 0.7 36.15 ? N3 AMP 2 A 1 HETATM 18 C C4 AMP . . . B 2 94.404 -121.29 34.381 0.7 37.18 ? C4 AMP 2 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 18 #