data_8HCG # _model_server_result.job_id 0_hkzygCk_7C8t1gWVHotw _model_server_result.datetime_utc '2024-11-27 01:06:03' _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 8hcg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":306}' # _entry.id 8HCG # _exptl.entry_id 8HCG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE-5'-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 8HCG _cell.length_a 92.585 _cell.length_b 92.585 _cell.length_c 67.44 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8HCG _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 22.48 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD1 ASP 8 A ASP 18 1_555 H MG MG . A MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc2 A OD2 ASP 8 A ASP 18 1_555 H MG MG . A MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc3 A OD2 ASP 8 A ASP 18 1_555 I MG MG . A MG 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc4 A OE2 GLU 10 A GLU 20 1_555 I MG MG . A MG 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc5 A OD2 ASP 190 A ASP 200 1_555 I MG MG . A MG 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc6 G O1P D5M . A D5M 306 1_555 H MG MG . A MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? metalc ? metalc7 G O1P D5M . A D5M 306 1_555 I MG MG . A MG 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc8 G O2P D5M . A D5M 306 1_555 I MG MG . A MG 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc9 H MG MG . A MG 307 1_555 J O HOH . A HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc10 H MG MG . A MG 307 1_555 J O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc11 H MG MG . A MG 307 1_555 J O HOH . A HOH 468 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? # _chem_comp.formula 'C10 H14 N5 O6 P' _chem_comp.formula_weight 331.222 _chem_comp.id D5M _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE-5'-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 O5' C5' D5M sing 120 n n O5' P D5M sing 121 n n C5' C4' D5M sing 122 n n C5' "H5'1" D5M sing 123 n n C5' "H5'2" D5M sing 124 n n C4' O4' D5M sing 125 n n C4' C3' D5M sing 126 n n C4' H4' D5M sing 127 n n O4' C1' D5M sing 128 n n C3' O3' D5M sing 129 n n C3' C2' D5M sing 130 n n C3' H1 D5M sing 131 n n O3' H3' D5M sing 132 n n C2' C1' D5M sing 133 n n C2' "H2'1" D5M sing 134 n n C2' "H2'2" D5M sing 135 n n C1' N9 D5M sing 136 n n C1' H1' D5M sing 137 n n N9 C8 D5M sing 138 n y N9 C4 D5M sing 139 n y C8 N7 D5M doub 140 n y C8 H8 D5M sing 141 n n N7 C5 D5M sing 142 n y C5 C6 D5M sing 143 n y C5 C4 D5M doub 144 n y C6 N6 D5M sing 145 n n C6 N1 D5M doub 146 n y N6 HN61 D5M sing 147 n n N6 HN62 D5M sing 148 n n N1 C2 D5M sing 149 n y C2 N3 D5M doub 150 n y C2 H2 D5M sing 151 n n N3 C4 D5M sing 152 n y P O1P D5M doub 153 n n P O3P D5M sing 154 n n P O2P D5M sing 155 n n O3P H3P D5M sing 156 n n O2P H2P D5M sing 157 n n # _atom_sites.entry_id 8HCG _atom_sites.fract_transf_matrix[1][1] 0.010801 _atom_sites.fract_transf_matrix[1][2] 0.006236 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012472 _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] 0.014828 _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 B 2 1PE A 1 301 302 1PE 1PE . C 2 1PE A 1 302 303 1PE 1PE . D 2 1PE A 1 303 304 1PE 1PE . E 3 NA A 1 304 305 NA NA . F 3 NA A 1 305 306 NA NA . G 4 D5M A 1 306 307 D5M D5M . H 5 MG A 1 307 3 MG MG . I 5 MG A 1 308 4 MG MG . J 6 HOH A 1 401 89 HOH HOH . J 6 HOH A 2 402 85 HOH HOH . J 6 HOH A 3 403 13 HOH HOH . J 6 HOH A 4 404 20 HOH HOH . J 6 HOH A 5 405 38 HOH HOH . J 6 HOH A 6 406 28 HOH HOH . J 6 HOH A 7 407 9 HOH HOH . J 6 HOH A 8 408 30 HOH HOH . J 6 HOH A 9 409 81 HOH HOH . J 6 HOH A 10 410 6 HOH HOH . J 6 HOH A 11 411 46 HOH HOH . J 6 HOH A 12 412 79 HOH HOH . J 6 HOH A 13 413 32 HOH HOH . J 6 HOH A 14 414 64 HOH HOH . J 6 HOH A 15 415 14 HOH HOH . J 6 HOH A 16 416 22 HOH HOH . J 6 HOH A 17 417 16 HOH HOH . J 6 HOH A 18 418 15 HOH HOH . J 6 HOH A 19 419 70 HOH HOH . J 6 HOH A 20 420 3 HOH HOH . J 6 HOH A 21 421 54 HOH HOH . J 6 HOH A 22 422 96 HOH HOH . J 6 HOH A 23 423 74 HOH HOH . J 6 HOH A 24 424 37 HOH HOH . J 6 HOH A 25 425 59 HOH HOH . J 6 HOH A 26 426 26 HOH HOH . J 6 HOH A 27 427 51 HOH HOH . J 6 HOH A 28 428 1 HOH HOH . J 6 HOH A 29 429 2 HOH HOH . J 6 HOH A 30 430 58 HOH HOH . J 6 HOH A 31 431 43 HOH HOH . J 6 HOH A 32 432 8 HOH HOH . J 6 HOH A 33 433 31 HOH HOH . J 6 HOH A 34 434 23 HOH HOH . J 6 HOH A 35 435 41 HOH HOH . J 6 HOH A 36 436 10 HOH HOH . J 6 HOH A 37 437 48 HOH HOH . J 6 HOH A 38 438 67 HOH HOH . J 6 HOH A 39 439 75 HOH HOH . J 6 HOH A 40 440 55 HOH HOH . J 6 HOH A 41 441 29 HOH HOH . J 6 HOH A 42 442 42 HOH HOH . J 6 HOH A 43 443 4 HOH HOH . J 6 HOH A 44 444 56 HOH HOH . J 6 HOH A 45 445 17 HOH HOH . J 6 HOH A 46 446 27 HOH HOH . J 6 HOH A 47 447 50 HOH HOH . J 6 HOH A 48 448 95 HOH HOH . J 6 HOH A 49 449 24 HOH HOH . J 6 HOH A 50 450 12 HOH HOH . J 6 HOH A 51 451 62 HOH HOH . J 6 HOH A 52 452 19 HOH HOH . J 6 HOH A 53 453 35 HOH HOH . J 6 HOH A 54 454 7 HOH HOH . J 6 HOH A 55 455 69 HOH HOH . J 6 HOH A 56 456 5 HOH HOH . J 6 HOH A 57 457 34 HOH HOH . J 6 HOH A 58 458 21 HOH HOH . J 6 HOH A 59 459 18 HOH HOH . J 6 HOH A 60 460 40 HOH HOH . J 6 HOH A 61 461 47 HOH HOH . J 6 HOH A 62 462 25 HOH HOH . J 6 HOH A 63 463 97 HOH HOH . J 6 HOH A 64 464 94 HOH HOH . J 6 HOH A 65 465 77 HOH HOH . J 6 HOH A 66 466 33 HOH HOH . J 6 HOH A 67 467 82 HOH HOH . J 6 HOH A 68 468 80 HOH HOH . J 6 HOH A 69 469 57 HOH HOH . J 6 HOH A 70 470 45 HOH HOH . J 6 HOH A 71 471 72 HOH HOH . J 6 HOH A 72 472 65 HOH HOH . J 6 HOH A 73 473 60 HOH HOH . J 6 HOH A 74 474 76 HOH HOH . J 6 HOH A 75 475 86 HOH HOH . J 6 HOH A 76 476 66 HOH HOH . J 6 HOH A 77 477 36 HOH HOH . J 6 HOH A 78 478 39 HOH HOH . J 6 HOH A 79 479 91 HOH HOH . J 6 HOH A 80 480 63 HOH HOH . J 6 HOH A 81 481 11 HOH HOH . J 6 HOH A 82 482 68 HOH HOH . J 6 HOH A 83 483 83 HOH HOH . J 6 HOH A 84 484 106 HOH HOH . J 6 HOH A 85 485 44 HOH HOH . J 6 HOH A 86 486 92 HOH HOH . J 6 HOH A 87 487 105 HOH HOH . J 6 HOH A 88 488 84 HOH HOH . J 6 HOH A 89 489 102 HOH HOH . J 6 HOH A 90 490 78 HOH HOH . J 6 HOH A 91 491 100 HOH HOH . J 6 HOH A 92 492 52 HOH HOH . J 6 HOH A 93 493 98 HOH HOH . J 6 HOH A 94 494 71 HOH HOH . J 6 HOH A 95 495 73 HOH HOH . J 6 HOH A 96 496 99 HOH HOH . J 6 HOH A 97 497 90 HOH HOH . J 6 HOH A 98 498 93 HOH HOH . J 6 HOH A 99 499 53 HOH HOH . J 6 HOH A 100 500 49 HOH HOH . J 6 HOH A 101 501 61 HOH HOH . J 6 HOH A 102 502 87 HOH HOH . J 6 HOH A 103 503 88 HOH HOH . J 6 HOH A 104 504 103 HOH HOH . J 6 HOH A 105 505 101 HOH HOH . J 6 HOH A 106 506 104 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 O5' D5M . . . G 4 -47.08 17.356 17.108 1 22.66 ? O5' D5M 306 A 1 HETATM 2 C C5' D5M . . . G 4 -45.742 16.998 17.372 1 22.64 ? C5' D5M 306 A 1 HETATM 3 C C4' D5M . . . G 4 -45.354 17.421 18.769 1 22.59 ? C4' D5M 306 A 1 HETATM 4 O O4' D5M . . . G 4 -45.627 18.834 18.96 1 22.4 ? O4' D5M 306 A 1 HETATM 5 C C3' D5M . . . G 4 -46.073 16.722 19.872 1 21.18 ? C3' D5M 306 A 1 HETATM 6 O O3' D5M . . . G 4 -45.43 15.464 20.115 1 22.53 ? O3' D5M 306 A 1 HETATM 7 C C2' D5M . . . G 4 -45.843 17.661 21.033 1 20.46 ? C2' D5M 306 A 1 HETATM 8 C C1' D5M . . . G 4 -46.089 19.033 20.347 1 22.44 ? C1' D5M 306 A 1 HETATM 9 N N9 D5M . . . G 4 -47.431 19.504 20.336 1 22.59 ? N9 D5M 306 A 1 HETATM 10 C C8 D5M . . . G 4 -48.249 19.514 19.285 1 23.78 ? C8 D5M 306 A 1 HETATM 11 N N7 D5M . . . G 4 -49.466 20.048 19.604 1 28.55 ? N7 D5M 306 A 1 HETATM 12 C C5 D5M . . . G 4 -49.268 20.404 21.025 1 24.08 ? C5 D5M 306 A 1 HETATM 13 C C6 D5M . . . G 4 -50.057 20.982 21.976 1 38.28 ? C6 D5M 306 A 1 HETATM 14 N N6 D5M . . . G 4 -51.398 21.354 21.596 1 36.95 ? N6 D5M 306 A 1 HETATM 15 N N1 D5M . . . G 4 -49.586 21.186 23.201 1 33.47 ? N1 D5M 306 A 1 HETATM 16 C C2 D5M . . . G 4 -48.32 20.807 23.444 1 42.67 ? C2 D5M 306 A 1 HETATM 17 N N3 D5M . . . G 4 -47.429 20.215 22.607 1 28.88 ? N3 D5M 306 A 1 HETATM 18 C C4 D5M . . . G 4 -47.962 20.053 21.424 1 26.13 ? C4 D5M 306 A 1 HETATM 19 P P D5M . . . G 4 -47.983 16.312 16.245 1 23.95 ? P D5M 306 A 1 HETATM 20 O O1P D5M . . . G 4 -47.411 15.849 15.03 1 24.68 ? O1P D5M 306 A 1 HETATM 21 O O3P D5M . . . G 4 -49.285 16.997 15.938 1 24.19 ? O3P D5M 306 A 1 HETATM 22 O O2P D5M . . . G 4 -48.364 15.148 17.094 1 22.38 ? O2P D5M 306 A 1 HETATM 23 H "H5'1" D5M . . . G 4 -45.093 17.489 16.656 1 27.16 ? "H5'1" D5M 306 A 1 HETATM 24 H "H5'2" D5M . . . G 4 -45.635 15.924 17.281 1 27.16 ? "H5'2" D5M 306 A 1 HETATM 25 H H4' D5M . . . G 4 -44.303 17.17 18.84 1 27.1 ? H4' D5M 306 A 1 HETATM 26 H H1 D5M . . . G 4 -47.12 16.528 19.68 1 25.41 ? H1 D5M 306 A 1 HETATM 27 H H3' D5M . . . G 4 -46.025 14.76 19.903 1 27.03 ? H3' D5M 306 A 1 HETATM 28 H "H2'1" D5M . . . G 4 -44.826 17.584 21.404 1 24.54 ? "H2'1" D5M 306 A 1 HETATM 29 H "H2'2" D5M . . . G 4 -46.56 17.485 21.828 1 24.54 ? "H2'2" D5M 306 A 1 HETATM 30 H H1' D5M . . . G 4 -45.554 19.79 20.907 1 26.92 ? H1' D5M 306 A 1 HETATM 31 H H8 D5M . . . G 4 -47.983 19.146 18.301 1 28.53 ? H8 D5M 306 A 1 HETATM 32 H HN61 D5M . . . G 4 -51.705 21.221 20.65 1 44.33 ? HN61 D5M 306 A 1 HETATM 33 H HN62 D5M . . . G 4 -52.021 21.746 22.277 1 44.33 ? HN62 D5M 306 A 1 HETATM 34 H H2 D5M . . . G 4 -47.96 21.001 24.446 1 51.19 ? H2 D5M 306 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #