data_9JN3 # _model_server_result.job_id '_q0hTzBdEsDQa6xOgmofRA' _model_server_result.datetime_utc '2025-02-23 17:02:10' _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 9jn3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 9JN3 # _exptl.entry_id 9JN3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL _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 101.12 _cell.angle_gamma 90 _cell.entry_id 9JN3 _cell.length_a 43.302 _cell.length_b 95.114 _cell.length_c 70.988 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JN3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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,I 1 1 B,F,G,H,J 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 OD1 ASP 91 A ASP 91 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc2 A OD2 ASP 91 A ASP 91 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc3 C O2A UPG . A UPG 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc4 C O1B UPG . A UPG 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc5 E MG MG . A MG 403 1_555 I O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc6 E MG MG . A MG 403 1_555 I O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc7 B OD1 ASP 91 B ASP 91 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc8 B OD2 ASP 91 B ASP 91 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc9 F O2A UPG . B UPG 401 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc10 F O1B UPG . B UPG 401 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc11 H MG MG . B MG 403 1_555 J O HOH . B HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc12 H MG MG . B MG 403 1_555 J O HOH . B HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id RAB _chem_comp.mon_nstd_flag . _chem_comp.name 2-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 9-BETA-D-ARABINOFURANOSYL-ADENINE # 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' RAB sing 277 n n O5' H5' RAB sing 278 n n C5' C4' RAB sing 279 n n C5' "H5'1" RAB sing 280 n n C5' "H5'2" RAB sing 281 n n C4' O4' RAB sing 282 n n C4' C3' RAB sing 283 n n C4' H4' RAB sing 284 n n O4' C1' RAB sing 285 n n C1' N9 RAB sing 286 n n C1' C2' RAB sing 287 n n C1' H1' RAB sing 288 n n N9 C4 RAB sing 289 n y N9 C8 RAB sing 290 n y C4 N3 RAB doub 291 n y C4 C5 RAB sing 292 n y N3 C2 RAB sing 293 n y C2 N1 RAB doub 294 n y C2 H2 RAB sing 295 n n N1 C6 RAB sing 296 n y C6 N6 RAB sing 297 n n C6 C5 RAB doub 298 n y N6 HN61 RAB sing 299 n n N6 HN62 RAB sing 300 n n C5 N7 RAB sing 301 n y N7 C8 RAB doub 302 n y C8 H8 RAB sing 303 n n C2' O2' RAB sing 304 n n C2' C3' RAB sing 305 n n C2' H2' RAB sing 306 n n O2' H1 RAB sing 307 n n C3' O3' RAB sing 308 n n C3' H3' RAB sing 309 n n O3' H3 RAB sing 310 n n # _atom_sites.entry_id 9JN3 _atom_sites.fract_transf_matrix[1][1] 0.023094 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004538 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010514 _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] 0.014356 _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 UPG A 1 401 401 UPG DRG . D 3 RAB A 1 402 501 RAB Ara . E 4 MG A 1 403 2 MG MG . F 2 UPG B 1 401 401 UPG DRG . G 3 RAB B 1 402 501 RAB Ara . H 4 MG B 1 403 1 MG MG . I 5 HOH A 1 501 129 HOH HOH . I 5 HOH A 2 502 114 HOH HOH . I 5 HOH A 3 503 128 HOH HOH . I 5 HOH A 4 504 22 HOH HOH . I 5 HOH A 5 505 65 HOH HOH . I 5 HOH A 6 506 54 HOH HOH . I 5 HOH A 7 507 44 HOH HOH . I 5 HOH A 8 508 68 HOH HOH . I 5 HOH A 9 509 111 HOH HOH . I 5 HOH A 10 510 46 HOH HOH . I 5 HOH A 11 511 24 HOH HOH . I 5 HOH A 12 512 132 HOH HOH . I 5 HOH A 13 513 82 HOH HOH . I 5 HOH A 14 514 59 HOH HOH . I 5 HOH A 15 515 43 HOH HOH . I 5 HOH A 16 516 13 HOH HOH . I 5 HOH A 17 517 126 HOH HOH . I 5 HOH A 18 518 40 HOH HOH . I 5 HOH A 19 519 103 HOH HOH . I 5 HOH A 20 520 20 HOH HOH . I 5 HOH A 21 521 77 HOH HOH . I 5 HOH A 22 522 57 HOH HOH . I 5 HOH A 23 523 48 HOH HOH . I 5 HOH A 24 524 67 HOH HOH . I 5 HOH A 25 525 3 HOH HOH . I 5 HOH A 26 526 12 HOH HOH . I 5 HOH A 27 527 35 HOH HOH . I 5 HOH A 28 528 42 HOH HOH . I 5 HOH A 29 529 10 HOH HOH . I 5 HOH A 30 530 11 HOH HOH . I 5 HOH A 31 531 94 HOH HOH . I 5 HOH A 32 532 38 HOH HOH . I 5 HOH A 33 533 99 HOH HOH . I 5 HOH A 34 534 97 HOH HOH . I 5 HOH A 35 535 98 HOH HOH . I 5 HOH A 36 536 31 HOH HOH . I 5 HOH A 37 537 47 HOH HOH . I 5 HOH A 38 538 101 HOH HOH . I 5 HOH A 39 539 8 HOH HOH . I 5 HOH A 40 540 133 HOH HOH . I 5 HOH A 41 541 29 HOH HOH . I 5 HOH A 42 542 137 HOH HOH . I 5 HOH A 43 543 23 HOH HOH . I 5 HOH A 44 544 53 HOH HOH . I 5 HOH A 45 545 34 HOH HOH . I 5 HOH A 46 546 89 HOH HOH . I 5 HOH A 47 547 100 HOH HOH . I 5 HOH A 48 548 93 HOH HOH . I 5 HOH A 49 549 30 HOH HOH . I 5 HOH A 50 550 21 HOH HOH . I 5 HOH A 51 551 25 HOH HOH . I 5 HOH A 52 552 49 HOH HOH . I 5 HOH A 53 553 102 HOH HOH . I 5 HOH A 54 554 96 HOH HOH . I 5 HOH A 55 555 62 HOH HOH . I 5 HOH A 56 556 139 HOH HOH . I 5 HOH A 57 557 134 HOH HOH . I 5 HOH A 58 558 79 HOH HOH . I 5 HOH A 59 559 105 HOH HOH . I 5 HOH A 60 560 135 HOH HOH . I 5 HOH A 61 561 87 HOH HOH . I 5 HOH A 62 562 136 HOH HOH . I 5 HOH A 63 563 80 HOH HOH . I 5 HOH A 64 564 63 HOH HOH . I 5 HOH A 65 565 130 HOH HOH . J 5 HOH B 1 501 84 HOH HOH . J 5 HOH B 2 502 55 HOH HOH . J 5 HOH B 3 503 119 HOH HOH . J 5 HOH B 4 504 74 HOH HOH . J 5 HOH B 5 505 4 HOH HOH . J 5 HOH B 6 506 112 HOH HOH . J 5 HOH B 7 507 104 HOH HOH . J 5 HOH B 8 508 14 HOH HOH . J 5 HOH B 9 509 75 HOH HOH . J 5 HOH B 10 510 70 HOH HOH . J 5 HOH B 11 511 71 HOH HOH . J 5 HOH B 12 512 107 HOH HOH . J 5 HOH B 13 513 45 HOH HOH . J 5 HOH B 14 514 52 HOH HOH . J 5 HOH B 15 515 122 HOH HOH . J 5 HOH B 16 516 9 HOH HOH . J 5 HOH B 17 517 64 HOH HOH . J 5 HOH B 18 518 33 HOH HOH . J 5 HOH B 19 519 118 HOH HOH . J 5 HOH B 20 520 36 HOH HOH . J 5 HOH B 21 521 41 HOH HOH . J 5 HOH B 22 522 39 HOH HOH . J 5 HOH B 23 523 28 HOH HOH . J 5 HOH B 24 524 76 HOH HOH . J 5 HOH B 25 525 16 HOH HOH . J 5 HOH B 26 526 6 HOH HOH . J 5 HOH B 27 527 26 HOH HOH . J 5 HOH B 28 528 83 HOH HOH . J 5 HOH B 29 529 85 HOH HOH . J 5 HOH B 30 530 72 HOH HOH . J 5 HOH B 31 531 61 HOH HOH . J 5 HOH B 32 532 19 HOH HOH . J 5 HOH B 33 533 5 HOH HOH . J 5 HOH B 34 534 88 HOH HOH . J 5 HOH B 35 535 66 HOH HOH . J 5 HOH B 36 536 116 HOH HOH . J 5 HOH B 37 537 18 HOH HOH . J 5 HOH B 38 538 81 HOH HOH . J 5 HOH B 39 539 51 HOH HOH . J 5 HOH B 40 540 7 HOH HOH . J 5 HOH B 41 541 37 HOH HOH . J 5 HOH B 42 542 91 HOH HOH . J 5 HOH B 43 543 27 HOH HOH . J 5 HOH B 44 544 60 HOH HOH . J 5 HOH B 45 545 86 HOH HOH . J 5 HOH B 46 546 1 HOH HOH . J 5 HOH B 47 547 50 HOH HOH . J 5 HOH B 48 548 73 HOH HOH . J 5 HOH B 49 549 90 HOH HOH . J 5 HOH B 50 550 17 HOH HOH . J 5 HOH B 51 551 2 HOH HOH . J 5 HOH B 52 552 32 HOH HOH . J 5 HOH B 53 553 125 HOH HOH . J 5 HOH B 54 554 120 HOH HOH . J 5 HOH B 55 555 78 HOH HOH . J 5 HOH B 56 556 58 HOH HOH . J 5 HOH B 57 557 92 HOH HOH . J 5 HOH B 58 558 121 HOH HOH . J 5 HOH B 59 559 110 HOH HOH . J 5 HOH B 60 560 56 HOH HOH . J 5 HOH B 61 561 138 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' RAB . . . D 3 18.594 -7.158 3.771 1 66.79 ? O5' RAB 402 A 1 HETATM 2 C C5' RAB . . . D 3 18.942 -8.448 4.253 1 68.5 ? C5' RAB 402 A 1 HETATM 3 C C4' RAB . . . D 3 20.372 -8.927 4.085 1 67.37 ? C4' RAB 402 A 1 HETATM 4 O O4' RAB . . . D 3 20.648 -9.906 5.108 1 66.3 ? O4' RAB 402 A 1 HETATM 5 C C1' RAB . . . D 3 20.33 -11.202 4.594 1 66.02 ? C1' RAB 402 A 1 HETATM 6 N N9 RAB . . . D 3 19.332 -11.857 5.45 1 63.2 ? N9 RAB 402 A 1 HETATM 7 C C4 RAB . . . D 3 18.565 -11.323 6.465 1 57.64 ? C4 RAB 402 A 1 HETATM 8 N N3 RAB . . . D 3 18.507 -10.045 6.882 1 55.08 ? N3 RAB 402 A 1 HETATM 9 C C2 RAB . . . D 3 17.649 -9.904 7.887 1 56.76 ? C2 RAB 402 A 1 HETATM 10 N N1 RAB . . . D 3 16.892 -10.83 8.485 1 53.03 ? N1 RAB 402 A 1 HETATM 11 C C6 RAB . . . D 3 16.966 -12.111 8.049 1 50.75 ? C6 RAB 402 A 1 HETATM 12 N N6 RAB . . . D 3 16.229 -13.044 8.651 1 52.44 ? N6 RAB 402 A 1 HETATM 13 C C5 RAB . . . D 3 17.845 -12.383 6.988 1 56.05 ? C5 RAB 402 A 1 HETATM 14 N N7 RAB . . . D 3 18.15 -13.562 6.321 1 58.59 ? N7 RAB 402 A 1 HETATM 15 C C8 RAB . . . D 3 19.037 -13.197 5.426 1 61.26 ? C8 RAB 402 A 1 HETATM 16 C C2' RAB . . . D 3 20.058 -11.067 3.092 1 65.29 ? C2' RAB 402 A 1 HETATM 17 O O2' RAB . . . D 3 18.675 -11.161 2.815 1 65.67 ? O2' RAB 402 A 1 HETATM 18 C C3' RAB . . . D 3 20.7 -9.703 2.805 1 68.64 ? C3' RAB 402 A 1 HETATM 19 O O3' RAB . . . D 3 22.108 -9.903 2.773 1 59.48 ? O3' RAB 402 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 19 #