data_1NJ5 # _model_server_result.job_id 1uFZygSccdQiZrAjcYR6Qw _model_server_result.datetime_utc '2024-11-30 19:52:06' _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 1nj5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":510}' # _entry.id 1NJ5 # _exptl.entry_id 1NJ5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.435 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "'5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE" _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 1NJ5 _cell.length_a 143.955 _cell.length_b 143.955 _cell.length_c 163.936 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NJ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 7_554 y,x,-z-1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 -54.645333 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 SG CYS 456 A CYS 436 1_555 B ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc2 A SG CYS 461 A CYS 441 1_555 B ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc3 A OE2 GLU 466 A GLU 446 1_555 C MG MG . A MG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc4 A OD2 ASP 472 A ASP 452 1_555 C MG MG . A MG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc5 A SG CYS 484 A CYS 464 1_555 B ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc6 A SG CYS 487 A CYS 467 1_555 B ZN ZN . A ZN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc7 E O HOH . A HOH 491 1_555 C MG MG . A MG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc8 E O HOH . A HOH 492 1_555 C MG MG . A MG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? # _chem_comp.formula 'C15 H21 N7 O7 S' _chem_comp.formula_weight 443.435 _chem_comp.id P5A _chem_comp.mon_nstd_flag . _chem_comp.name "'5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE" _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 CB CG P5A sing 237 n n CB CA P5A sing 238 n n CB HB1 P5A sing 239 n n CB HB2 P5A sing 240 n n CG CD P5A sing 241 n n CG HG1 P5A sing 242 n n CG HG2 P5A sing 243 n n C O P5A doub 244 n n C CA P5A sing 245 n n C N3S P5A sing 246 n n N CD P5A sing 247 n n N CA P5A sing 248 n n N HT1 P5A sing 249 n n CD HD1 P5A sing 250 n n CD HD2 P5A sing 251 n n CA HA P5A sing 252 n n N3S S P5A sing 253 n n N3S H3S P5A sing 254 n n S O1S P5A doub 255 n n S O2S P5A doub 256 n n S O5' P5A sing 257 n n O5' C5' P5A sing 258 n n C5' C4' P5A sing 259 n n C5' "H1'1" P5A sing 260 n n C5' "H1'2" P5A sing 261 n n C4' O4' P5A sing 262 n n C4' C3' P5A sing 263 n n C4' H4' P5A sing 264 n n O4' C1' P5A sing 265 n n C1' N9 P5A sing 266 n n C1' C2' P5A sing 267 n n C1' H1' P5A sing 268 n n N9 C4 P5A sing 269 n y N9 C8 P5A sing 270 n y C4 N3 P5A doub 271 n y C4 C5 P5A sing 272 n y N3 C2 P5A sing 273 n y C2 N1 P5A doub 274 n y C2 H2 P5A sing 275 n n N1 C6 P5A sing 276 n y C6 N6 P5A sing 277 n n C6 C5 P5A doub 278 n y N6 H61 P5A sing 279 n n N6 H62 P5A sing 280 n n C5 N7 P5A sing 281 n y N7 C8 P5A doub 282 n y C8 H8 P5A sing 283 n n C2' O2' P5A sing 284 n n C2' C3' P5A sing 285 n n C2' H2' P5A sing 286 n n O2' "HO'2" P5A sing 287 n n C3' O3' P5A sing 288 n n C3' H3' P5A sing 289 n n O3' H3T P5A sing 290 n n # _atom_sites.entry_id 1NJ5 _atom_sites.fract_transf_matrix[1][1] 0.006947 _atom_sites.fract_transf_matrix[1][2] 0.004011 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008021 _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] 0.0061 _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 ZN A 1 511 511 ZN ZN . C 3 MG A 1 512 512 MG MG . D 4 P5A A 1 510 510 P5A P5A . E 5 HOH A 1 482 482 HOH HOH . E 5 HOH A 2 483 483 HOH HOH . E 5 HOH A 3 484 484 HOH HOH . E 5 HOH A 4 485 485 HOH HOH . E 5 HOH A 5 486 486 HOH HOH . E 5 HOH A 6 487 487 HOH HOH . E 5 HOH A 7 488 488 HOH HOH . E 5 HOH A 8 489 489 HOH HOH . E 5 HOH A 9 490 490 HOH HOH . E 5 HOH A 10 491 491 HOH HOH . E 5 HOH A 11 492 492 HOH HOH . E 5 HOH A 12 493 493 HOH HOH . E 5 HOH A 13 494 494 HOH HOH . E 5 HOH A 14 495 495 HOH HOH . E 5 HOH A 15 496 496 HOH HOH . E 5 HOH A 16 497 497 HOH HOH . E 5 HOH A 17 498 498 HOH HOH . E 5 HOH A 18 499 499 HOH HOH . E 5 HOH A 19 500 500 HOH HOH . E 5 HOH A 20 501 501 HOH HOH . E 5 HOH A 21 502 502 HOH HOH . E 5 HOH A 22 503 503 HOH HOH . E 5 HOH A 23 504 504 HOH HOH . E 5 HOH A 24 505 505 HOH HOH . E 5 HOH A 25 506 506 HOH HOH . E 5 HOH A 26 507 507 HOH HOH . E 5 HOH A 27 508 508 HOH HOH . E 5 HOH A 28 509 509 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 C CB P5A . . . D 4 -33.812 -78.633 -41.035 1 61.15 ? CB P5A 510 A 1 HETATM 2 C CG P5A . . . D 4 -34.699 -77.756 -40.166 1 60.94 ? CG P5A 510 A 1 HETATM 3 C C P5A . . . D 4 -34.225 -80.896 -39.973 1 63.18 ? C P5A 510 A 1 HETATM 4 O O P5A . . . D 4 -35.035 -81.179 -39.082 1 65 ? O P5A 510 A 1 HETATM 5 N N P5A . . . D 4 -36.037 -79.552 -40.999 1 59.44 ? N P5A 510 A 1 HETATM 6 C CD P5A . . . D 4 -36.159 -78.162 -40.51 1 60.98 ? CD P5A 510 A 1 HETATM 7 C CA P5A . . . D 4 -34.619 -79.93 -41.103 1 61.48 ? CA P5A 510 A 1 HETATM 8 N N3S P5A . . . D 4 -32.982 -81.391 -40.011 1 64.85 ? N3S P5A 510 A 1 HETATM 9 S S P5A . . . D 4 -32.365 -82.386 -38.938 1 64.49 ? S P5A 510 A 1 HETATM 10 O O1S P5A . . . D 4 -33.281 -83.53 -38.748 1 62.76 ? O1S P5A 510 A 1 HETATM 11 O O2S P5A . . . D 4 -30.978 -82.645 -39.454 1 66.75 ? O2S P5A 510 A 1 HETATM 12 O O5' P5A . . . D 4 -32.231 -81.575 -37.57 1 66.58 ? O5' P5A 510 A 1 HETATM 13 C C5' P5A . . . D 4 -31.492 -80.337 -37.511 1 67.99 ? C5' P5A 510 A 1 HETATM 14 C C4' P5A . . . D 4 -30.365 -80.388 -36.496 1 67.79 ? C4' P5A 510 A 1 HETATM 15 O O4' P5A . . . D 4 -30.901 -80.647 -35.177 1 66.75 ? O4' P5A 510 A 1 HETATM 16 C C1' P5A . . . D 4 -29.989 -81.402 -34.406 1 66.97 ? C1' P5A 510 A 1 HETATM 17 N N9 P5A . . . D 4 -30.673 -82.567 -33.815 1 66.59 ? N9 P5A 510 A 1 HETATM 18 C C4 P5A . . . D 4 -30.771 -82.81 -32.451 1 65.13 ? C4 P5A 510 A 1 HETATM 19 N N3 P5A . . . D 4 -30.267 -82.051 -31.423 1 63.33 ? N3 P5A 510 A 1 HETATM 20 C C2 P5A . . . D 4 -30.551 -82.582 -30.224 1 62.84 ? C2 P5A 510 A 1 HETATM 21 N N1 P5A . . . D 4 -31.247 -83.716 -29.955 1 63.6 ? N1 P5A 510 A 1 HETATM 22 C C6 P5A . . . D 4 -31.741 -84.457 -30.994 1 64.23 ? C6 P5A 510 A 1 HETATM 23 N N6 P5A . . . D 4 -32.422 -85.561 -30.7 1 63.4 ? N6 P5A 510 A 1 HETATM 24 C C5 P5A . . . D 4 -31.506 -83.994 -32.331 1 65.24 ? C5 P5A 510 A 1 HETATM 25 N N7 P5A . . . D 4 -31.85 -84.487 -33.58 1 66.3 ? N7 P5A 510 A 1 HETATM 26 C C8 P5A . . . D 4 -31.34 -83.61 -34.421 1 66.97 ? C8 P5A 510 A 1 HETATM 27 C C2' P5A . . . D 4 -28.771 -81.67 -35.295 1 68.5 ? C2' P5A 510 A 1 HETATM 28 O O2' P5A . . . D 4 -27.778 -80.732 -34.919 1 68.53 ? O2' P5A 510 A 1 HETATM 29 C C3' P5A . . . D 4 -29.342 -81.494 -36.697 1 69.44 ? C3' P5A 510 A 1 HETATM 30 O O3' P5A . . . D 4 -28.354 -81.054 -37.625 1 72.23 ? O3' P5A 510 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #