data_1NJ1 # _model_server_result.job_id IQg9gYRWv0OtHzL8lL98KQ _model_server_result.datetime_utc '2024-11-30 22:39:28' _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 1nj1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":512}' # _entry.id 1NJ1 # _exptl.entry_id 1NJ1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 449.463 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-(N-(L-CYSTEINYL)-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 1NJ1 _cell.length_a 143.75 _cell.length_b 143.75 _cell.length_c 163.89 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NJ1 _symmetry.cell_setting hexagonal _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 -54.63 # _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 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc2 A SG CYS 461 A CYS 441 1_555 B ZN ZN . A ZN 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc3 A OE2 GLU 466 A GLU 446 1_555 C MG MG . A MG 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc4 A OD2 ASP 472 A ASP 452 1_555 C MG MG . A MG 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc5 A SG CYS 484 A CYS 464 1_555 B ZN ZN . A ZN 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc6 A SG CYS 487 A CYS 467 1_555 B ZN ZN . A ZN 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc7 E O HOH . A HOH 492 1_555 C MG MG . A MG 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc8 E O HOH . A HOH 493 1_555 C MG MG . A MG 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? # _chem_comp.formula 'C13 H19 N7 O7 S2' _chem_comp.formula_weight 449.463 _chem_comp.id 5CA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-(N-(L-CYSTEINYL)-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 N CA 5CA sing 1 n n N H 5CA sing 2 n n N HN2 5CA sing 3 n n CA CB 5CA sing 4 n n CA C 5CA sing 5 n n CA HA 5CA sing 6 n n CB SG 5CA sing 7 n n CB HB1 5CA sing 8 n n CB HB2 5CA sing 9 n n SG HG 5CA sing 10 n n C O 5CA doub 11 n n C N3S 5CA sing 12 n n N3S S 5CA sing 13 n n N3S H3S 5CA sing 14 n n S O1S 5CA doub 15 n n S O2S 5CA doub 16 n n S O5' 5CA sing 17 n n O5' C5' 5CA sing 18 n n C5' C4' 5CA sing 19 n n C5' "H5'1" 5CA sing 20 n n C5' "H5'2" 5CA sing 21 n n C4' O4' 5CA sing 22 n n C4' C3' 5CA sing 23 n n C4' H4' 5CA sing 24 n n O4' C1' 5CA sing 25 n n C3' O3' 5CA sing 26 n n C3' C2' 5CA sing 27 n n C3' H3' 5CA sing 28 n n O3' H3T 5CA sing 29 n n C2' O2' 5CA sing 30 n n C2' C1' 5CA sing 31 n n C2' H2' 5CA sing 32 n n O2' "HO'2" 5CA sing 33 n n C1' N9 5CA sing 34 n n C1' H1' 5CA sing 35 n n N9 C8 5CA sing 36 n y N9 C4 5CA sing 37 n y C8 N7 5CA doub 38 n y C8 H8 5CA sing 39 n n N7 C5 5CA sing 40 n y C5 C6 5CA doub 41 n y C5 C4 5CA sing 42 n y C6 N6 5CA sing 43 n n C6 N1 5CA sing 44 n y N6 H61 5CA sing 45 n n N6 H62 5CA sing 46 n n N1 C2 5CA doub 47 n y C2 N3 5CA sing 48 n y C2 H2 5CA sing 49 n n N3 C4 5CA doub 50 n y # _atom_sites.entry_id 1NJ1 _atom_sites.fract_transf_matrix[1][1] 0.006957 _atom_sites.fract_transf_matrix[1][2] 0.004016 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008033 _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] 0.006102 _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 1 513 513 ZN ZN . C 3 MG A 1 514 514 MG MG . D 4 5CA A 1 512 512 5CA 5CA . 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 . E 5 HOH A 29 510 510 HOH HOH . E 5 HOH A 30 511 511 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 N N 5CA . . . D 4 -35.976 -79.826 -41.089 1 63.89 ? N 5CA 512 A 1 HETATM 2 C CA 5CA . . . D 4 -34.52 -79.919 -41.026 1 67.64 ? CA 5CA 512 A 1 HETATM 3 C CB 5CA . . . D 4 -33.881 -78.549 -40.98 1 68.94 ? CB 5CA 512 A 1 HETATM 4 S SG 5CA . . . D 4 -34.861 -77.405 -40.007 1 75.51 ? SG 5CA 512 A 1 HETATM 5 C C 5CA . . . D 4 -34.146 -80.651 -39.771 1 67.35 ? C 5CA 512 A 1 HETATM 6 O O 5CA . . . D 4 -34.916 -81.11 -38.964 1 69.52 ? O 5CA 512 A 1 HETATM 7 N N3S 5CA . . . D 4 -32.912 -81.225 -39.893 1 67.49 ? N3S 5CA 512 A 1 HETATM 8 S S 5CA . . . D 4 -32.261 -82.296 -38.89 1 67.04 ? S 5CA 512 A 1 HETATM 9 O O1S 5CA . . . D 4 -33.181 -83.435 -38.714 1 64.56 ? O1S 5CA 512 A 1 HETATM 10 O O2S 5CA . . . D 4 -30.916 -82.576 -39.492 1 70.91 ? O2S 5CA 512 A 1 HETATM 11 O O5' 5CA . . . D 4 -32.04 -81.571 -37.477 1 67.67 ? O5' 5CA 512 A 1 HETATM 12 C C5' 5CA . . . D 4 -31.475 -80.25 -37.387 1 65.47 ? C5' 5CA 512 A 1 HETATM 13 C C4' 5CA . . . D 4 -30.327 -80.198 -36.402 1 63.69 ? C4' 5CA 512 A 1 HETATM 14 O O4' 5CA . . . D 4 -30.798 -80.442 -35.051 1 60.9 ? O4' 5CA 512 A 1 HETATM 15 C C3' 5CA . . . D 4 -29.237 -81.223 -36.63 1 64.74 ? C3' 5CA 512 A 1 HETATM 16 O O3' 5CA . . . D 4 -28.275 -80.693 -37.544 1 69.08 ? O3' 5CA 512 A 1 HETATM 17 C C2' 5CA . . . D 4 -28.675 -81.488 -35.242 1 62.46 ? C2' 5CA 512 A 1 HETATM 18 O O2' 5CA . . . D 4 -27.565 -80.671 -34.924 1 64.91 ? O2' 5CA 512 A 1 HETATM 19 C C1' 5CA . . . D 4 -29.841 -81.192 -34.316 1 60.75 ? C1' 5CA 512 A 1 HETATM 20 N N9 5CA . . . D 4 -30.532 -82.374 -33.732 1 56.77 ? N9 5CA 512 A 1 HETATM 21 C C8 5CA . . . D 4 -31.191 -83.411 -34.368 1 55.58 ? C8 5CA 512 A 1 HETATM 22 N N7 5CA . . . D 4 -31.709 -84.3 -33.538 1 53.91 ? N7 5CA 512 A 1 HETATM 23 C C5 5CA . . . D 4 -31.376 -83.828 -32.279 1 51.11 ? C5 5CA 512 A 1 HETATM 24 C C6 5CA . . . D 4 -31.632 -84.31 -30.951 1 49.81 ? C6 5CA 512 A 1 HETATM 25 N N6 5CA . . . D 4 -32.315 -85.424 -30.689 1 51.43 ? N6 5CA 512 A 1 HETATM 26 N N1 5CA . . . D 4 -31.151 -83.589 -29.888 1 49.75 ? N1 5CA 512 A 1 HETATM 27 C C2 5CA . . . D 4 -30.453 -82.446 -30.13 1 50.36 ? C2 5CA 512 A 1 HETATM 28 N N3 5CA . . . D 4 -30.155 -81.898 -31.336 1 51.33 ? N3 5CA 512 A 1 HETATM 29 C C4 5CA . . . D 4 -30.646 -82.64 -32.375 1 52.49 ? C4 5CA 512 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #