data_1NJ6 # _model_server_result.job_id 2Z_DwaDX6NjJ7WwZcUjddw _model_server_result.datetime_utc '2024-11-28 01:28:58' _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 1nj6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":508}' # _entry.id 1NJ6 # _exptl.entry_id 1NJ6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 417.398 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "'5'-O-(N-(L-ALANYL)-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 1NJ6 _cell.length_a 143.539 _cell.length_b 143.539 _cell.length_c 164.178 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NJ6 _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 -54.726 # _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 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc2 A SG CYS 461 A CYS 441 1_555 B ZN ZN . A ZN 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc3 A OE2 GLU 466 A GLU 446 1_555 C MG MG . A MG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc4 A OD2 ASP 472 A ASP 452 1_555 C MG MG . A MG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc5 A SG CYS 484 A CYS 464 1_555 B ZN ZN . A ZN 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc6 A SG CYS 487 A CYS 467 1_555 B ZN ZN . A ZN 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? # _chem_comp.formula 'C13 H19 N7 O7 S' _chem_comp.formula_weight 417.398 _chem_comp.id A5A _chem_comp.mon_nstd_flag . _chem_comp.name "'5'-O-(N-(L-ALANYL)-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 A5A sing 1 n n N H A5A sing 2 n n N HN2 A5A sing 3 n n CA CB A5A sing 4 n n CA C A5A sing 5 n n CA HA A5A sing 6 n n CB HB1 A5A sing 7 n n CB HB2 A5A sing 8 n n CB HB3 A5A sing 9 n n C O A5A doub 10 n n C N3S A5A sing 11 n n N3S S A5A sing 12 n n N3S H3S A5A sing 13 n n S O1S A5A doub 14 n n S O2S A5A doub 15 n n S O5' A5A sing 16 n n O5' C5' A5A sing 17 n n C5' C4' A5A sing 18 n n C5' "H5'1" A5A sing 19 n n C5' "H5'2" A5A sing 20 n n C4' O4' A5A sing 21 n n C4' C3' A5A sing 22 n n C4' H4' A5A sing 23 n n O4' C1' A5A sing 24 n n C3' O3' A5A sing 25 n n C3' C2' A5A sing 26 n n C3' H3' A5A sing 27 n n O3' H3T A5A sing 28 n n C2' O2' A5A sing 29 n n C2' C1' A5A sing 30 n n C2' H2' A5A sing 31 n n O2' "HO'2" A5A sing 32 n n C1' N9 A5A sing 33 n n C1' H1' A5A sing 34 n n N9 C8 A5A sing 35 n y N9 C4 A5A sing 36 n y C8 N7 A5A doub 37 n y C8 H8 A5A sing 38 n n N7 C5 A5A sing 39 n y C5 C6 A5A doub 40 n y C5 C4 A5A sing 41 n y C6 N6 A5A sing 42 n n C6 N1 A5A sing 43 n y N6 H61 A5A sing 44 n n N6 H62 A5A sing 45 n n N1 C2 A5A doub 46 n y C2 N3 A5A sing 47 n y C2 H2 A5A sing 48 n n N3 C4 A5A doub 49 n y # _atom_sites.entry_id 1NJ6 _atom_sites.fract_transf_matrix[1][1] 0.006967 _atom_sites.fract_transf_matrix[1][2] 0.004022 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008045 _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] 0.006091 _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 1 509 509 ZN ZN . C 3 MG A 1 510 510 MG MG . D 4 A5A A 1 508 508 A5A A5A . 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 . # 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 A5A . . . D 4 -35.916 -79.543 -41.286 1 69.32 ? N A5A 508 A 1 HETATM 2 C CA A5A . . . D 4 -34.465 -79.622 -41.18 1 72.03 ? CA A5A 508 A 1 HETATM 3 C CB A5A . . . D 4 -33.846 -78.226 -41.044 1 72.08 ? CB A5A 508 A 1 HETATM 4 C C A5A . . . D 4 -34.129 -80.393 -39.939 1 72.91 ? C A5A 508 A 1 HETATM 5 O O A5A . . . D 4 -34.92 -80.869 -39.162 1 74.85 ? O A5A 508 A 1 HETATM 6 N N3S A5A . . . D 4 -32.908 -81.004 -40.05 1 74.24 ? N3S A5A 508 A 1 HETATM 7 S S A5A . . . D 4 -32.32 -82.112 -39.035 1 75.35 ? S A5A 508 A 1 HETATM 8 O O1S A5A . . . D 4 -33.3 -83.197 -38.833 1 72.69 ? O1S A5A 508 A 1 HETATM 9 O O2S A5A . . . D 4 -30.983 -82.467 -39.622 1 75.84 ? O2S A5A 508 A 1 HETATM 10 O O5' A5A . . . D 4 -32.041 -81.372 -37.648 1 74.54 ? O5' A5A 508 A 1 HETATM 11 C C5' A5A . . . D 4 -31.265 -80.166 -37.623 1 76.04 ? C5' A5A 508 A 1 HETATM 12 C C4' A5A . . . D 4 -30.221 -80.182 -36.527 1 77.03 ? C4' A5A 508 A 1 HETATM 13 O O4' A5A . . . D 4 -30.829 -80.429 -35.227 1 76.76 ? O4' A5A 508 A 1 HETATM 14 C C3' A5A . . . D 4 -29.142 -81.242 -36.644 1 78.12 ? C3' A5A 508 A 1 HETATM 15 O O3' A5A . . . D 4 -28.123 -80.814 -37.549 1 81.27 ? O3' A5A 508 A 1 HETATM 16 C C2' A5A . . . D 4 -28.664 -81.414 -35.206 1 77.6 ? C2' A5A 508 A 1 HETATM 17 O O2' A5A . . . D 4 -27.612 -80.532 -34.832 1 77.32 ? O2' A5A 508 A 1 HETATM 18 C C1' A5A . . . D 4 -29.92 -81.144 -34.393 1 77.46 ? C1' A5A 508 A 1 HETATM 19 N N9 A5A . . . D 4 -30.608 -82.342 -33.855 1 76.37 ? N9 A5A 508 A 1 HETATM 20 C C8 A5A . . . D 4 -31.269 -83.354 -34.529 1 77.11 ? C8 A5A 508 A 1 HETATM 21 N N7 A5A . . . D 4 -31.787 -84.276 -33.735 1 76.83 ? N7 A5A 508 A 1 HETATM 22 C C5 A5A . . . D 4 -31.451 -83.852 -32.457 1 75.91 ? C5 A5A 508 A 1 HETATM 23 C C6 A5A . . . D 4 -31.704 -84.385 -31.147 1 75.2 ? C6 A5A 508 A 1 HETATM 24 N N6 A5A . . . D 4 -32.39 -85.513 -30.931 1 76.17 ? N6 A5A 508 A 1 HETATM 25 N N1 A5A . . . D 4 -31.218 -83.7 -30.055 1 74.38 ? N1 A5A 508 A 1 HETATM 26 C C2 A5A . . . D 4 -30.519 -82.546 -30.255 1 73.91 ? C2 A5A 508 A 1 HETATM 27 N N3 A5A . . . D 4 -30.221 -81.951 -31.437 1 74.14 ? N3 A5A 508 A 1 HETATM 28 C C4 A5A . . . D 4 -30.718 -82.657 -32.508 1 75.76 ? C4 A5A 508 A 1 # _model_server_stats.io_time_ms 107 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #