data_3B9L # _model_server_result.job_id -31zFIRYtIK8QpLWzN26UQ _model_server_result.datetime_utc '2024-10-14 14:13:29' _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 3b9l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1009}' # _entry.id 3B9L # _exptl.entry_id 3B9L _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 "3'-azido-3'-deoxythymidine" _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 104.35 _cell.angle_gamma 90 _cell.entry_id 3B9L _cell.length_a 183.9 _cell.length_b 38.696 _cell.length_c 95.867 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3B9L _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 I N N ? 3 J 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 disulf ? disulf1 A SG CYS 53 A CYS 53 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 124 A CYS 124 1_555 A SG CYS 169 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf5 A SG CYS 168 A CYS 168 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 A SG CYS 200 A CYS 200 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 A SG CYS 245 A CYS 245 1_555 A SG CYS 253 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf8 A SG CYS 265 A CYS 265 1_555 A SG CYS 279 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 A SG CYS 278 A CYS 278 1_555 A SG CYS 289 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf10 A SG CYS 316 A CYS 316 1_555 A SG CYS 361 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 A SG CYS 360 A CYS 360 1_555 A SG CYS 369 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 A SG CYS 392 A CYS 392 1_555 A SG CYS 438 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 A SG CYS 437 A CYS 437 1_555 A SG CYS 448 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf14 A SG CYS 461 A CYS 461 1_555 A SG CYS 477 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf15 A SG CYS 476 A CYS 476 1_555 A SG CYS 487 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf16 A SG CYS 514 A CYS 514 1_555 A SG CYS 559 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf17 A SG CYS 558 A CYS 558 1_555 A SG CYS 567 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id AZZ _chem_comp.mon_nstd_flag . _chem_comp.name "3'-azido-3'-deoxythymidine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Azidothymidine;Zidovudine # 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' AZZ sing 70 n n C5' C4' AZZ sing 71 n n C4' O4' AZZ sing 72 n n C4' C3' AZZ sing 73 n n O4' C1' AZZ sing 74 n n C3' N3' AZZ sing 75 n n C3' C2' AZZ sing 76 n n N3' N4' AZZ doub 77 n n N4' N5' AZZ doub 78 n n C2' C1' AZZ sing 79 n n C1' N1 AZZ sing 80 n n N1 C2 AZZ sing 81 n n N1 C6 AZZ sing 82 n n C2 O2 AZZ doub 83 n n C2 N3 AZZ sing 84 n n N3 C4 AZZ sing 85 n n C4 O4 AZZ doub 86 n n C4 C5 AZZ sing 87 n n C5 C5A AZZ sing 88 n n C5 C6 AZZ doub 89 n n O5' HO5' AZZ sing 90 n n C5' H5' AZZ sing 91 n n C5' "H5'A" AZZ sing 92 n n C4' H4' AZZ sing 93 n n C3' H3' AZZ sing 94 n n C2' H2' AZZ sing 95 n n C2' "H2'A" AZZ sing 96 n n C1' H1' AZZ sing 97 n n N3 HN3 AZZ sing 98 n n C5A H5A AZZ sing 99 n n C5A H5AA AZZ sing 100 n n C5A H5AB AZZ sing 101 n n C6 H6 AZZ sing 102 n n # _atom_sites.entry_id 3B9L _atom_sites.fract_transf_matrix[1][1] 0.005438 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001391 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025842 _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] 0.010767 _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 MYR A 1 1001 1001 MYR MYR . C 2 MYR A 1 1002 1002 MYR MYR . D 2 MYR A 1 1003 1003 MYR MYR . E 2 MYR A 1 1004 1004 MYR MYR . F 2 MYR A 1 1005 1005 MYR MYR . G 2 MYR A 1 1006 1006 MYR MYR . H 2 MYR A 1 1007 1007 MYR MYR . I 3 AZZ A 1 1009 1009 AZZ AZZ . J 3 AZZ A 1 1010 1010 AZZ AZZ . # 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' AZZ . . . I 3 35.524 2.484 18.43 1 87.7 ? O5' AZZ 1009 A 1 HETATM 2 C C5' AZZ . . . I 3 35.628 2.473 17.017 1 101.07 ? C5' AZZ 1009 A 1 HETATM 3 C C4' AZZ . . . I 3 34.662 1.459 16.443 1 95.07 ? C4' AZZ 1009 A 1 HETATM 4 O O4' AZZ . . . I 3 33.31 1.849 16.765 1 101.78 ? O4' AZZ 1009 A 1 HETATM 5 C C3' AZZ . . . I 3 34.77 1.446 14.915 1 104.04 ? C3' AZZ 1009 A 1 HETATM 6 N N3' AZZ . . . I 3 35.796 0.495 14.451 1 95.2 ? N3' AZZ 1009 A 1 HETATM 7 N N4' AZZ . . . I 3 36.02 0.377 13.345 1 95.97 ? N4' AZZ 1009 A 1 HETATM 8 N N5' AZZ . . . I 3 36.254 0.269 12.246 1 90.79 ? N5' AZZ 1009 A 1 HETATM 9 C C2' AZZ . . . I 3 33.328 1.114 14.453 1 111.15 ? C2' AZZ 1009 A 1 HETATM 10 C C1' AZZ . . . I 3 32.438 1.417 15.698 1 109.96 ? C1' AZZ 1009 A 1 HETATM 11 N N1 AZZ . . . I 3 31.435 2.521 15.454 1 108.98 ? N1 AZZ 1009 A 1 HETATM 12 C C2 AZZ . . . I 3 30.669 2.985 16.51 1 95.81 ? C2 AZZ 1009 A 1 HETATM 13 O O2 AZZ . . . I 3 30.798 2.505 17.63 1 69.73 ? O2 AZZ 1009 A 1 HETATM 14 N N3 AZZ . . . I 3 29.755 3.991 16.316 1 95.98 ? N3 AZZ 1009 A 1 HETATM 15 C C4 AZZ . . . I 3 29.574 4.562 15.08 1 111.1 ? C4 AZZ 1009 A 1 HETATM 16 O O4 AZZ . . . I 3 28.752 5.459 14.937 1 113.83 ? O4 AZZ 1009 A 1 HETATM 17 C C5 AZZ . . . I 3 30.357 4.1 13.963 1 116.25 ? C5 AZZ 1009 A 1 HETATM 18 C C5A AZZ . . . I 3 30.188 4.706 12.589 1 121.9 ? C5A AZZ 1009 A 1 HETATM 19 C C6 AZZ . . . I 3 31.268 3.092 14.171 1 110.88 ? C6 AZZ 1009 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 471 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #