data_5YB1 # _model_server_result.job_id lt2t-4wuJ9IKBwWqyMzFKw _model_server_result.datetime_utc '2024-10-19 16:36:14' _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 5yb1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":608}' # _entry.id 5YB1 # _exptl.entry_id 5YB1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 285.856 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N},~{N},12-trimethyl-3$l^{3}-thia-1$l^{4},5,6$l^{4}-triaza-2$l^{3}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),3,6,9,11-pentaen-4-amine _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 104.67 _cell.angle_beta 101.43 _cell.angle_gamma 89.97 _cell.entry_id 5YB1 _cell.length_a 38.492 _cell.length_b 95.653 _cell.length_c 96.642 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YB1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,F,G,H,I,J,S 1 1 B,K,L,M,N,O,P,Q,R,T 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 J N N ? 3 R 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 51 A CYS 53 1_555 A SG CYS 60 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 73 A CYS 75 1_555 A SG CYS 89 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf3 A SG CYS 88 A CYS 90 1_555 A SG CYS 99 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf4 A SG CYS 122 A CYS 124 1_555 A SG CYS 167 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf5 A SG CYS 166 A CYS 168 1_555 A SG CYS 175 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 A SG CYS 198 A CYS 200 1_555 A SG CYS 244 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf7 A SG CYS 243 A CYS 245 1_555 A SG CYS 251 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 A SG CYS 263 A CYS 265 1_555 A SG CYS 277 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf9 A SG CYS 276 A CYS 278 1_555 A SG CYS 287 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf10 A SG CYS 314 A CYS 316 1_555 A SG CYS 359 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 A SG CYS 358 A CYS 360 1_555 A SG CYS 367 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf12 A SG CYS 390 A CYS 392 1_555 A SG CYS 436 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf13 A SG CYS 435 A CYS 437 1_555 A SG CYS 446 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf14 A SG CYS 459 A CYS 461 1_555 A SG CYS 475 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf15 A SG CYS 474 A CYS 476 1_555 A SG CYS 485 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf16 A SG CYS 512 A CYS 514 1_555 A SG CYS 557 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf17 A SG CYS 556 A CYS 558 1_555 A SG CYS 565 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf18 B SG CYS 51 B CYS 53 1_555 B SG CYS 60 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf19 B SG CYS 73 B CYS 75 1_555 B SG CYS 89 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf20 B SG CYS 88 B CYS 90 1_555 B SG CYS 99 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf21 B SG CYS 122 B CYS 124 1_555 B SG CYS 167 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf22 B SG CYS 166 B CYS 168 1_555 B SG CYS 175 B CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf23 B SG CYS 198 B CYS 200 1_555 B SG CYS 244 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf24 B SG CYS 243 B CYS 245 1_555 B SG CYS 251 B CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf25 B SG CYS 263 B CYS 265 1_555 B SG CYS 277 B CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf26 B SG CYS 276 B CYS 278 1_555 B SG CYS 287 B CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf27 B SG CYS 314 B CYS 316 1_555 B SG CYS 359 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf28 B SG CYS 358 B CYS 360 1_555 B SG CYS 367 B CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf29 B SG CYS 390 B CYS 392 1_555 B SG CYS 436 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf30 B SG CYS 435 B CYS 437 1_555 B SG CYS 446 B CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf31 B SG CYS 459 B CYS 461 1_555 B SG CYS 475 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf32 B SG CYS 474 B CYS 476 1_555 B SG CYS 485 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf33 B SG CYS 512 B CYS 514 1_555 B SG CYS 557 B CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf34 B SG CYS 556 B CYS 558 1_555 B SG CYS 565 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc1 A NE2 HIS 144 A HIS 146 1_555 J CU1 8ZR . A 8ZR 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc2 B NE2 HIS 144 B HIS 146 1_555 R CU1 8ZR . B 8ZR 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? # _chem_comp.formula 'C10 H14 Cu N4 S' _chem_comp.formula_weight 285.856 _chem_comp.id 8ZR _chem_comp.mon_nstd_flag . _chem_comp.name ~{N},~{N},12-trimethyl-3$l^{3}-thia-1$l^{4},5,6$l^{4}-triaza-2$l^{3}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),3,6,9,11-pentaen-4-amine _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 C10 C11 8ZR doub 1 n y C10 C9 8ZR sing 2 n y C11 C12 8ZR sing 3 n y C12 C13 8ZR doub 4 n y C13 C14 8ZR sing 5 n n C13 N15 8ZR sing 6 n y C2 N1 8ZR sing 7 n n C3 N1 8ZR sing 8 n n C4 N1 8ZR sing 9 n n C4 N6 8ZR sing 10 n n C4 S5 8ZR doub 11 n n C8 C9 8ZR sing 12 n n C8 N7 8ZR doub 13 n n C9 N15 8ZR doub 14 n y N15 CU1 8ZR sing 15 n n N6 N7 8ZR sing 16 n n N7 CU1 8ZR sing 17 n n S5 CU1 8ZR sing 18 n n C10 H10 8ZR sing 19 n n C11 H11 8ZR sing 20 n n C12 H12 8ZR sing 21 n n C14 H13 8ZR sing 22 n n C14 H14 8ZR sing 23 n n C14 H15 8ZR sing 24 n n C2 H22 8ZR sing 25 n n C2 H23 8ZR sing 26 n n C2 H21 8ZR sing 27 n n C3 H32 8ZR sing 28 n n C3 H31 8ZR sing 29 n n C3 H30 8ZR sing 30 n n C8 H2 8ZR sing 31 n n N6 H3 8ZR sing 32 n n # _atom_sites.entry_id 5YB1 _atom_sites.fract_transf_matrix[1][1] 0.025979 _atom_sites.fract_transf_matrix[1][2] -0.000015 _atom_sites.fract_transf_matrix[1][3] 0.005433 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010454 _atom_sites.fract_transf_matrix[2][3] 0.002796 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010928 _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 PLM A 1 601 1 PLM PLM . D 2 PLM A 1 602 2 PLM PLM . E 2 PLM A 1 603 3 PLM PLM . F 2 PLM A 1 604 4 PLM PLM . G 2 PLM A 1 605 5 PLM PLM . H 2 PLM A 1 606 6 PLM PLM . I 2 PLM A 1 607 13 PLM PLM . J 3 8ZR A 1 608 2 8ZR CUL . K 2 PLM B 1 601 7 PLM PLM . L 2 PLM B 1 602 8 PLM PLM . M 2 PLM B 1 603 9 PLM PLM . N 2 PLM B 1 604 10 PLM PLM . O 2 PLM B 1 605 11 PLM PLM . P 2 PLM B 1 606 12 PLM PLM . Q 2 PLM B 1 607 14 PLM PLM . R 3 8ZR B 1 608 1 8ZR CUL . S 4 HOH A 1 701 32 HOH HOH . S 4 HOH A 2 702 13 HOH HOH . S 4 HOH A 3 703 11 HOH HOH . S 4 HOH A 4 704 34 HOH HOH . S 4 HOH A 5 705 1 HOH HOH . S 4 HOH A 6 706 6 HOH HOH . S 4 HOH A 7 707 19 HOH HOH . S 4 HOH A 8 708 2 HOH HOH . S 4 HOH A 9 709 14 HOH HOH . S 4 HOH A 10 710 7 HOH HOH . S 4 HOH A 11 711 10 HOH HOH . S 4 HOH A 12 712 25 HOH HOH . S 4 HOH A 13 713 30 HOH HOH . S 4 HOH A 14 714 8 HOH HOH . S 4 HOH A 15 715 33 HOH HOH . S 4 HOH A 16 716 21 HOH HOH . S 4 HOH A 17 717 28 HOH HOH . S 4 HOH A 18 718 29 HOH HOH . S 4 HOH A 19 719 26 HOH HOH . S 4 HOH A 20 720 24 HOH HOH . T 4 HOH B 1 701 16 HOH HOH . T 4 HOH B 2 702 12 HOH HOH . T 4 HOH B 3 703 31 HOH HOH . T 4 HOH B 4 704 35 HOH HOH . T 4 HOH B 5 705 15 HOH HOH . T 4 HOH B 6 706 5 HOH HOH . T 4 HOH B 7 707 17 HOH HOH . T 4 HOH B 8 708 36 HOH HOH . T 4 HOH B 9 709 4 HOH HOH . T 4 HOH B 10 710 22 HOH HOH . T 4 HOH B 11 711 3 HOH HOH . T 4 HOH B 12 712 9 HOH HOH . T 4 HOH B 13 713 23 HOH HOH . T 4 HOH B 14 714 18 HOH HOH . T 4 HOH B 15 715 20 HOH HOH . T 4 HOH B 16 716 27 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 C10 8ZR . . . J 3 2.284 8.847 8.744 1 110.36 ? C10 8ZR 608 A 1 HETATM 2 C C11 8ZR . . . J 3 2.597 7.533 8.682 1 110.16 ? C11 8ZR 608 A 1 HETATM 3 C C12 8ZR . . . J 3 1.612 6.608 8.62 1 110.02 ? C12 8ZR 608 A 1 HETATM 4 C C13 8ZR . . . J 3 0.276 7.004 8.617 1 110.61 ? C13 8ZR 608 A 1 HETATM 5 C C14 8ZR . . . J 3 -0.83 5.94 8.549 1 111.03 ? C14 8ZR 608 A 1 HETATM 6 C C2 8ZR . . . J 3 -2.674 14.692 8.166 1 113.11 ? C2 8ZR 608 A 1 HETATM 7 C C3 8ZR . . . J 3 -4.412 13.66 9.698 1 113.84 ? C3 8ZR 608 A 1 HETATM 8 C C4 8ZR . . . J 3 -2.463 12.246 8.846 1 112.72 ? C4 8ZR 608 A 1 HETATM 9 C C8 8ZR . . . J 3 0.72 10.623 8.809 1 111.85 ? C8 8ZR 608 A 1 HETATM 10 C C9 8ZR . . . J 3 0.951 9.248 8.743 1 110.89 ? C9 8ZR 608 A 1 HETATM 11 N N1 8ZR . . . J 3 -3.184 13.528 8.901 1 113.36 ? N1 8ZR 608 A 1 HETATM 12 N N15 8ZR . . . J 3 -0.054 8.333 8.682 1 111 ? N15 8ZR 608 A 1 HETATM 13 N N6 8ZR . . . J 3 -1.207 12.102 8.857 1 112.94 ? N6 8ZR 608 A 1 HETATM 14 N N7 8ZR . . . J 3 -0.604 10.852 8.801 1 112.47 ? N7 8ZR 608 A 1 HETATM 15 S S5 8ZR . . . J 3 -3.114 10.721 8.762 1 111.52 ? S5 8ZR 608 A 1 HETATM 16 CU CU1 8ZR . . . J 3 -1.837 9.192 8.683 1 111.37 ? CU1 8ZR 608 A 1 HETATM 17 H H10 8ZR . . . J 3 2.961 9.484 8.787 1 132.32 ? H10 8ZR 608 A 1 HETATM 18 H H11 8ZR . . . J 3 3.487 7.266 8.681 1 132.07 ? H11 8ZR 608 A 1 HETATM 19 H H12 8ZR . . . J 3 1.828 5.705 8.575 1 131.9 ? H12 8ZR 608 A 1 HETATM 20 H H13 8ZR . . . J 3 -1.521 6.151 9.196 1 133.12 ? H13 8ZR 608 A 1 HETATM 21 H H14 8ZR . . . J 3 -0.453 5.069 8.75 1 133.12 ? H14 8ZR 608 A 1 HETATM 22 H H15 8ZR . . . J 3 -1.213 5.929 7.658 1 133.12 ? H15 8ZR 608 A 1 HETATM 23 H H22 8ZR . . . J 3 -2.792 15.491 8.705 1 135.61 ? H22 8ZR 608 A 1 HETATM 24 H H23 8ZR . . . J 3 -3.163 14.789 7.334 1 135.61 ? H23 8ZR 608 A 1 HETATM 25 H H21 8ZR . . . J 3 -1.732 14.567 7.975 1 135.61 ? H21 8ZR 608 A 1 HETATM 26 H H32 8ZR . . . J 3 -4.929 14.414 9.374 1 136.48 ? H32 8ZR 608 A 1 HETATM 27 H H31 8ZR . . . J 3 -4.18 13.803 10.628 1 136.48 ? H31 8ZR 608 A 1 HETATM 28 H H30 8ZR . . . J 3 -4.939 12.849 9.617 1 136.48 ? H30 8ZR 608 A 1 HETATM 29 H H3 8ZR . . . J 3 -0.71 12.802 8.9 1 135.41 ? H3 8ZR 608 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 90 _model_server_stats.query_time_ms 414 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 29 #