data_9DM1 # _model_server_result.job_id 8shdrYkK1xVwqUc9Qrpy6g _model_server_result.datetime_utc '2025-10-01 11:42:13' _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 9dm1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"MB","auth_seq_id":401}' # _entry.id 9DM1 # _exptl.entry_id 9DM1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 63.546 _entity.id 14 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'COPPER (II) ION' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 25-meric _pdbx_struct_assembly.oligomeric_count 25 _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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC,MC _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 ? 14 Z N N ? 14 SA N N ? 14 AB N N ? 14 BB N N ? 14 MB N N ? 14 NB 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 V SG CYS 312 Y CYS 351 1_555 V SG CYS 328 Y CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 X SG CYS 312 M CYS 351 1_555 X SG CYS 328 M CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 E N CYS 1 D CYS 21 1_555 WA C1 PLM . D PLM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.539 ? covale ? covale2 F N CYS 1 G CYS 21 1_555 YA C1 PLM . G PLM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.535 ? covale ? covale3 F SG CYS 1 G CYS 21 1_555 ZA C37 9XX . G 9XX 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.553 ? covale ? covale4 T N CYS 1 c CYS 24 1_555 XB C1 PLM . c PLM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.551 ? covale ? covale5 T SG CYS 1 c CYS 24 1_555 YB C37 9XX . c 9XX 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.566 ? covale ? covale6 W N CYS 1 W CYS 24 1_555 HC C1 PLM . W PLM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.543 ? metalc ? metalc1 A NE2 HIS 77 R HIS 86 1_555 BA FE HEA . R HEA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc2 A ND1 HIS 255 R HIS 264 1_555 Z CU CU . R CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc3 A NE2 HIS 304 R HIS 313 1_555 Z CU CU . R CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc4 A NE2 HIS 305 R HIS 314 1_555 Z CU CU . R CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 A NE2 HIS 388 R HIS 397 1_555 AA FE HEA . R HEA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc6 A NE2 HIS 390 R HIS 399 1_555 BA FE HEA . R HEA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc7 B NE2 HIS 106 E HIS 109 1_555 EA FE HEM . E HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc8 B NE2 HIS 120 E HIS 123 1_555 DA FE HEM . E HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc9 B NE2 HIS 208 E HIS 211 1_555 EA FE HEM . E HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc10 B NE2 HIS 223 E HIS 226 1_555 DA FE HEM . E HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc11 C NE2 HIS 106 F HIS 109 1_555 LA FE HEM . F HEM 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc12 C NE2 HIS 120 F HIS 123 1_555 KA FE HEM . F HEM 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc13 C NE2 HIS 208 F HIS 211 1_555 LA FE HEM . F HEM 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc14 C NE2 HIS 223 F HIS 226 1_555 KA FE HEM . F HEM 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc15 D NE2 HIS 77 L HIS 86 1_555 UA FE HEA . L HEA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc16 D NE2 HIS 255 L HIS 264 1_555 SA CU CU . L CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc17 D NE2 HIS 304 L HIS 313 1_555 SA CU CU . L CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc18 D NE2 HIS 305 L HIS 314 1_555 SA CU CU . L CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc19 D NE2 HIS 388 L HIS 397 1_555 TA FE HEA . L HEA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc20 D NE2 HIS 390 L HIS 399 1_555 UA FE HEA . L HEA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc21 G ND1 HIS 206 Q HIS 232 1_555 BB CU CU . Q CU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc22 G NE2 HIS 206 Q HIS 232 1_555 BB CU CU . Q CU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc23 G SG CYS 247 Q CYS 273 1_555 AB CU CU . Q CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc24 G SG CYS 251 Q CYS 277 1_555 AB CU CU . Q CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc25 G ND1 HIS 255 Q HIS 281 1_555 AB CU CU . Q CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc26 M NE2 HIS 20 O HIS 91 1_555 JB FE HEC . O HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc27 M NE2 HIS 121 O HIS 192 1_555 KB FE HEC . O HEC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc28 N ND1 HIS 206 K HIS 232 1_555 NB CU CU . K CU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc29 N SG CYS 247 K CYS 273 1_555 MB CU CU . K CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc30 N O GLU 249 K GLU 275 1_555 MB CU CU . K CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc31 N SG CYS 251 K CYS 277 1_555 MB CU CU . K CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc32 N ND1 HIS 255 K HIS 281 1_555 MB CU CU . K CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc33 U NE2 HIS 121 I HIS 192 1_555 BC FE HEC . I HEC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc34 V SG CYS 307 Y CYS 346 1_555 EC FE2 FES . Y FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc35 V ND1 HIS 309 Y HIS 348 1_555 EC FE1 FES . Y FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc36 V SG CYS 326 Y CYS 365 1_555 EC FE2 FES . Y FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc37 V ND1 HIS 329 Y HIS 368 1_555 EC FE1 FES . Y FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc38 X SG CYS 307 M CYS 346 1_555 MC FE2 FES . M FES 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc39 X ND1 HIS 309 M HIS 348 1_555 MC FE1 FES . M FES 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc40 X SG CYS 326 M CYS 365 1_555 MC FE2 FES . M FES 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc41 X ND1 HIS 329 M HIS 368 1_555 MC FE1 FES . M FES 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? # _chem_comp.formula 'Cu 2' _chem_comp.formula_weight 63.546 _chem_comp.id CU _chem_comp.mon_nstd_flag ? _chem_comp.name 'COPPER (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 9DM1 _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 Z 14 CU R 1 601 601 CU CU ? AA 15 HEA R 1 602 602 HEA HEA ? BA 15 HEA R 1 603 603 HEA HEA ? CA 16 CDL R 1 604 604 CDL CDL ? DA 17 HEM E 1 601 601 HEM HEM ? EA 17 HEM E 1 602 602 HEM HEM ? FA 18 MQ9 E 1 603 603 MQ9 MQ9 ? GA 18 MQ9 E 1 604 604 MQ9 MQ9 ? HA 16 CDL E 1 605 605 CDL CDL ? IA 16 CDL E 1 606 606 CDL CDL ? JA 18 MQ9 F 1 701 701 MQ9 MQ9 ? KA 17 HEM F 1 702 702 HEM HEM ? LA 17 HEM F 1 703 703 HEM HEM ? MA 16 CDL F 1 704 704 CDL CDL ? NA 16 CDL F 1 705 705 CDL CDL ? OA 19 9Y0 F 1 706 706 9Y0 9Y0 ? PA 18 MQ9 F 1 707 707 MQ9 MQ9 ? QA 18 MQ9 F 1 708 708 MQ9 MQ9 ? RA 18 MQ9 F 1 709 709 MQ9 MQ9 ? SA 14 CU L 1 601 601 CU CU ? TA 15 HEA L 1 602 602 HEA HEA ? UA 15 HEA L 1 603 603 HEA HEA ? VA 16 CDL L 1 604 604 CDL CDL ? WA 20 PLM D 1 301 301 PLM PLM ? XA 21 9XX D 1 302 302 9XX 9XX ? YA 20 PLM G 1 301 301 PLM PLM ? ZA 21 9XX G 1 302 302 9XX 9XX ? AB 14 CU Q 1 401 401 CU CU ? BB 14 CU Q 1 402 402 CU CU ? CB 16 CDL S 1 301 301 CDL CDL ? DB 19 9Y0 S 1 302 302 9Y0 9Y0 ? EB 16 CDL T 1 201 201 CDL CDL ? FB 16 CDL T 1 202 202 CDL CDL ? GB 16 CDL T 1 203 203 CDL CDL ? HB 16 CDL P 1 201 201 CDL CDL ? IB 19 9Y0 P 1 202 202 9Y0 9Y0 ? JB 22 HEC O 1 301 301 HEC HEC ? KB 22 HEC O 1 302 302 HEC HEC ? LB 23 9YF O 1 303 303 9YF 9YF ? MB 14 CU K 1 401 401 CU CU ? NB 14 CU K 1 402 402 CU CU ? OB 16 CDL X 1 301 301 CDL CDL ? PB 16 CDL X 1 302 302 CDL CDL ? QB 19 9Y0 X 1 303 303 9Y0 9Y0 ? RB 18 MQ9 Z 1 201 201 MQ9 MQ9 ? SB 16 CDL Z 1 202 202 CDL CDL ? TB 16 CDL Z 1 203 203 CDL CDL ? UB 16 CDL J 1 201 201 CDL CDL ? VB 19 9Y0 J 1 202 202 9Y0 9Y0 ? WB 19 9Y0 J 1 203 203 9Y0 9Y0 ? XB 20 PLM c 1 201 201 PLM PLM ? YB 21 9XX c 1 202 202 9XX 9XX ? ZB 23 9YF c 1 203 203 9YF 9YF ? AC 22 HEC I 1 301 301 HEC HEC ? BC 22 HEC I 1 302 302 HEC HEC ? CC 18 MQ9 I 1 303 303 MQ9 MQ9 ? DC 23 9YF I 1 304 304 9YF 9YF ? EC 24 FES Y 1 501 501 FES FES ? FC 23 9YF Y 1 502 502 9YF 9YF ? GC 23 9YF Y 1 503 503 9YF 9YF ? HC 20 PLM W 1 201 201 PLM PLM ? IC 21 9XX W 1 202 202 9XX 9XX ? JC 23 9YF W 1 203 203 9YF 9YF ? KC 23 9YF M 1 501 501 9YF 9YF ? LC 23 9YF M 1 502 502 9YF 9YF ? MC 24 FES M 1 503 503 FES FES ? # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CU _atom_site.label_atom_id CU _atom_site.label_comp_id CU _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id MB _atom_site.label_entity_id 14 _atom_site.Cartn_x 145.749 _atom_site.Cartn_y 132.3 _atom_site.Cartn_z 192.691 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 67.6 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CU _atom_site.auth_comp_id CU _atom_site.auth_seq_id 401 _atom_site.auth_asym_id K _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #