data_7YML # _model_server_result.job_id 3TBoYxjiqXzL08kiUyfjRg _model_server_result.datetime_utc '2025-02-26 07:38:00' _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 7yml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":302}' # _entry.id 7YML # _exptl.entry_id 7YML _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 889.215 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BACTERIOPHEOPHYTIN A' _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 90 _cell.angle_gamma 90 _cell.entry_id 7YML _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YML _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 _pdbx_struct_assembly.details author_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,NC,OC,PC,QC,RC,SC,TC,UC,VC,WC,XC,YC,ZC,AD,BD,CD,DD,ED,FD,GD,HD,ID,JD,KD _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 ? _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 ? 8 Z N N ? 8 NA 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 covale ? covale1 D C FME 1 A FME 1 1_555 D N SER 2 A SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 F C FME 1 D FME 1 1_555 F N SER 2 D SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 H C FME 1 F FME 1 1_555 H N SER 2 F SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 J C FME 1 I FME 1 1_555 J N SER 2 I SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 L C FME 1 K FME 1 1_555 L N SER 2 K SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 N C FME 1 O FME 1 1_555 N N SER 2 O SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 P C FME 1 Q FME 1 1_555 P N SER 2 Q SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 R C FME 1 S FME 1 1_555 R N SER 2 S SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 T C FME 1 V FME 1 1_555 T N SER 2 V SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A NE2 HIS 191 L HIS 191 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc2 A NE2 HIS 231 L HIS 231 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc3 B NE2 HIS 218 M HIS 218 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc4 B OE1 GLU 233 M GLU 233 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc5 B OE2 GLU 233 M GLU 233 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc6 B NE2 HIS 265 M HIS 265 1_555 OA FE FE . M FE 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc7 RB MG BCL . F BCL 101 1_555 SB O1 MYR . F MYR 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? # _chem_comp.formula 'C55 H76 N4 O6' _chem_comp.formula_weight 889.215 _chem_comp.id BPH _chem_comp.mon_nstd_flag . _chem_comp.name 'BACTERIOPHEOPHYTIN A' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7YML _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 Y 7 BCL L 1 301 301 BCL BCL . Z 8 BPH L 1 302 302 BPH BPH . AA 9 U10 L 1 303 310 U10 U10 . BA 9 U10 L 1 304 312 U10 U10 . CA 10 PGV L 1 305 316 PGV PGV . DA 11 PEE L 1 306 317 PEE PEE . EA 12 LDA L 1 307 318 LDA LDA . FA 13 LMT L 1 308 319 LMT LMT . GA 13 LMT L 1 309 320 LMT LMT . HA 7 BCL L 1 310 401 BCL BCL . IA 13 LMT L 1 311 307 LMT LMT . JA 9 U10 M 1 401 311 U10 U10 . KA 10 PGV M 1 402 315 PGV PGV . LA 7 BCL M 1 403 402 BCL BCL . MA 7 BCL M 1 404 403 BCL BCL . NA 8 BPH M 1 405 404 BPH BPH . OA 14 FE M 1 406 410 FE FE . PA 9 U10 M 1 407 411 U10 U10 . QA 15 SPO M 1 408 412 SPO SPO . RA 13 LMT M 1 409 418 LMT LMT . SA 13 LMT M 1 410 420 LMT LMT . TA 13 LMT M 1 411 422 LMT LMT . UA 13 LMT M 1 412 423 LMT LMT . VA 10 PGV M 1 413 424 PGV PGV . WA 10 PGV M 1 414 425 PGV PGV . XA 10 PGV M 1 415 426 PGV PGV . YA 12 LDA M 1 416 428 LDA LDA . ZA 13 LMT M 1 417 429 LMT LMT . AB 12 LDA M 1 418 430 LDA LDA . BB 12 LDA M 1 419 431 LDA LDA . CB 12 LDA M 1 420 433 LDA LDA . DB 12 LDA H 1 301 413 LDA LDA . EB 12 LDA H 1 302 416 LDA LDA . FB 10 PGV H 1 303 305 PGV PGV . GB 10 PGV H 1 304 306 PGV PGV . HB 7 BCL A 1 101 101 BCL BCL . IB 13 LMT A 1 102 201 LMT LMT . JB 7 BCL B 1 101 101 BCL BCL . KB 15 SPO D 1 101 110 SPO SPO . LB 7 BCL D 1 102 101 BCL BCL . MB 15 SPO D 1 103 110 SPO SPO . NB 12 LDA D 1 104 112 LDA LDA . OB 15 SPO D 1 105 110 SPO SPO . PB 15 SPO E 1 101 111 SPO SPO . QB 7 BCL E 1 102 101 BCL BCL . RB 7 BCL F 1 101 310 BCL BCL . SB 16 MYR F 1 102 311 MYR MYR . TB 7 BCL F 1 103 101 BCL BCL . UB 15 SPO F 1 104 111 SPO SPO . VB 7 BCL G 1 101 101 BCL BCL . WB 15 SPO G 1 102 111 SPO SPO . XB 13 LMT I 1 101 314 LMT LMT . YB 7 BCL I 1 102 101 BCL BCL . ZB 15 SPO I 1 103 110 SPO SPO . AC 15 SPO I 1 104 110 SPO SPO . BC 7 BCL J 1 101 101 BCL BCL . CC 13 LMT K 1 101 302 LMT LMT . DC 7 BCL K 1 102 101 BCL BCL . EC 15 SPO N 1 101 111 SPO SPO . FC 7 BCL N 1 102 101 BCL BCL . GC 12 LDA O 1 101 435 LDA LDA . HC 7 BCL O 1 102 101 BCL BCL . IC 15 SPO O 1 103 110 SPO SPO . JC 15 SPO O 1 104 110 SPO SPO . KC 15 SPO P 1 101 111 SPO SPO . LC 7 BCL P 1 102 101 BCL BCL . MC 13 LMT Q 1 101 414 LMT LMT . NC 12 LDA Q 1 102 417 LDA LDA . OC 10 PGV Q 1 103 427 PGV PGV . PC 12 LDA Q 1 104 434 LDA LDA . QC 7 BCL Q 1 105 101 BCL BCL . RC 15 SPO R 1 101 111 SPO SPO . SC 7 BCL R 1 102 101 BCL BCL . TC 13 LMT S 1 101 415 LMT LMT . UC 13 LMT S 1 102 419 LMT LMT . VC 7 BCL S 1 103 101 BCL BCL . WC 15 SPO S 1 104 110 SPO SPO . XC 15 SPO S 1 105 110 SPO SPO . YC 15 SPO T 1 101 111 SPO SPO . ZC 7 BCL T 1 102 101 BCL BCL . AD 7 BCL V 1 101 101 BCL BCL . BD 15 SPO W 1 101 111 SPO SPO . CD 7 BCL W 1 102 101 BCL BCL . DD 13 LMT Y 1 101 421 LMT LMT . ED 7 BCL Y 1 102 101 BCL BCL . FD 13 LMT Y 1 103 432 LMT LMT . GD 7 BCL Z 1 101 101 BCL BCL . HD 13 LMT X 1 101 321 LMT LMT . ID 13 LMT X 1 102 301 LMT LMT . JD 17 HOH L 1 401 1 HOH HOH . JD 17 HOH L 2 402 3 HOH HOH . JD 17 HOH L 3 403 4 HOH HOH . JD 17 HOH L 4 404 2 HOH HOH . KD 17 HOH M 1 501 6 HOH HOH . KD 17 HOH M 2 502 5 HOH HOH . KD 17 HOH M 3 503 7 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 O O1D BPH . . . Z 8 167.467 157.823 180.696 1 39.29 ? O1D BPH 302 L 1 HETATM 2 C CGD BPH . . . Z 8 166.764 157.268 179.9 1 30.78 ? CGD BPH 302 L 1 HETATM 3 O O2D BPH . . . Z 8 166.068 157.894 178.957 1 37.85 ? O2D BPH 302 L 1 HETATM 4 C CED BPH . . . Z 8 166.387 159.289 178.756 1 29.96 ? CED BPH 302 L 1 HETATM 5 C CBD BPH . . . Z 8 166.626 155.792 179.786 1 25.14 ? CBD BPH 302 L 1 HETATM 6 C CHA BPH . . . Z 8 166.696 155.362 178.331 1 24.86 ? CHA BPH 302 L 1 HETATM 7 C C4D BPH . . . Z 8 165.482 154.653 178.057 1 25.01 ? C4D BPH 302 L 1 HETATM 8 C C3D BPH . . . Z 8 164.606 154.644 179.14 1 28.87 ? C3D BPH 302 L 1 HETATM 9 C CAD BPH . . . Z 8 165.23 155.368 180.25 1 27.97 ? CAD BPH 302 L 1 HETATM 10 O OBD BPH . . . Z 8 164.783 155.597 181.351 1 36.72 ? OBD BPH 302 L 1 HETATM 11 C C2D BPH . . . Z 8 163.465 153.934 178.735 1 27.79 ? C2D BPH 302 L 1 HETATM 12 C CMD BPH . . . Z 8 162.243 153.659 179.556 1 25.73 ? CMD BPH 302 L 1 HETATM 13 C C1D BPH . . . Z 8 163.682 153.53 177.42 1 27.27 ? C1D BPH 302 L 1 HETATM 14 N ND BPH . . . Z 8 164.917 153.978 177.032 1 24.45 ? ND BPH 302 L 1 HETATM 15 C CHD BPH . . . Z 8 162.874 152.81 176.554 1 26.56 ? CHD BPH 302 L 1 HETATM 16 C C4C BPH . . . Z 8 163.151 152.501 175.219 1 28.11 ? C4C BPH 302 L 1 HETATM 17 C C3C BPH . . . Z 8 162.172 151.854 174.263 1 28.33 ? C3C BPH 302 L 1 HETATM 18 C CAC BPH . . . Z 8 161.352 150.713 174.868 1 30.09 ? CAC BPH 302 L 1 HETATM 19 C CBC BPH . . . Z 8 162.197 149.603 175.448 1 30.49 ? CBC BPH 302 L 1 HETATM 20 C C2C BPH . . . Z 8 163.073 151.462 173.093 1 24.06 ? C2C BPH 302 L 1 HETATM 21 C CMC BPH . . . Z 8 162.498 151.721 171.705 1 30.98 ? CMC BPH 302 L 1 HETATM 22 C C1C BPH . . . Z 8 164.31 152.293 173.344 1 27.78 ? C1C BPH 302 L 1 HETATM 23 N NC BPH . . . Z 8 164.352 152.795 174.612 1 32.33 ? NC BPH 302 L 1 HETATM 24 C CHC BPH . . . Z 8 165.305 152.487 172.385 1 20.81 ? CHC BPH 302 L 1 HETATM 25 C C4B BPH . . . Z 8 166.494 153.295 172.401 1 22.39 ? C4B BPH 302 L 1 HETATM 26 C C3B BPH . . . Z 8 167.463 153.492 171.362 1 29.26 ? C3B BPH 302 L 1 HETATM 27 C CAB BPH . . . Z 8 167.474 152.917 169.997 1 32.4 ? CAB BPH 302 L 1 HETATM 28 C CBB BPH . . . Z 8 166.288 152.187 169.457 1 32.81 ? CBB BPH 302 L 1 HETATM 29 O OBB BPH . . . Z 8 168.472 153.002 169.293 1 30.62 ? OBB BPH 302 L 1 HETATM 30 C C2B BPH . . . Z 8 168.441 154.368 171.884 1 36.41 ? C2B BPH 302 L 1 HETATM 31 C CMB BPH . . . Z 8 169.669 154.896 171.2 1 33.25 ? CMB BPH 302 L 1 HETATM 32 C C1B BPH . . . Z 8 168.083 154.686 173.211 1 30.61 ? C1B BPH 302 L 1 HETATM 33 N NB BPH . . . Z 8 166.907 154.028 173.491 1 27.84 ? NB BPH 302 L 1 HETATM 34 C CHB BPH . . . Z 8 168.776 155.513 174.061 1 28.6 ? CHB BPH 302 L 1 HETATM 35 C C4A BPH . . . Z 8 168.545 155.774 175.413 1 30.83 ? C4A BPH 302 L 1 HETATM 36 C C3A BPH . . . Z 8 169.335 156.772 176.231 1 30.72 ? C3A BPH 302 L 1 HETATM 37 C CMA BPH . . . Z 8 168.951 158.18 175.791 1 28.27 ? CMA BPH 302 L 1 HETATM 38 C C2A BPH . . . Z 8 168.94 156.402 177.651 1 27.58 ? C2A BPH 302 L 1 HETATM 39 C C1A BPH . . . Z 8 167.67 155.628 177.417 1 30.86 ? C1A BPH 302 L 1 HETATM 40 N NA BPH . . . Z 8 167.552 155.173 176.14 1 35.49 ? NA BPH 302 L 1 HETATM 41 C CAA BPH . . . Z 8 169.946 155.55 178.417 1 22.78 ? CAA BPH 302 L 1 HETATM 42 C CBA BPH . . . Z 8 171.242 156.302 178.682 1 29.83 ? CBA BPH 302 L 1 HETATM 43 C CGA BPH . . . Z 8 172.303 155.405 179.242 1 42.73 ? CGA BPH 302 L 1 HETATM 44 O O1A BPH . . . Z 8 172.422 154.238 178.994 1 47.68 ? O1A BPH 302 L 1 HETATM 45 O O2A BPH . . . Z 8 173.099 156.052 180.074 1 53.04 ? O2A BPH 302 L 1 HETATM 46 C C1 BPH . . . Z 8 174.29 155.361 180.492 1 38.43 ? C1 BPH 302 L 1 HETATM 47 C C2 BPH . . . Z 8 175.268 155.308 179.369 1 37.66 ? C2 BPH 302 L 1 HETATM 48 C C3 BPH . . . Z 8 175.779 156.378 178.772 1 42.12 ? C3 BPH 302 L 1 HETATM 49 C C4 BPH . . . Z 8 175.477 157.783 179.196 1 34.58 ? C4 BPH 302 L 1 HETATM 50 C C5 BPH . . . Z 8 176.726 156.248 177.62 1 35.75 ? C5 BPH 302 L 1 HETATM 51 C C6 BPH . . . Z 8 177.213 154.855 177.426 1 30.35 ? C6 BPH 302 L 1 HETATM 52 C C7 BPH . . . Z 8 178.216 154.755 176.299 1 33.22 ? C7 BPH 302 L 1 HETATM 53 C C8 BPH . . . Z 8 178.958 153.431 176.191 1 38.95 ? C8 BPH 302 L 1 HETATM 54 C C9 BPH . . . Z 8 179.758 153.129 177.445 1 42.97 ? C9 BPH 302 L 1 HETATM 55 C C10 BPH . . . Z 8 179.831 153.407 174.943 1 38.7 ? C10 BPH 302 L 1 HETATM 56 C C11 BPH . . . Z 8 179.08 153.255 173.655 1 35.09 ? C11 BPH 302 L 1 HETATM 57 C C12 BPH . . . Z 8 178.509 151.875 173.511 1 37.6 ? C12 BPH 302 L 1 HETATM 58 C C13 BPH . . . Z 8 177.468 151.701 172.417 1 34.73 ? C13 BPH 302 L 1 HETATM 59 C C14 BPH . . . Z 8 177.143 150.238 172.182 1 35.58 ? C14 BPH 302 L 1 HETATM 60 C C15 BPH . . . Z 8 177.87 152.415 171.134 1 33.74 ? C15 BPH 302 L 1 HETATM 61 C C16 BPH . . . Z 8 177.069 152.05 169.917 1 34.88 ? C16 BPH 302 L 1 HETATM 62 C C17 BPH . . . Z 8 177.056 153.102 168.846 1 34.68 ? C17 BPH 302 L 1 HETATM 63 C C18 BPH . . . Z 8 176.496 152.658 167.501 1 33.3 ? C18 BPH 302 L 1 HETATM 64 C C19 BPH . . . Z 8 176.113 153.848 166.639 1 31.84 ? C19 BPH 302 L 1 HETATM 65 C C20 BPH . . . Z 8 175.326 151.704 167.665 1 25.64 ? C20 BPH 302 L 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 65 #