data_5GPN # _model_server_result.job_id IXJpbSr2mwpaSBh4OhzFGQ _model_server_result.datetime_utc '2025-03-04 21:32:10' _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 5gpn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"VC","auth_seq_id":502}' # _entry.id 5GPN # _exptl.entry_id 5GPN _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 456.344 _entity.id 68 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FLAVIN MONONUCLEOTIDE' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 84-meric _pdbx_struct_assembly.oligomeric_count 84 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 68 _struct_asym.id VC _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 covale ? covale1 K CB ARG 11 K ARG 11 1_555 DB CB ALA 26 7 ALA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 W NH2 ARG 101 W ARG 101 1_555 W O VAL 159 W VAL 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.264 ? covale ? covale3 W CB LYS 161 W LYS 161 1_555 Y CG ASN 285 Z ASN 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.642 ? covale ? covale4 W CB LYS 161 W LYS 161 1_555 Y OD1 ASN 285 Z ASN 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? covale ? covale5 Z SD MET 106 a MET 106 1_555 Z CE2 PHE 113 a PHE 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.651 ? metalc ? metalc1 X SG CYS 64 Y CYS 64 1_555 QC FE1 FES . Y FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc2 X O ASN 74 Y ASN 74 1_555 QC FE1 FES . Y FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc3 X O CYS 75 Y CYS 75 1_555 QC FE1 FES . Y FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc4 X NE2 HIS 124 Y HIS 124 1_555 OC FE2 SF4 . Y SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc5 X NE2 HIS 124 Y HIS 124 1_555 OC FE3 SF4 . Y SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc6 X O ILE 177 Y ILE 177 1_555 PC FE1 SF4 . Y SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc7 Z SG CYS 92 a CYS 92 1_555 RC FE1 SF4 . a SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc8 Z SG CYS 186 a CYS 186 1_555 RC FE2 SF4 . a SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc9 AA SG CYS 113 b CYS 113 1_555 SC FE1 SF4 . b SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc10 AA N CYS 155 b CYS 155 1_555 TC FE4 SF4 . b SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc11 AA N GLY 156 b GLY 156 1_555 TC FE4 SF4 . b SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc12 BA O SER 378 c SER 378 1_555 UC FE3 SF4 . c SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc13 BA OG1 THR 423 c THR 423 1_555 UC FE1 SF4 . c SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc14 IB O GLU 198 z GLU 198 1_555 ED CU CU . z CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc15 DD CU CU . z CU 301 1_555 ED CU CU . z CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? # _chem_comp.formula 'C17 H21 N4 O9 P' _chem_comp.formula_weight 456.344 _chem_comp.id FMN _chem_comp.mon_nstd_flag . _chem_comp.name 'FLAVIN MONONUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVIN MONOPHOSPHATE' # 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 N1 C2 FMN sing 87 n n N1 C10 FMN doub 88 n n C2 O2 FMN doub 89 n n C2 N3 FMN sing 90 n n N3 C4 FMN sing 91 n n N3 HN3 FMN sing 92 n n C4 O4 FMN doub 93 n n C4 C4A FMN sing 94 n n C4A N5 FMN doub 95 n n C4A C10 FMN sing 96 n n N5 C5A FMN sing 97 n n C5A C6 FMN doub 98 n y C5A C9A FMN sing 99 n y C6 C7 FMN sing 100 n y C6 H6 FMN sing 101 n n C7 C7M FMN sing 102 n n C7 C8 FMN doub 103 n y C7M HM71 FMN sing 104 n n C7M HM72 FMN sing 105 n n C7M HM73 FMN sing 106 n n C8 C8M FMN sing 107 n n C8 C9 FMN sing 108 n y C8M HM81 FMN sing 109 n n C8M HM82 FMN sing 110 n n C8M HM83 FMN sing 111 n n C9 C9A FMN doub 112 n y C9 H9 FMN sing 113 n n C9A N10 FMN sing 114 n n N10 C10 FMN sing 115 n n N10 C1' FMN sing 116 n n C1' C2' FMN sing 117 n n C1' "H1'1" FMN sing 118 n n C1' "H1'2" FMN sing 119 n n C2' O2' FMN sing 120 n n C2' C3' FMN sing 121 n n C2' H2' FMN sing 122 n n O2' HO2' FMN sing 123 n n C3' O3' FMN sing 124 n n C3' C4' FMN sing 125 n n C3' H3' FMN sing 126 n n O3' HO3' FMN sing 127 n n C4' O4' FMN sing 128 n n C4' C5' FMN sing 129 n n C4' H4' FMN sing 130 n n O4' HO4' FMN sing 131 n n C5' O5' FMN sing 132 n n C5' "H5'1" FMN sing 133 n n C5' "H5'2" FMN sing 134 n n O5' P FMN sing 135 n n P O1P FMN doub 136 n n P O2P FMN sing 137 n n P O3P FMN sing 138 n n O2P HOP2 FMN sing 139 n n O3P HOP3 FMN sing 140 n n # _atom_sites.entry_id 5GPN _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 GC 64 HEM C 1 401 380 HEM HEM . HC 64 HEM C 1 402 381 HEM HEM . IC 65 HEC D 1 301 242 HEC HEC . JC 66 FES E 1 201 197 FES FES . KC 64 HEM O 1 401 380 HEM HEM . LC 64 HEM O 1 402 381 HEM HEM . MC 65 HEC P 1 301 242 HEC HEC . NC 66 FES Q 1 201 197 FES FES . OC 67 SF4 Y 1 801 717 SF4 SF4 . PC 67 SF4 Y 1 802 718 SF4 SF4 . QC 66 FES Y 1 803 719 FES FES . RC 67 SF4 a 1 301 208 SF4 SF4 . SC 67 SF4 b 1 301 213 SF4 SF4 . TC 67 SF4 b 1 302 214 SF4 SF4 . UC 67 SF4 c 1 501 457 SF4 SF4 . VC 68 FMN c 1 502 458 FMN FMN . WC 66 FES d 1 301 217 FES FES . XC 69 NDP p 1 401 378 NDP NDP . YC 70 ZN 3 1 101 99 ZN ZN . ZC 71 HEA y 1 601 515 HEA HEA . AD 71 HEA y 1 602 516 HEA HEA . BD 72 CU y 1 603 517 CU CU . CD 73 MG y 1 604 518 MG MG . DD 72 CU z 1 301 228 CU CU . ED 72 CU z 1 302 229 CU CU . # 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 N1 FMN . . . VC 68 190.385 136.859 357.494 1 53.86 ? N1 FMN 502 c 1 HETATM 2 C C2 FMN . . . VC 68 190.204 137.192 356.194 1 50.53 ? C2 FMN 502 c 1 HETATM 3 O O2 FMN . . . VC 68 191.179 137.602 355.543 1 39.87 ? O2 FMN 502 c 1 HETATM 4 N N3 FMN . . . VC 68 189.025 137.104 355.571 1 47.75 ? N3 FMN 502 c 1 HETATM 5 C C4 FMN . . . VC 68 187.939 136.671 356.201 1 39.8 ? C4 FMN 502 c 1 HETATM 6 O O4 FMN . . . VC 68 186.858 136.593 355.598 1 37.12 ? O4 FMN 502 c 1 HETATM 7 C C4A FMN . . . VC 68 188.04 136.284 357.622 1 30.06 ? C4A FMN 502 c 1 HETATM 8 N N5 FMN . . . VC 68 186.978 135.842 358.318 1 12.59 ? N5 FMN 502 c 1 HETATM 9 C C5A FMN . . . VC 68 187.106 135.497 359.613 1 33.02 ? C5A FMN 502 c 1 HETATM 10 C C6 FMN . . . VC 68 185.998 135.043 360.305 1 40.71 ? C6 FMN 502 c 1 HETATM 11 C C7 FMN . . . VC 68 186.119 134.688 361.637 1 55.27 ? C7 FMN 502 c 1 HETATM 12 C C7M FMN . . . VC 68 184.909 134.199 362.382 1 61.58 ? C7M FMN 502 c 1 HETATM 13 C C8 FMN . . . VC 68 187.432 134.796 362.32 1 63.17 ? C8 FMN 502 c 1 HETATM 14 C C8M FMN . . . VC 68 187.564 134.411 363.764 1 71.41 ? C8M FMN 502 c 1 HETATM 15 C C9 FMN . . . VC 68 188.542 135.249 361.631 1 55.82 ? C9 FMN 502 c 1 HETATM 16 C C9A FMN . . . VC 68 188.417 135.601 360.3 1 45.2 ? C9A FMN 502 c 1 HETATM 17 N N10 FMN . . . VC 68 189.529 136.06 359.595 1 40.75 ? N10 FMN 502 c 1 HETATM 18 C C10 FMN . . . VC 68 189.367 136.408 358.249 1 45.69 ? C10 FMN 502 c 1 HETATM 19 C C1' FMN . . . VC 68 190.823 136.164 360.252 1 21.62 ? C1' FMN 502 c 1 HETATM 20 C C2' FMN . . . VC 68 190.998 137.598 360.702 1 13.62 ? C2' FMN 502 c 1 HETATM 21 O O2' FMN . . . VC 68 191.364 138.376 359.566 1 7.11 ? O2' FMN 502 c 1 HETATM 22 C C3' FMN . . . VC 68 192.065 137.701 361.779 1 24.7 ? C3' FMN 502 c 1 HETATM 23 O O3' FMN . . . VC 68 193.37 137.635 361.203 1 31.01 ? O3' FMN 502 c 1 HETATM 24 C C4' FMN . . . VC 68 191.908 136.546 362.75 1 20.68 ? C4' FMN 502 c 1 HETATM 25 O O4' FMN . . . VC 68 190.521 136.399 363.074 1 10.67 ? O4' FMN 502 c 1 HETATM 26 C C5' FMN . . . VC 68 192.732 136.779 364.007 1 35.3 ? C5' FMN 502 c 1 HETATM 27 O O5' FMN . . . VC 68 193.516 135.616 364.246 1 55.76 ? O5' FMN 502 c 1 HETATM 28 P P FMN . . . VC 68 193.907 135.181 365.739 1 33.3 ? P FMN 502 c 1 HETATM 29 O O1P FMN . . . VC 68 194.678 133.904 365.547 1 46.6 ? O1P FMN 502 c 1 HETATM 30 O O2P FMN . . . VC 68 192.573 135.011 366.418 1 26.8 ? O2P FMN 502 c 1 HETATM 31 O O3P FMN . . . VC 68 194.739 136.322 366.259 1 0 ? O3P FMN 502 c 1 # _model_server_stats.io_time_ms 134 _model_server_stats.parse_time_ms 41 _model_server_stats.create_model_time_ms 398 _model_server_stats.query_time_ms 1481 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 31 #