data_4R38 # _model_server_result.job_id JMoBGtwjlSIclIFyDXd-4g _model_server_result.datetime_utc '2024-11-17 14:19:14' _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 4r38 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":201}' # _entry.id 4R38 # _exptl.entry_id 4R38 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.364 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RIBOFLAVIN _entity.pdbx_number_of_molecules 4 _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 4R38 _cell.length_a 41.081 _cell.length_b 89.383 _cell.length_c 122.404 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4R38 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 PISA dimeric 2 software_defined_assembly 5 PISA dimeric 2 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 1 A,C,E,G,I,K 5 1 B,D,F,H,J,L 6 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 84 A CYS 78 1_555 A SG CYS 117 A CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 B SG CYS 84 B CYS 78 1_555 B SG CYS 117 B CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 C SG CYS 84 C CYS 78 1_555 C SG CYS 117 C CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 D SG CYS 84 D CYS 78 1_555 D SG CYS 117 D CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? # _chem_comp.formula 'C17 H20 N4 O6' _chem_comp.formula_weight 376.364 _chem_comp.id RBF _chem_comp.mon_nstd_flag . _chem_comp.name RIBOFLAVIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVINE;VITAMIN B2' # 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 RBF sing 277 n n N1 C10 RBF doub 278 n n C2 O2 RBF doub 279 n n C2 N3 RBF sing 280 n n N3 C4 RBF sing 281 n n N3 HN3 RBF sing 282 n n C4 O4 RBF doub 283 n n C4 C4A RBF sing 284 n n C4A N5 RBF doub 285 n n C4A C10 RBF sing 286 n n N5 C5A RBF sing 287 n n C5A C6 RBF doub 288 n y C5A C9A RBF sing 289 n y C6 C7 RBF sing 290 n y C6 HC6 RBF sing 291 n n C7 C7M RBF sing 292 n n C7 C8 RBF doub 293 n y C7M HC71 RBF sing 294 n n C7M HC72 RBF sing 295 n n C7M HC73 RBF sing 296 n n C8 C8M RBF sing 297 n n C8 C9 RBF sing 298 n y C8M HC81 RBF sing 299 n n C8M HC82 RBF sing 300 n n C8M HC83 RBF sing 301 n n C9 C9A RBF doub 302 n y C9 HC9 RBF sing 303 n n C9A N10 RBF sing 304 n n N10 C10 RBF sing 305 n n N10 C1' RBF sing 306 n n C1' C2' RBF sing 307 n n C1' HC11 RBF sing 308 n n C1' HC12 RBF sing 309 n n C2' O2' RBF sing 310 n n C2' C3' RBF sing 311 n n C2' HC2' RBF sing 312 n n O2' HO2' RBF sing 313 n n C3' O3' RBF sing 314 n n C3' C4' RBF sing 315 n n C3' HC3' RBF sing 316 n n O3' HO3' RBF sing 317 n n C4' O4' RBF sing 318 n n C4' C5' RBF sing 319 n n C4' HC4' RBF sing 320 n n O4' HO4' RBF sing 321 n n C5' O5' RBF sing 322 n n C5' HC51 RBF sing 323 n n C5' HC52 RBF sing 324 n n O5' HO5' RBF sing 325 n n # _atom_sites.entry_id 4R38 _atom_sites.fract_transf_matrix[1][1] 0.024342 _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] 0.011188 _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] 0.00817 _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 E 2 RBF A 1 201 201 RBF RBF . F 2 RBF B 1 201 201 RBF RBF . G 2 RBF C 1 201 201 RBF RBF . H 2 RBF D 1 201 201 RBF RBF . I 3 HOH A 1 301 15 HOH HOH . I 3 HOH A 2 302 19 HOH HOH . I 3 HOH A 3 303 20 HOH HOH . I 3 HOH A 4 304 24 HOH HOH . I 3 HOH A 5 305 32 HOH HOH . I 3 HOH A 6 306 34 HOH HOH . I 3 HOH A 7 307 35 HOH HOH . I 3 HOH A 8 308 42 HOH HOH . I 3 HOH A 9 309 43 HOH HOH . I 3 HOH A 10 310 45 HOH HOH . I 3 HOH A 11 311 46 HOH HOH . I 3 HOH A 12 312 48 HOH HOH . I 3 HOH A 13 313 51 HOH HOH . I 3 HOH A 14 314 57 HOH HOH . I 3 HOH A 15 315 59 HOH HOH . I 3 HOH A 16 316 62 HOH HOH . I 3 HOH A 17 317 65 HOH HOH . I 3 HOH A 18 318 70 HOH HOH . I 3 HOH A 19 319 71 HOH HOH . I 3 HOH A 20 320 75 HOH HOH . I 3 HOH A 21 321 82 HOH HOH . I 3 HOH A 22 322 86 HOH HOH . I 3 HOH A 23 323 88 HOH HOH . I 3 HOH A 24 324 95 HOH HOH . I 3 HOH A 25 325 102 HOH HOH . I 3 HOH A 26 326 103 HOH HOH . I 3 HOH A 27 327 105 HOH HOH . I 3 HOH A 28 328 109 HOH HOH . I 3 HOH A 29 329 115 HOH HOH . I 3 HOH A 30 330 117 HOH HOH . I 3 HOH A 31 331 124 HOH HOH . I 3 HOH A 32 332 133 HOH HOH . I 3 HOH A 33 333 137 HOH HOH . I 3 HOH A 34 334 142 HOH HOH . I 3 HOH A 35 335 144 HOH HOH . I 3 HOH A 36 336 145 HOH HOH . J 3 HOH B 1 301 25 HOH HOH . J 3 HOH B 2 302 44 HOH HOH . J 3 HOH B 3 303 56 HOH HOH . J 3 HOH B 4 304 78 HOH HOH . J 3 HOH B 5 305 89 HOH HOH . J 3 HOH B 6 306 122 HOH HOH . J 3 HOH B 7 307 126 HOH HOH . J 3 HOH B 8 308 135 HOH HOH . J 3 HOH B 9 309 138 HOH HOH . J 3 HOH B 10 310 143 HOH HOH . K 3 HOH C 1 301 1 HOH HOH . K 3 HOH C 2 302 6 HOH HOH . K 3 HOH C 3 303 7 HOH HOH . K 3 HOH C 4 304 8 HOH HOH . K 3 HOH C 5 305 10 HOH HOH . K 3 HOH C 6 306 12 HOH HOH . K 3 HOH C 7 307 14 HOH HOH . K 3 HOH C 8 308 22 HOH HOH . K 3 HOH C 9 309 26 HOH HOH . K 3 HOH C 10 310 29 HOH HOH . K 3 HOH C 11 311 31 HOH HOH . K 3 HOH C 12 312 36 HOH HOH . K 3 HOH C 13 313 37 HOH HOH . K 3 HOH C 14 314 39 HOH HOH . K 3 HOH C 15 315 50 HOH HOH . K 3 HOH C 16 316 55 HOH HOH . K 3 HOH C 17 317 63 HOH HOH . K 3 HOH C 18 318 68 HOH HOH . K 3 HOH C 19 319 73 HOH HOH . K 3 HOH C 20 320 74 HOH HOH . K 3 HOH C 21 321 84 HOH HOH . K 3 HOH C 22 322 85 HOH HOH . K 3 HOH C 23 323 91 HOH HOH . K 3 HOH C 24 324 92 HOH HOH . K 3 HOH C 25 325 93 HOH HOH . K 3 HOH C 26 326 94 HOH HOH . K 3 HOH C 27 327 97 HOH HOH . K 3 HOH C 28 328 98 HOH HOH . K 3 HOH C 29 329 104 HOH HOH . K 3 HOH C 30 330 108 HOH HOH . K 3 HOH C 31 331 112 HOH HOH . K 3 HOH C 32 332 116 HOH HOH . K 3 HOH C 33 333 125 HOH HOH . K 3 HOH C 34 334 128 HOH HOH . K 3 HOH C 35 335 130 HOH HOH . K 3 HOH C 36 336 134 HOH HOH . K 3 HOH C 37 337 139 HOH HOH . K 3 HOH C 38 338 140 HOH HOH . K 3 HOH C 39 339 141 HOH HOH . L 3 HOH D 1 301 2 HOH HOH . L 3 HOH D 2 302 3 HOH HOH . L 3 HOH D 3 303 4 HOH HOH . L 3 HOH D 4 304 5 HOH HOH . L 3 HOH D 5 305 9 HOH HOH . L 3 HOH D 6 306 11 HOH HOH . L 3 HOH D 7 307 13 HOH HOH . L 3 HOH D 8 308 16 HOH HOH . L 3 HOH D 9 309 17 HOH HOH . L 3 HOH D 10 310 18 HOH HOH . L 3 HOH D 11 311 21 HOH HOH . L 3 HOH D 12 312 23 HOH HOH . L 3 HOH D 13 313 27 HOH HOH . L 3 HOH D 14 314 28 HOH HOH . L 3 HOH D 15 315 30 HOH HOH . L 3 HOH D 16 316 33 HOH HOH . L 3 HOH D 17 317 38 HOH HOH . L 3 HOH D 18 318 40 HOH HOH . L 3 HOH D 19 319 41 HOH HOH . L 3 HOH D 20 320 47 HOH HOH . L 3 HOH D 21 321 49 HOH HOH . L 3 HOH D 22 322 52 HOH HOH . L 3 HOH D 23 323 53 HOH HOH . L 3 HOH D 24 324 54 HOH HOH . L 3 HOH D 25 325 58 HOH HOH . L 3 HOH D 26 326 60 HOH HOH . L 3 HOH D 27 327 61 HOH HOH . L 3 HOH D 28 328 64 HOH HOH . L 3 HOH D 29 329 66 HOH HOH . L 3 HOH D 30 330 67 HOH HOH . L 3 HOH D 31 331 69 HOH HOH . L 3 HOH D 32 332 72 HOH HOH . L 3 HOH D 33 333 76 HOH HOH . L 3 HOH D 34 334 77 HOH HOH . L 3 HOH D 35 335 79 HOH HOH . L 3 HOH D 36 336 80 HOH HOH . L 3 HOH D 37 337 81 HOH HOH . L 3 HOH D 38 338 83 HOH HOH . L 3 HOH D 39 339 87 HOH HOH . L 3 HOH D 40 340 90 HOH HOH . L 3 HOH D 41 341 96 HOH HOH . L 3 HOH D 42 342 99 HOH HOH . L 3 HOH D 43 343 100 HOH HOH . L 3 HOH D 44 344 101 HOH HOH . L 3 HOH D 45 345 106 HOH HOH . L 3 HOH D 46 346 107 HOH HOH . L 3 HOH D 47 347 110 HOH HOH . L 3 HOH D 48 348 111 HOH HOH . L 3 HOH D 49 349 113 HOH HOH . L 3 HOH D 50 350 114 HOH HOH . L 3 HOH D 51 351 118 HOH HOH . L 3 HOH D 52 352 119 HOH HOH . L 3 HOH D 53 353 120 HOH HOH . L 3 HOH D 54 354 121 HOH HOH . L 3 HOH D 55 355 123 HOH HOH . L 3 HOH D 56 356 127 HOH HOH . L 3 HOH D 57 357 129 HOH HOH . L 3 HOH D 58 358 131 HOH HOH . L 3 HOH D 59 359 132 HOH HOH . L 3 HOH D 60 360 136 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 N N1 RBF . . . H 2 5.567 7.356 68.139 1 29.32 ? N1 RBF 201 D 1 HETATM 2 C C2 RBF . . . H 2 4.304 7.06 68.567 1 33.54 ? C2 RBF 201 D 1 HETATM 3 O O2 RBF . . . H 2 4.07 6.992 69.772 1 31.34 ? O2 RBF 201 D 1 HETATM 4 N N3 RBF . . . H 2 3.333 6.767 67.684 1 32.75 ? N3 RBF 201 D 1 HETATM 5 C C4 RBF . . . H 2 3.571 6.768 66.335 1 27.92 ? C4 RBF 201 D 1 HETATM 6 O O4 RBF . . . H 2 2.698 6.476 65.509 1 30.67 ? O4 RBF 201 D 1 HETATM 7 C C4A RBF . . . H 2 4.833 7.191 65.854 1 28.44 ? C4A RBF 201 D 1 HETATM 8 N N5 RBF . . . H 2 5.09 7.326 64.539 1 29.78 ? N5 RBF 201 D 1 HETATM 9 C C5A RBF . . . H 2 6.31 7.745 64.116 1 29.22 ? C5A RBF 201 D 1 HETATM 10 C C6 RBF . . . H 2 6.57 7.904 62.727 1 31.13 ? C6 RBF 201 D 1 HETATM 11 C C7 RBF . . . H 2 7.83 8.33 62.281 1 31.12 ? C7 RBF 201 D 1 HETATM 12 C C7M RBF . . . H 2 8.095 8.483 60.76 1 33.6 ? C7M RBF 201 D 1 HETATM 13 C C8 RBF . . . H 2 8.828 8.629 63.196 1 30.02 ? C8 RBF 201 D 1 HETATM 14 C C8M RBF . . . H 2 10.228 9.104 62.774 1 27.88 ? C8M RBF 201 D 1 HETATM 15 C C9 RBF . . . H 2 8.593 8.492 64.557 1 27.86 ? C9 RBF 201 D 1 HETATM 16 C C9A RBF . . . H 2 7.323 8.064 65.054 1 28.06 ? C9A RBF 201 D 1 HETATM 17 N N10 RBF . . . H 2 7.102 7.907 66.412 1 26.77 ? N10 RBF 201 D 1 HETATM 18 C C10 RBF . . . H 2 5.832 7.491 66.826 1 28.94 ? C10 RBF 201 D 1 HETATM 19 C C1' RBF . . . H 2 8.1 8.117 67.463 1 27.67 ? C1' RBF 201 D 1 HETATM 20 C C2' RBF . . . H 2 8.256 9.479 68.092 1 27.83 ? C2' RBF 201 D 1 HETATM 21 O O2' RBF . . . H 2 8.07 10.389 67.047 1 30.14 ? O2' RBF 201 D 1 HETATM 22 C C3' RBF . . . H 2 9.648 9.613 68.689 1 30.08 ? C3' RBF 201 D 1 HETATM 23 O O3' RBF . . . H 2 10.557 9.496 67.627 1 34.93 ? O3' RBF 201 D 1 HETATM 24 C C4' RBF . . . H 2 9.97 8.531 69.732 1 29.69 ? C4' RBF 201 D 1 HETATM 25 O O4' RBF . . . H 2 9.035 8.554 70.773 1 32.28 ? O4' RBF 201 D 1 HETATM 26 C C5' RBF . . . H 2 11.363 8.76 70.299 1 31.36 ? C5' RBF 201 D 1 HETATM 27 O O5' RBF . . . H 2 11.343 9.946 71.015 1 36.17 ? O5' RBF 201 D 1 HETATM 28 H HN3 RBF . . . H 2 2.5 6.516 67.996 1 39.3 ? HN3 RBF 201 D 1 HETATM 29 H HC6 RBF . . . H 2 5.866 7.71 62.076 1 37.35 ? HC6 RBF 201 D 1 HETATM 30 H HC71 RBF . . . H 2 7.281 8.255 60.268 1 40.31 ? HC71 RBF 201 D 1 HETATM 31 H HC72 RBF . . . H 2 8.344 9.412 60.561 1 40.31 ? HC72 RBF 201 D 1 HETATM 32 H HC73 RBF . . . H 2 8.818 7.874 60.488 1 40.31 ? HC73 RBF 201 D 1 HETATM 33 H HC81 RBF . . . H 2 10.632 8.444 62.176 1 33.46 ? HC81 RBF 201 D 1 HETATM 34 H HC82 RBF . . . H 2 10.789 9.2 63.571 1 33.46 ? HC82 RBF 201 D 1 HETATM 35 H HC83 RBF . . . H 2 10.16 9.97 62.321 1 33.46 ? HC83 RBF 201 D 1 HETATM 36 H HC9 RBF . . . H 2 9.316 8.68 65.188 1 33.44 ? HC9 RBF 201 D 1 HETATM 37 H HC11 RBF . . . H 2 7.889 7.498 68.182 1 33.21 ? HC11 RBF 201 D 1 HETATM 38 H HC12 RBF . . . H 2 8.975 7.858 67.095 1 33.21 ? HC12 RBF 201 D 1 HETATM 39 H HC2' RBF . . . H 2 7.578 9.613 68.781 1 33.39 ? HC2' RBF 201 D 1 HETATM 40 H HO2' RBF . . . H 2 7.761 11.153 67.372 1 36.17 ? HO2' RBF 201 D 1 HETATM 41 H HC3' RBF . . . H 2 9.741 10.496 69.099 1 36.09 ? HC3' RBF 201 D 1 HETATM 42 H HO3' RBF . . . H 2 11.078 10.215 67.602 1 41.92 ? HO3' RBF 201 D 1 HETATM 43 H HC4' RBF . . . H 2 9.943 7.66 69.303 1 35.63 ? HC4' RBF 201 D 1 HETATM 44 H HO4' RBF . . . H 2 9.085 7.795 71.234 1 38.74 ? HO4' RBF 201 D 1 HETATM 45 H HC51 RBF . . . H 2 12.014 8.826 69.566 1 37.63 ? HC51 RBF 201 D 1 HETATM 46 H HC52 RBF . . . H 2 11.606 8.02 70.891 1 37.63 ? HC52 RBF 201 D 1 HETATM 47 H HO5' RBF . . . H 2 12.081 10.004 71.517 1 43.41 ? HO5' RBF 201 D 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 47 #