data_5LBR # _model_server_result.job_id ep_CltWyhG0cFCDHLgaucw _model_server_result.datetime_utc '2024-11-08 00:41:43' _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 5lbr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5LBR # _exptl.entry_id 5LBR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 585.67 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.84 _cell.angle_gamma 90 _cell.entry_id 5LBR _cell.length_a 96.22 _cell.length_b 55.49 _cell.length_c 71.63 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LBR _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 38 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 24 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id CBA _struct_conn.ptnr2_label_comp_id LBV _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id LBV _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 1.617 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C33 H37 N4 O6 1' _chem_comp.formula_weight 585.67 _chem_comp.id LBV _chem_comp.mon_nstd_flag . _chem_comp.name '3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2(R),3(E)- PHYTOCHROMOBILIN' # 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 C1A N_A LBV sing 179 n n C1A C2A LBV sing 180 n n C1B C2B LBV doub 181 n y C1B CHB LBV sing 182 n n O1B CGB LBV doub 183 n n C1C CHC LBV doub 184 z n C1D CHD LBV doub 185 z n C2A CMA LBV sing 186 n n C2A C3A LBV sing 187 n n C2B CMB LBV sing 188 n n C2C C1C LBV sing 189 n n O2C CGC LBV doub 190 n n C2D C1D LBV sing 191 n n C2D CMD LBV sing 192 n n C3A CAA LBV doub 193 e n C3B C2B LBV sing 194 n y C3B CAB LBV sing 195 n n C3C C2C LBV doub 196 n n C3C C4C LBV sing 197 n n C3D C2D LBV doub 198 n n C4A C3A LBV sing 199 n n C4A CHB LBV doub 200 z n C4B C3B LBV doub 201 n y C4B N_B LBV sing 202 n y C4C N_C LBV doub 203 n n C4D C3D LBV sing 204 n n C4D N_D LBV sing 205 n n CAA CBA LBV sing 206 n n CAC C2C LBV sing 207 n n CAC CBC LBV sing 208 n n CAD C3D LBV sing 209 n n CBB CAB LBV sing 210 n n CBB CGB LBV sing 211 n n CBD CAD LBV doub 212 n n CGB O2B LBV sing 213 n n CGC O1C LBV sing 214 n n CGC CBC LBV sing 215 n n CHC C4B LBV sing 216 n n CHD C4C LBV sing 217 n n CMC C3C LBV sing 218 n n N_A C4A LBV sing 219 n n O_A C1A LBV doub 220 n n N_B C1B LBV sing 221 n y N_C C1C LBV sing 222 n n N_D C1D LBV sing 223 n n O_D C4D LBV doub 224 n n O1C HO1C LBV sing 225 n n C2A H2A LBV sing 226 n n O2B HO2B LBV sing 227 n n CAA HAA1 LBV sing 228 n n CAB HAB1 LBV sing 229 n n CAB HAB2 LBV sing 230 n n CAC HAC1 LBV sing 231 n n CAC HAC2 LBV sing 232 n n CAD HAD1 LBV sing 233 n n CBA HBA1 LBV sing 234 n n CBA HBA2 LBV sing 235 n n CBA HBA3 LBV sing 236 n n CBB HBB1 LBV sing 237 n n CBB HBB2 LBV sing 238 n n CBC HBC1 LBV sing 239 n n CBC HBC2 LBV sing 240 n n CBD HBD1 LBV sing 241 n n CBD HBD2 LBV sing 242 n n CHB HHB1 LBV sing 243 n n CHC HHC1 LBV sing 244 n n CHD HHD1 LBV sing 245 n n CMA HMA1 LBV sing 246 n n CMA HMA2 LBV sing 247 n n CMA HMA3 LBV sing 248 n n CMB HMB1 LBV sing 249 n n CMB HMB2 LBV sing 250 n n CMB HMB3 LBV sing 251 n n CMC HMC1 LBV sing 252 n n CMC HMC2 LBV sing 253 n n CMC HMC3 LBV sing 254 n n CMD HMD1 LBV sing 255 n n CMD HMD2 LBV sing 256 n n CMD HMD3 LBV sing 257 n n N_A HAD LBV sing 258 n n N_B HAE LBV sing 259 n n N_C HAF LBV sing 260 n n N_D HAG LBV sing 261 n n # _atom_sites.entry_id 5LBR _atom_sites.fract_transf_matrix[1][1] 0.010393 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000516 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018021 _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] 0.013978 _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 B 2 LBV A 1 401 405 LBV LBV . C 3 ACT A 1 402 1 ACT ACT . D 4 HOH A 1 501 55 HOH HOH . D 4 HOH A 2 502 268 HOH HOH . D 4 HOH A 3 503 74 HOH HOH . D 4 HOH A 4 504 114 HOH HOH . D 4 HOH A 5 505 196 HOH HOH . D 4 HOH A 6 506 105 HOH HOH . D 4 HOH A 7 507 50 HOH HOH . D 4 HOH A 8 508 66 HOH HOH . D 4 HOH A 9 509 26 HOH HOH . D 4 HOH A 10 510 96 HOH HOH . D 4 HOH A 11 511 122 HOH HOH . D 4 HOH A 12 512 44 HOH HOH . D 4 HOH A 13 513 19 HOH HOH . D 4 HOH A 14 514 92 HOH HOH . D 4 HOH A 15 515 121 HOH HOH . D 4 HOH A 16 516 317 HOH HOH . D 4 HOH A 17 517 29 HOH HOH . D 4 HOH A 18 518 15 HOH HOH . D 4 HOH A 19 519 17 HOH HOH . D 4 HOH A 20 520 87 HOH HOH . D 4 HOH A 21 521 109 HOH HOH . D 4 HOH A 22 522 33 HOH HOH . D 4 HOH A 23 523 7 HOH HOH . D 4 HOH A 24 524 11 HOH HOH . D 4 HOH A 25 525 52 HOH HOH . D 4 HOH A 26 526 286 HOH HOH . D 4 HOH A 27 527 3 HOH HOH . D 4 HOH A 28 528 160 HOH HOH . D 4 HOH A 29 529 70 HOH HOH . D 4 HOH A 30 530 319 HOH HOH . D 4 HOH A 31 531 8 HOH HOH . D 4 HOH A 32 532 155 HOH HOH . D 4 HOH A 33 533 21 HOH HOH . D 4 HOH A 34 534 177 HOH HOH . D 4 HOH A 35 535 42 HOH HOH . D 4 HOH A 36 536 20 HOH HOH . D 4 HOH A 37 537 2 HOH HOH . D 4 HOH A 38 538 78 HOH HOH . D 4 HOH A 39 539 5 HOH HOH . D 4 HOH A 40 540 10 HOH HOH . D 4 HOH A 41 541 212 HOH HOH . D 4 HOH A 42 542 57 HOH HOH . D 4 HOH A 43 543 4 HOH HOH . D 4 HOH A 44 544 85 HOH HOH . D 4 HOH A 45 545 82 HOH HOH . D 4 HOH A 46 546 89 HOH HOH . D 4 HOH A 47 547 22 HOH HOH . D 4 HOH A 48 548 12 HOH HOH . D 4 HOH A 49 549 27 HOH HOH . D 4 HOH A 50 550 46 HOH HOH . D 4 HOH A 51 551 129 HOH HOH . D 4 HOH A 52 552 45 HOH HOH . D 4 HOH A 53 553 98 HOH HOH . D 4 HOH A 54 554 83 HOH HOH . D 4 HOH A 55 555 30 HOH HOH . D 4 HOH A 56 556 99 HOH HOH . D 4 HOH A 57 557 90 HOH HOH . D 4 HOH A 58 558 228 HOH HOH . D 4 HOH A 59 559 208 HOH HOH . D 4 HOH A 60 560 43 HOH HOH . D 4 HOH A 61 561 40 HOH HOH . D 4 HOH A 62 562 34 HOH HOH . D 4 HOH A 63 563 101 HOH HOH . D 4 HOH A 64 564 88 HOH HOH . D 4 HOH A 65 565 36 HOH HOH . D 4 HOH A 66 566 25 HOH HOH . D 4 HOH A 67 567 108 HOH HOH . D 4 HOH A 68 568 18 HOH HOH . D 4 HOH A 69 569 272 HOH HOH . D 4 HOH A 70 570 76 HOH HOH . D 4 HOH A 71 571 51 HOH HOH . D 4 HOH A 72 572 16 HOH HOH . D 4 HOH A 73 573 303 HOH HOH . D 4 HOH A 74 574 178 HOH HOH . D 4 HOH A 75 575 67 HOH HOH . D 4 HOH A 76 576 116 HOH HOH . D 4 HOH A 77 577 24 HOH HOH . D 4 HOH A 78 578 65 HOH HOH . D 4 HOH A 79 579 69 HOH HOH . D 4 HOH A 80 580 32 HOH HOH . D 4 HOH A 81 581 64 HOH HOH . D 4 HOH A 82 582 111 HOH HOH . D 4 HOH A 83 583 124 HOH HOH . D 4 HOH A 84 584 181 HOH HOH . D 4 HOH A 85 585 125 HOH HOH . D 4 HOH A 86 586 239 HOH HOH . D 4 HOH A 87 587 241 HOH HOH . D 4 HOH A 88 588 13 HOH HOH . D 4 HOH A 89 589 126 HOH HOH . D 4 HOH A 90 590 84 HOH HOH . D 4 HOH A 91 591 28 HOH HOH . D 4 HOH A 92 592 6 HOH HOH . D 4 HOH A 93 593 75 HOH HOH . D 4 HOH A 94 594 100 HOH HOH . D 4 HOH A 95 595 213 HOH HOH . D 4 HOH A 96 596 86 HOH HOH . D 4 HOH A 97 597 59 HOH HOH . D 4 HOH A 98 598 227 HOH HOH . D 4 HOH A 99 599 156 HOH HOH . D 4 HOH A 100 600 230 HOH HOH . D 4 HOH A 101 601 56 HOH HOH . D 4 HOH A 102 602 134 HOH HOH . D 4 HOH A 103 603 38 HOH HOH . D 4 HOH A 104 604 315 HOH HOH . D 4 HOH A 105 605 164 HOH HOH . D 4 HOH A 106 606 305 HOH HOH . D 4 HOH A 107 607 47 HOH HOH . D 4 HOH A 108 608 277 HOH HOH . D 4 HOH A 109 609 58 HOH HOH . D 4 HOH A 110 610 9 HOH HOH . D 4 HOH A 111 611 41 HOH HOH . D 4 HOH A 112 612 39 HOH HOH . D 4 HOH A 113 613 48 HOH HOH . D 4 HOH A 114 614 152 HOH HOH . D 4 HOH A 115 615 206 HOH HOH . D 4 HOH A 116 616 207 HOH HOH . D 4 HOH A 117 617 278 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 C1A LBV . . . B 2 -7.743 16.879 3.989 1 41.28 ? C1A LBV 401 A 1 HETATM 2 C C1B LBV . . . B 2 -8.206 19.106 7.953 1 33.04 ? C1B LBV 401 A 1 HETATM 3 O O1B LBV . . . B 2 -9.073 24.492 11.596 1 30.52 ? O1B LBV 401 A 1 HETATM 4 C C1C LBV . . . B 2 -12.772 19.458 8.048 1 30.71 ? C1C LBV 401 A 1 HETATM 5 O O1C LBV . . . B 2 -15.509 23.275 7.493 1 32.07 ? O1C LBV 401 A 1 HETATM 6 C C1D LBV . . . B 2 -15.265 17.465 4.445 1 33.05 ? C1D LBV 401 A 1 HETATM 7 C C2A LBV . . . B 2 -6.236 16.568 4.062 1 42.1 ? C2A LBV 401 A 1 HETATM 8 C C2B LBV . . . B 2 -8.025 19.86 9.119 1 32.8 ? C2B LBV 401 A 1 HETATM 9 O O2B LBV . . . B 2 -10.895 23.439 12.28 1 30.19 ? O2B LBV 401 A 1 HETATM 10 C C2C LBV . . . B 2 -14.115 19.663 8.377 1 30.38 ? C2C LBV 401 A 1 HETATM 11 O O2C LBV . . . B 2 -16.92 22.281 8.826 1 31.73 ? O2C LBV 401 A 1 HETATM 12 C C2D LBV . . . B 2 -15.534 16.448 3.511 1 34.8 ? C2D LBV 401 A 1 HETATM 13 C C3A LBV . . . B 2 -5.915 17.218 5.344 1 43.37 ? C3A LBV 401 A 1 HETATM 14 C C3B LBV . . . B 2 -9.281 20.264 9.531 1 31.52 ? C3B LBV 401 A 1 HETATM 15 C C3C LBV . . . B 2 -14.894 18.938 7.46 1 30.16 ? C3C LBV 401 A 1 HETATM 16 C C3D LBV . . . B 2 -16.586 16.886 2.72 1 35.47 ? C3D LBV 401 A 1 HETATM 17 C C4A LBV . . . B 2 -7.047 17.856 5.965 1 38.62 ? C4A LBV 401 A 1 HETATM 18 C C4B LBV . . . B 2 -10.213 19.762 8.629 1 31.05 ? C4B LBV 401 A 1 HETATM 19 C C4C LBV . . . B 2 -13.996 18.329 6.576 1 31.06 ? C4C LBV 401 A 1 HETATM 20 C C4D LBV . . . B 2 -16.915 18.159 3.191 1 34.38 ? C4D LBV 401 A 1 HETATM 21 C CAA LBV . . . B 2 -4.615 17.517 5.741 1 47.99 ? CAA LBV 401 A 1 HETATM 22 C CAB LBV . . . B 2 -9.572 21.135 10.714 1 30.98 ? CAB LBV 401 A 1 HETATM 23 C CAC LBV . . . B 2 -14.615 20.524 9.535 1 31.69 ? CAC LBV 401 A 1 HETATM 24 C CAD LBV . . . B 2 -17.204 16.129 1.566 1 37.18 ? CAD LBV 401 A 1 HETATM 25 C CBA LBV . . . B 2 -3.424 16.667 5.395 1 54.48 ? CBA LBV 401 A 1 HETATM 26 C CBB LBV . . . B 2 -9.812 22.58 10.341 1 29.38 ? CBB LBV 401 A 1 HETATM 27 C CBC LBV . . . B 2 -14.623 22.018 9.336 1 31.23 ? CBC LBV 401 A 1 HETATM 28 C CBD LBV . . . B 2 -18.515 16.313 1.19 1 39.61 ? CBD LBV 401 A 1 HETATM 29 C CGB LBV . . . B 2 -9.933 23.563 11.467 1 30.33 ? CGB LBV 401 A 1 HETATM 30 C CGC LBV . . . B 2 -15.742 22.561 8.507 1 32.16 ? CGC LBV 401 A 1 HETATM 31 C CHB LBV . . . B 2 -7.032 18.465 7.225 1 34.64 ? CHB LBV 401 A 1 HETATM 32 C CHC LBV . . . B 2 -11.701 20.049 8.763 1 31.55 ? CHC LBV 401 A 1 HETATM 33 C CHD LBV . . . B 2 -14.247 17.376 5.398 1 32.36 ? CHD LBV 401 A 1 HETATM 34 C CMA LBV . . . B 2 -5.611 17.248 2.888 1 43.04 ? CMA LBV 401 A 1 HETATM 35 C CMB LBV . . . B 2 -6.738 20.182 9.81 1 32.95 ? CMB LBV 401 A 1 HETATM 36 C CMC LBV . . . B 2 -16.381 18.852 7.437 1 30.5 ? CMC LBV 401 A 1 HETATM 37 C CMD LBV . . . B 2 -14.82 15.137 3.395 1 34.8 ? CMD LBV 401 A 1 HETATM 38 N N_A LBV . . . B 2 -8.174 17.661 5.169 1 39.81 ? N_A LBV 401 A 1 HETATM 39 O O_A LBV . . . B 2 -8.506 16.554 3.092 1 43.34 ? O_A LBV 401 A 1 HETATM 40 N N_B LBV . . . B 2 -9.542 19.065 7.684 1 33.07 ? N_B LBV 401 A 1 HETATM 41 N N_C LBV . . . B 2 -12.741 18.65 6.957 1 31.7 ? N_C LBV 401 A 1 HETATM 42 N N_D LBV . . . B 2 -16.11 18.482 4.231 1 34.14 ? N_D LBV 401 A 1 HETATM 43 O O_D LBV . . . B 2 -17.781 18.868 2.751 1 33.3 ? O_D LBV 401 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #