data_4Y3I # _model_server_result.job_id wpC-VqunxvDMkHzCwEWrZQ _model_server_result.datetime_utc '2024-11-05 00:36:30' _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 4y3i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4Y3I # _exptl.entry_id 4Y3I _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 116.22 _cell.angle_gamma 90 _cell.entry_id 4Y3I _cell.length_a 89.481 _cell.length_b 51.917 _cell.length_c 80.339 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y3I _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 21 _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 1.66 _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 173 n n C1A C2A LBV sing 174 n n C1B C2B LBV doub 175 n y C1B CHB LBV sing 176 n n O1B CGB LBV doub 177 n n C1C CHC LBV doub 178 z n C1D CHD LBV doub 179 z n C2A CMA LBV sing 180 n n C2A C3A LBV sing 181 n n C2B CMB LBV sing 182 n n C2C C1C LBV sing 183 n n O2C CGC LBV doub 184 n n C2D C1D LBV sing 185 n n C2D CMD LBV sing 186 n n C3A CAA LBV doub 187 e n C3B C2B LBV sing 188 n y C3B CAB LBV sing 189 n n C3C C2C LBV doub 190 n n C3C C4C LBV sing 191 n n C3D C2D LBV doub 192 n n C4A C3A LBV sing 193 n n C4A CHB LBV doub 194 z n C4B C3B LBV doub 195 n y C4B N_B LBV sing 196 n y C4C N_C LBV doub 197 n n C4D C3D LBV sing 198 n n C4D N_D LBV sing 199 n n CAA CBA LBV sing 200 n n CAC C2C LBV sing 201 n n CAC CBC LBV sing 202 n n CAD C3D LBV sing 203 n n CBB CAB LBV sing 204 n n CBB CGB LBV sing 205 n n CBD CAD LBV doub 206 n n CGB O2B LBV sing 207 n n CGC O1C LBV sing 208 n n CGC CBC LBV sing 209 n n CHC C4B LBV sing 210 n n CHD C4C LBV sing 211 n n CMC C3C LBV sing 212 n n N_A C4A LBV sing 213 n n O_A C1A LBV doub 214 n n N_B C1B LBV sing 215 n y N_C C1C LBV sing 216 n n N_D C1D LBV sing 217 n n O_D C4D LBV doub 218 n n O1C HO1C LBV sing 219 n n C2A H2A LBV sing 220 n n O2B HO2B LBV sing 221 n n CAA HAA1 LBV sing 222 n n CAB HAB1 LBV sing 223 n n CAB HAB2 LBV sing 224 n n CAC HAC1 LBV sing 225 n n CAC HAC2 LBV sing 226 n n CAD HAD1 LBV sing 227 n n CBA HBA1 LBV sing 228 n n CBA HBA2 LBV sing 229 n n CBA HBA3 LBV sing 230 n n CBB HBB1 LBV sing 231 n n CBB HBB2 LBV sing 232 n n CBC HBC1 LBV sing 233 n n CBC HBC2 LBV sing 234 n n CBD HBD1 LBV sing 235 n n CBD HBD2 LBV sing 236 n n CHB HHB1 LBV sing 237 n n CHC HHC1 LBV sing 238 n n CHD HHD1 LBV sing 239 n n CMA HMA1 LBV sing 240 n n CMA HMA2 LBV sing 241 n n CMA HMA3 LBV sing 242 n n CMB HMB1 LBV sing 243 n n CMB HMB2 LBV sing 244 n n CMB HMB3 LBV sing 245 n n CMC HMC1 LBV sing 246 n n CMC HMC2 LBV sing 247 n n CMC HMC3 LBV sing 248 n n CMD HMD1 LBV sing 249 n n CMD HMD2 LBV sing 250 n n CMD HMD3 LBV sing 251 n n N_A HAD LBV sing 252 n n N_B HAE LBV sing 253 n n N_C HAF LBV sing 254 n n N_D HAG LBV sing 255 n n # _atom_sites.entry_id 4Y3I _atom_sites.fract_transf_matrix[1][1] 0.011176 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005505 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019262 _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] 0.013876 _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 1 LBV LBV . C 3 HOH A 1 501 73 HOH HOH . C 3 HOH A 2 502 60 HOH HOH . C 3 HOH A 3 503 93 HOH HOH . C 3 HOH A 4 504 58 HOH HOH . C 3 HOH A 5 505 98 HOH HOH . C 3 HOH A 6 506 102 HOH HOH . C 3 HOH A 7 507 55 HOH HOH . C 3 HOH A 8 508 69 HOH HOH . C 3 HOH A 9 509 86 HOH HOH . C 3 HOH A 10 510 54 HOH HOH . C 3 HOH A 11 511 12 HOH HOH . C 3 HOH A 12 512 82 HOH HOH . C 3 HOH A 13 513 119 HOH HOH . C 3 HOH A 14 514 71 HOH HOH . C 3 HOH A 15 515 78 HOH HOH . C 3 HOH A 16 516 32 HOH HOH . C 3 HOH A 17 517 74 HOH HOH . C 3 HOH A 18 518 45 HOH HOH . C 3 HOH A 19 519 112 HOH HOH . C 3 HOH A 20 520 46 HOH HOH . C 3 HOH A 21 521 34 HOH HOH . C 3 HOH A 22 522 108 HOH HOH . C 3 HOH A 23 523 20 HOH HOH . C 3 HOH A 24 524 62 HOH HOH . C 3 HOH A 25 525 35 HOH HOH . C 3 HOH A 26 526 84 HOH HOH . C 3 HOH A 27 527 88 HOH HOH . C 3 HOH A 28 528 91 HOH HOH . C 3 HOH A 29 529 33 HOH HOH . C 3 HOH A 30 530 116 HOH HOH . C 3 HOH A 31 531 90 HOH HOH . C 3 HOH A 32 532 83 HOH HOH . C 3 HOH A 33 533 118 HOH HOH . C 3 HOH A 34 534 1 HOH HOH . C 3 HOH A 35 535 2 HOH HOH . C 3 HOH A 36 536 3 HOH HOH . C 3 HOH A 37 537 4 HOH HOH . C 3 HOH A 38 538 5 HOH HOH . C 3 HOH A 39 539 6 HOH HOH . C 3 HOH A 40 540 7 HOH HOH . C 3 HOH A 41 541 8 HOH HOH . C 3 HOH A 42 542 9 HOH HOH . C 3 HOH A 43 543 10 HOH HOH . C 3 HOH A 44 544 11 HOH HOH . C 3 HOH A 45 545 13 HOH HOH . C 3 HOH A 46 546 14 HOH HOH . C 3 HOH A 47 547 15 HOH HOH . C 3 HOH A 48 548 16 HOH HOH . C 3 HOH A 49 549 17 HOH HOH . C 3 HOH A 50 550 18 HOH HOH . C 3 HOH A 51 551 19 HOH HOH . C 3 HOH A 52 552 21 HOH HOH . C 3 HOH A 53 553 22 HOH HOH . C 3 HOH A 54 554 23 HOH HOH . C 3 HOH A 55 555 24 HOH HOH . C 3 HOH A 56 556 25 HOH HOH . C 3 HOH A 57 557 26 HOH HOH . C 3 HOH A 58 558 27 HOH HOH . C 3 HOH A 59 559 28 HOH HOH . C 3 HOH A 60 560 29 HOH HOH . C 3 HOH A 61 561 30 HOH HOH . C 3 HOH A 62 562 31 HOH HOH . C 3 HOH A 63 563 36 HOH HOH . C 3 HOH A 64 564 37 HOH HOH . C 3 HOH A 65 565 38 HOH HOH . C 3 HOH A 66 566 39 HOH HOH . C 3 HOH A 67 567 40 HOH HOH . C 3 HOH A 68 568 41 HOH HOH . C 3 HOH A 69 569 42 HOH HOH . C 3 HOH A 70 570 43 HOH HOH . C 3 HOH A 71 571 44 HOH HOH . C 3 HOH A 72 572 47 HOH HOH . C 3 HOH A 73 573 48 HOH HOH . C 3 HOH A 74 574 49 HOH HOH . C 3 HOH A 75 575 50 HOH HOH . C 3 HOH A 76 576 51 HOH HOH . C 3 HOH A 77 577 52 HOH HOH . C 3 HOH A 78 578 53 HOH HOH . C 3 HOH A 79 579 56 HOH HOH . C 3 HOH A 80 580 57 HOH HOH . C 3 HOH A 81 581 59 HOH HOH . C 3 HOH A 82 582 61 HOH HOH . C 3 HOH A 83 583 63 HOH HOH . C 3 HOH A 84 584 64 HOH HOH . C 3 HOH A 85 585 65 HOH HOH . C 3 HOH A 86 586 66 HOH HOH . C 3 HOH A 87 587 67 HOH HOH . C 3 HOH A 88 588 68 HOH HOH . C 3 HOH A 89 589 70 HOH HOH . C 3 HOH A 90 590 72 HOH HOH . C 3 HOH A 91 591 75 HOH HOH . C 3 HOH A 92 592 76 HOH HOH . C 3 HOH A 93 593 77 HOH HOH . C 3 HOH A 94 594 79 HOH HOH . C 3 HOH A 95 595 80 HOH HOH . C 3 HOH A 96 596 81 HOH HOH . C 3 HOH A 97 597 85 HOH HOH . C 3 HOH A 98 598 87 HOH HOH . C 3 HOH A 99 599 89 HOH HOH . C 3 HOH A 100 600 92 HOH HOH . C 3 HOH A 101 601 94 HOH HOH . C 3 HOH A 102 602 95 HOH HOH . C 3 HOH A 103 603 96 HOH HOH . C 3 HOH A 104 604 97 HOH HOH . C 3 HOH A 105 605 99 HOH HOH . C 3 HOH A 106 606 100 HOH HOH . C 3 HOH A 107 607 101 HOH HOH . C 3 HOH A 108 608 103 HOH HOH . C 3 HOH A 109 609 104 HOH HOH . C 3 HOH A 110 610 105 HOH HOH . C 3 HOH A 111 611 106 HOH HOH . C 3 HOH A 112 612 107 HOH HOH . C 3 HOH A 113 613 109 HOH HOH . C 3 HOH A 114 614 110 HOH HOH . C 3 HOH A 115 615 111 HOH HOH . C 3 HOH A 116 616 113 HOH HOH . C 3 HOH A 117 617 114 HOH HOH . C 3 HOH A 118 618 115 HOH HOH . C 3 HOH A 119 619 117 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 24.048 -9.415 20.561 1 17.4 ? C1A LBV 401 A 1 HETATM 2 C C1B LBV . . . B 2 19.926 -7.542 20.832 1 13.5 ? C1B LBV 401 A 1 HETATM 3 O O1B LBV . . . B 2 14.711 -3.612 19.276 1 12.03 ? O1B LBV 401 A 1 HETATM 4 C C1C LBV . . . B 2 18.823 -7.079 16.488 1 11.57 ? C1C LBV 401 A 1 HETATM 5 O O1C LBV . . . B 2 17.031 -4.179 12.762 1 10.4 ? O1C LBV 401 A 1 HETATM 6 C C1D LBV . . . B 2 21.735 -8.503 13.113 1 14 ? C1D LBV 401 A 1 HETATM 7 C C2A LBV . . . B 2 24.232 -9.748 21.981 1 17.2 ? C2A LBV 401 A 1 HETATM 8 C C2B LBV . . . B 2 18.73 -6.811 21.367 1 11.62 ? C2B LBV 401 A 1 HETATM 9 O O2B LBV . . . B 2 15.666 -2.591 21.011 1 11.22 ? O2B LBV 401 A 1 HETATM 10 C C2C LBV . . . B 2 18.159 -6.735 15.207 1 11.52 ? C2C LBV 401 A 1 HETATM 11 O O2C LBV . . . B 2 18.412 -3.005 14.045 1 13.2 ? O2C LBV 401 A 1 HETATM 12 C C2D LBV . . . B 2 22.54 -9.612 12.532 1 14.46 ? C2D LBV 401 A 1 HETATM 13 C C3A LBV . . . B 2 22.924 -9.283 22.566 1 16.72 ? C3A LBV 401 A 1 HETATM 14 C C3B LBV . . . B 2 18.005 -6.429 20.263 1 11.52 ? C3B LBV 401 A 1 HETATM 15 C C3C LBV . . . B 2 18.95 -7.293 14.225 1 12.04 ? C3C LBV 401 A 1 HETATM 16 C C3D LBV . . . B 2 23.175 -8.999 11.419 1 14.08 ? C3D LBV 401 A 1 HETATM 17 C C4A LBV . . . B 2 22.044 -8.853 21.388 1 15.86 ? C4A LBV 401 A 1 HETATM 18 C C4B LBV . . . B 2 18.748 -6.983 19.071 1 10.93 ? C4B LBV 401 A 1 HETATM 19 C C4C LBV . . . B 2 20.036 -7.93 14.916 1 13.18 ? C4C LBV 401 A 1 HETATM 20 C C4D LBV . . . B 2 22.669 -7.643 11.374 1 13.75 ? C4D LBV 401 A 1 HETATM 21 C CAA LBV . . . B 2 22.615 -9.384 23.893 1 20.14 ? CAA LBV 401 A 1 HETATM 22 C CAB LBV . . . B 2 16.722 -5.668 20.307 1 10.69 ? CAB LBV 401 A 1 HETATM 23 C CAC LBV . . . B 2 16.835 -6.033 14.987 1 11.53 ? CAC LBV 401 A 1 HETATM 24 C CAD LBV . . . B 2 24.055 -9.737 10.49 1 18.24 ? CAD LBV 401 A 1 HETATM 25 C CBA LBV . . . B 2 23.612 -9.976 24.948 1 24.14 ? CBA LBV 401 A 1 HETATM 26 C CBB LBV . . . B 2 16.968 -4.22 19.858 1 10 ? CBB LBV 401 A 1 HETATM 27 C CBC LBV . . . B 2 16.858 -4.491 15.143 1 10.69 ? CBC LBV 401 A 1 HETATM 28 C CBD LBV . . . B 2 24.686 -9.075 9.472 1 18.59 ? CBD LBV 401 A 1 HETATM 29 C CGB LBV . . . B 2 15.689 -3.428 20.039 1 11.74 ? CGB LBV 401 A 1 HETATM 30 C CGC LBV . . . B 2 17.52 -3.867 13.936 1 11.8 ? CGC LBV 401 A 1 HETATM 31 C CHB LBV . . . B 2 20.923 -7.995 21.809 1 14.01 ? CHB LBV 401 A 1 HETATM 32 C CHC LBV . . . B 2 18.198 -6.665 17.727 1 10.13 ? CHC LBV 401 A 1 HETATM 33 C CHD LBV . . . B 2 21.091 -8.779 14.351 1 13.43 ? CHD LBV 401 A 1 HETATM 34 C CMA LBV . . . B 2 25.464 -8.997 22.378 1 21.5 ? CMA LBV 401 A 1 HETATM 35 C CMB LBV . . . B 2 18.42 -6.564 22.856 1 13.26 ? CMB LBV 401 A 1 HETATM 36 C CMC LBV . . . B 2 18.717 -7.304 12.766 1 12.41 ? CMC LBV 401 A 1 HETATM 37 C CMD LBV . . . B 2 22.697 -11.032 12.97 1 15.51 ? CMD LBV 401 A 1 HETATM 38 N N_A LBV . . . B 2 22.885 -8.806 20.204 1 14.79 ? N_A LBV 401 A 1 HETATM 39 O O_A LBV . . . B 2 24.837 -9.628 19.7 1 16.01 ? O_A LBV 401 A 1 HETATM 40 N N_B LBV . . . B 2 19.88 -7.574 19.466 1 12.41 ? N_B LBV 401 A 1 HETATM 41 N N_C LBV . . . B 2 19.941 -7.799 16.27 1 11.22 ? N_C LBV 401 A 1 HETATM 42 N N_D LBV . . . B 2 21.809 -7.306 12.401 1 11.73 ? N_D LBV 401 A 1 HETATM 43 O O_D LBV . . . B 2 23.048 -6.841 10.483 1 12.91 ? O_D LBV 401 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #