data_3BV0 # _model_server_result.job_id HeRor4ykuqPbMCN3f3mOVg _model_server_result.datetime_utc '2024-11-16 23:28:36' _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 3bv0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 3BV0 # _exptl.entry_id 3BV0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 3BV0 _cell.length_a 63.047 _cell.length_b 66.47 _cell.length_c 203.377 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BV0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D 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 A NZ LYS 283 A LYS 283 1_555 C C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.265 ? covale ? covale2 B NZ LYS 283 B LYS 283 1_555 D C4A PLP . B PLP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.27 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 PLP doub 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 3BV0 _atom_sites.fract_transf_matrix[1][1] 0.015861 _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] 0.015044 _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] 0.004917 _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 C 2 PLP A 1 501 501 PLP PLP . D 2 PLP B 1 502 502 PLP PLP . E 3 HOH A 1 502 1 HOH HOH . E 3 HOH A 2 503 2 HOH HOH . E 3 HOH A 3 504 4 HOH HOH . E 3 HOH A 4 505 5 HOH HOH . E 3 HOH A 5 506 8 HOH HOH . E 3 HOH A 6 507 9 HOH HOH . E 3 HOH A 7 508 10 HOH HOH . E 3 HOH A 8 509 11 HOH HOH . E 3 HOH A 9 510 13 HOH HOH . E 3 HOH A 10 511 15 HOH HOH . E 3 HOH A 11 512 16 HOH HOH . E 3 HOH A 12 513 18 HOH HOH . E 3 HOH A 13 514 19 HOH HOH . E 3 HOH A 14 515 20 HOH HOH . E 3 HOH A 15 516 21 HOH HOH . E 3 HOH A 16 517 27 HOH HOH . E 3 HOH A 17 518 31 HOH HOH . E 3 HOH A 18 519 33 HOH HOH . E 3 HOH A 19 520 36 HOH HOH . E 3 HOH A 20 521 38 HOH HOH . E 3 HOH A 21 522 39 HOH HOH . E 3 HOH A 22 523 42 HOH HOH . E 3 HOH A 23 524 43 HOH HOH . E 3 HOH A 24 525 44 HOH HOH . E 3 HOH A 25 526 45 HOH HOH . E 3 HOH A 26 527 46 HOH HOH . E 3 HOH A 27 528 47 HOH HOH . E 3 HOH A 28 529 48 HOH HOH . E 3 HOH A 29 530 49 HOH HOH . E 3 HOH A 30 531 50 HOH HOH . E 3 HOH A 31 532 52 HOH HOH . E 3 HOH A 32 533 54 HOH HOH . E 3 HOH A 33 534 55 HOH HOH . E 3 HOH A 34 535 57 HOH HOH . E 3 HOH A 35 536 58 HOH HOH . E 3 HOH A 36 537 59 HOH HOH . E 3 HOH A 37 538 60 HOH HOH . E 3 HOH A 38 539 61 HOH HOH . E 3 HOH A 39 540 62 HOH HOH . E 3 HOH A 40 541 63 HOH HOH . E 3 HOH A 41 542 64 HOH HOH . E 3 HOH A 42 543 66 HOH HOH . E 3 HOH A 43 544 67 HOH HOH . E 3 HOH A 44 545 68 HOH HOH . E 3 HOH A 45 546 69 HOH HOH . E 3 HOH A 46 547 70 HOH HOH . E 3 HOH A 47 548 71 HOH HOH . E 3 HOH A 48 549 72 HOH HOH . E 3 HOH A 49 550 73 HOH HOH . E 3 HOH A 50 551 74 HOH HOH . E 3 HOH A 51 552 76 HOH HOH . E 3 HOH A 52 553 78 HOH HOH . E 3 HOH A 53 554 79 HOH HOH . E 3 HOH A 54 555 81 HOH HOH . E 3 HOH A 55 556 107 HOH HOH . E 3 HOH A 56 557 108 HOH HOH . E 3 HOH A 57 558 109 HOH HOH . E 3 HOH A 58 559 110 HOH HOH . E 3 HOH A 59 560 111 HOH HOH . E 3 HOH A 60 561 112 HOH HOH . E 3 HOH A 61 562 113 HOH HOH . E 3 HOH A 62 563 114 HOH HOH . E 3 HOH A 63 564 115 HOH HOH . E 3 HOH A 64 565 118 HOH HOH . E 3 HOH A 65 566 119 HOH HOH . E 3 HOH A 66 567 131 HOH HOH . E 3 HOH A 67 568 135 HOH HOH . E 3 HOH A 68 569 138 HOH HOH . E 3 HOH A 69 570 149 HOH HOH . E 3 HOH A 70 571 150 HOH HOH . E 3 HOH A 71 572 154 HOH HOH . E 3 HOH A 72 573 160 HOH HOH . E 3 HOH A 73 574 161 HOH HOH . E 3 HOH A 74 575 166 HOH HOH . E 3 HOH A 75 576 167 HOH HOH . E 3 HOH A 76 577 179 HOH HOH . E 3 HOH A 77 578 180 HOH HOH . E 3 HOH A 78 579 189 HOH HOH . E 3 HOH A 79 580 190 HOH HOH . E 3 HOH A 80 581 191 HOH HOH . E 3 HOH A 81 582 195 HOH HOH . E 3 HOH A 82 583 197 HOH HOH . E 3 HOH A 83 584 198 HOH HOH . E 3 HOH A 84 585 199 HOH HOH . E 3 HOH A 85 586 200 HOH HOH . E 3 HOH A 86 587 201 HOH HOH . E 3 HOH A 87 588 203 HOH HOH . E 3 HOH A 88 589 204 HOH HOH . E 3 HOH A 89 590 205 HOH HOH . E 3 HOH A 90 591 206 HOH HOH . E 3 HOH A 91 592 207 HOH HOH . E 3 HOH A 92 593 208 HOH HOH . E 3 HOH A 93 594 209 HOH HOH . E 3 HOH A 94 595 211 HOH HOH . E 3 HOH A 95 596 212 HOH HOH . E 3 HOH A 96 597 213 HOH HOH . E 3 HOH A 97 598 215 HOH HOH . E 3 HOH A 98 599 216 HOH HOH . E 3 HOH A 99 600 217 HOH HOH . E 3 HOH A 100 601 218 HOH HOH . E 3 HOH A 101 602 220 HOH HOH . E 3 HOH A 102 603 221 HOH HOH . E 3 HOH A 103 604 228 HOH HOH . E 3 HOH A 104 605 229 HOH HOH . E 3 HOH A 105 606 230 HOH HOH . E 3 HOH A 106 607 231 HOH HOH . E 3 HOH A 107 608 239 HOH HOH . E 3 HOH A 108 609 240 HOH HOH . F 3 HOH B 1 503 3 HOH HOH . F 3 HOH B 2 504 6 HOH HOH . F 3 HOH B 3 505 7 HOH HOH . F 3 HOH B 4 506 12 HOH HOH . F 3 HOH B 5 507 14 HOH HOH . F 3 HOH B 6 508 17 HOH HOH . F 3 HOH B 7 509 22 HOH HOH . F 3 HOH B 8 510 23 HOH HOH . F 3 HOH B 9 511 24 HOH HOH . F 3 HOH B 10 512 25 HOH HOH . F 3 HOH B 11 513 26 HOH HOH . F 3 HOH B 12 514 28 HOH HOH . F 3 HOH B 13 515 29 HOH HOH . F 3 HOH B 14 516 30 HOH HOH . F 3 HOH B 15 517 32 HOH HOH . F 3 HOH B 16 518 34 HOH HOH . F 3 HOH B 17 519 35 HOH HOH . F 3 HOH B 18 520 37 HOH HOH . F 3 HOH B 19 521 40 HOH HOH . F 3 HOH B 20 522 41 HOH HOH . F 3 HOH B 21 523 51 HOH HOH . F 3 HOH B 22 524 53 HOH HOH . F 3 HOH B 23 525 56 HOH HOH . F 3 HOH B 24 526 65 HOH HOH . F 3 HOH B 25 527 75 HOH HOH . F 3 HOH B 26 528 77 HOH HOH . F 3 HOH B 27 529 80 HOH HOH . F 3 HOH B 28 530 82 HOH HOH . F 3 HOH B 29 531 83 HOH HOH . F 3 HOH B 30 532 84 HOH HOH . F 3 HOH B 31 533 85 HOH HOH . F 3 HOH B 32 534 86 HOH HOH . F 3 HOH B 33 535 87 HOH HOH . F 3 HOH B 34 536 88 HOH HOH . F 3 HOH B 35 537 89 HOH HOH . F 3 HOH B 36 538 90 HOH HOH . F 3 HOH B 37 539 91 HOH HOH . F 3 HOH B 38 540 92 HOH HOH . F 3 HOH B 39 541 93 HOH HOH . F 3 HOH B 40 542 94 HOH HOH . F 3 HOH B 41 543 95 HOH HOH . F 3 HOH B 42 544 96 HOH HOH . F 3 HOH B 43 545 97 HOH HOH . F 3 HOH B 44 546 98 HOH HOH . F 3 HOH B 45 547 99 HOH HOH . F 3 HOH B 46 548 100 HOH HOH . F 3 HOH B 47 549 101 HOH HOH . F 3 HOH B 48 550 102 HOH HOH . F 3 HOH B 49 551 103 HOH HOH . F 3 HOH B 50 552 104 HOH HOH . F 3 HOH B 51 553 105 HOH HOH . F 3 HOH B 52 554 106 HOH HOH . F 3 HOH B 53 555 116 HOH HOH . F 3 HOH B 54 556 117 HOH HOH . F 3 HOH B 55 557 120 HOH HOH . F 3 HOH B 56 558 121 HOH HOH . F 3 HOH B 57 559 122 HOH HOH . F 3 HOH B 58 560 123 HOH HOH . F 3 HOH B 59 561 124 HOH HOH . F 3 HOH B 60 562 125 HOH HOH . F 3 HOH B 61 563 126 HOH HOH . F 3 HOH B 62 564 127 HOH HOH . F 3 HOH B 63 565 128 HOH HOH . F 3 HOH B 64 566 129 HOH HOH . F 3 HOH B 65 567 130 HOH HOH . F 3 HOH B 66 568 132 HOH HOH . F 3 HOH B 67 569 133 HOH HOH . F 3 HOH B 68 570 134 HOH HOH . F 3 HOH B 69 571 136 HOH HOH . F 3 HOH B 70 572 137 HOH HOH . F 3 HOH B 71 573 139 HOH HOH . F 3 HOH B 72 574 140 HOH HOH . F 3 HOH B 73 575 141 HOH HOH . F 3 HOH B 74 576 142 HOH HOH . F 3 HOH B 75 577 143 HOH HOH . F 3 HOH B 76 578 144 HOH HOH . F 3 HOH B 77 579 145 HOH HOH . F 3 HOH B 78 580 146 HOH HOH . F 3 HOH B 79 581 147 HOH HOH . F 3 HOH B 80 582 148 HOH HOH . F 3 HOH B 81 583 151 HOH HOH . F 3 HOH B 82 584 152 HOH HOH . F 3 HOH B 83 585 153 HOH HOH . F 3 HOH B 84 586 155 HOH HOH . F 3 HOH B 85 587 156 HOH HOH . F 3 HOH B 86 588 157 HOH HOH . F 3 HOH B 87 589 158 HOH HOH . F 3 HOH B 88 590 159 HOH HOH . F 3 HOH B 89 591 162 HOH HOH . F 3 HOH B 90 592 163 HOH HOH . F 3 HOH B 91 593 164 HOH HOH . F 3 HOH B 92 594 165 HOH HOH . F 3 HOH B 93 595 168 HOH HOH . F 3 HOH B 94 596 169 HOH HOH . F 3 HOH B 95 597 170 HOH HOH . F 3 HOH B 96 598 171 HOH HOH . F 3 HOH B 97 599 172 HOH HOH . F 3 HOH B 98 600 173 HOH HOH . F 3 HOH B 99 601 174 HOH HOH . F 3 HOH B 100 602 175 HOH HOH . F 3 HOH B 101 603 176 HOH HOH . F 3 HOH B 102 604 177 HOH HOH . F 3 HOH B 103 605 178 HOH HOH . F 3 HOH B 104 606 181 HOH HOH . F 3 HOH B 105 607 182 HOH HOH . F 3 HOH B 106 608 183 HOH HOH . F 3 HOH B 107 609 184 HOH HOH . F 3 HOH B 108 610 185 HOH HOH . F 3 HOH B 109 611 186 HOH HOH . F 3 HOH B 110 612 187 HOH HOH . F 3 HOH B 111 613 188 HOH HOH . F 3 HOH B 112 614 192 HOH HOH . F 3 HOH B 113 615 193 HOH HOH . F 3 HOH B 114 616 194 HOH HOH . F 3 HOH B 115 617 196 HOH HOH . F 3 HOH B 116 618 202 HOH HOH . F 3 HOH B 117 619 210 HOH HOH . F 3 HOH B 118 620 214 HOH HOH . F 3 HOH B 119 621 219 HOH HOH . F 3 HOH B 120 622 222 HOH HOH . F 3 HOH B 121 623 223 HOH HOH . F 3 HOH B 122 624 224 HOH HOH . F 3 HOH B 123 625 225 HOH HOH . F 3 HOH B 124 626 226 HOH HOH . F 3 HOH B 125 627 227 HOH HOH . F 3 HOH B 126 628 232 HOH HOH . F 3 HOH B 127 629 233 HOH HOH . F 3 HOH B 128 630 234 HOH HOH . F 3 HOH B 129 631 235 HOH HOH . F 3 HOH B 130 632 236 HOH HOH . F 3 HOH B 131 633 237 HOH HOH . F 3 HOH B 132 634 238 HOH HOH . F 3 HOH B 133 635 241 HOH HOH . F 3 HOH B 134 636 242 HOH HOH . F 3 HOH B 135 637 243 HOH HOH . F 3 HOH B 136 638 244 HOH HOH . F 3 HOH B 137 639 245 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 PLP . . . D 2 -37.714 -10.247 -27.092 1 15.63 ? N1 PLP 502 B 1 HETATM 2 C C2 PLP . . . D 2 -38.32 -11.072 -26.171 1 17.34 ? C2 PLP 502 B 1 HETATM 3 C C2A PLP . . . D 2 -38.9 -12.384 -26.604 1 8.69 ? C2A PLP 502 B 1 HETATM 4 C C3 PLP . . . D 2 -38.388 -10.692 -24.835 1 20.45 ? C3 PLP 502 B 1 HETATM 5 O O3 PLP . . . D 2 -38.997 -11.529 -23.93 1 21.07 ? O3 PLP 502 B 1 HETATM 6 C C4 PLP . . . D 2 -37.838 -9.475 -24.42 1 23.39 ? C4 PLP 502 B 1 HETATM 7 C C4A PLP . . . D 2 -37.82 -9.155 -22.939 1 22 ? C4A PLP 502 B 1 HETATM 8 C C5 PLP . . . D 2 -37.214 -8.647 -25.367 1 13.22 ? C5 PLP 502 B 1 HETATM 9 C C6 PLP . . . D 2 -37.166 -9.046 -26.699 1 12.77 ? C6 PLP 502 B 1 HETATM 10 C C5A PLP . . . D 2 -36.612 -7.304 -25.008 1 12.22 ? C5A PLP 502 B 1 HETATM 11 O O4P PLP . . . D 2 -35.505 -7.421 -24.121 1 21.35 ? O4P PLP 502 B 1 HETATM 12 P P PLP . . . D 2 -34.871 -6.141 -23.339 1 19.71 ? P PLP 502 B 1 HETATM 13 O O1P PLP . . . D 2 -35.912 -5.762 -22.299 1 15.28 ? O1P PLP 502 B 1 HETATM 14 O O2P PLP . . . D 2 -34.636 -4.982 -24.282 1 17.5 ? O2P PLP 502 B 1 HETATM 15 O O3P PLP . . . D 2 -33.53 -6.548 -22.747 1 14.5 ? O3P PLP 502 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 15 #