data_3VB7 # _model_server_result.job_id ExUTaSgmeS7ZyaU_hvVfZg _model_server_result.datetime_utc '2024-11-27 20:25:54' _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 3vb7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":403}' # _entry.id 3VB7 # _exptl.entry_id 3VB7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 103.3 _cell.angle_gamma 90 _cell.entry_id 3VB7 _cell.length_a 52.317 _cell.length_b 96.492 _cell.length_c 67.644 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VB7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G,H,I,J,K _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 4 _struct_asym.id H _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 A SG CYS 145 A CYS 145 1_555 C C 0JU 5 E 0JU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.659 ? covale ? covale2 B SG CYS 145 B CYS 145 1_555 D C 0JU 5 F 0JU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.66 ? covale ? covale3 C C LEU 4 E LEU 4 1_555 C N 0JU 5 E 0JU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 sing covale ? covale4 D C LEU 4 F LEU 4 1_555 D N 0JU 5 F 0JU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 sing # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 171 n n C1 C2 GOL sing 172 n n C1 H11 GOL sing 173 n n C1 H12 GOL sing 174 n n O1 HO1 GOL sing 175 n n C2 O2 GOL sing 176 n n C2 C3 GOL sing 177 n n C2 H2 GOL sing 178 n n O2 HO2 GOL sing 179 n n C3 O3 GOL sing 180 n n C3 H31 GOL sing 181 n n C3 H32 GOL sing 182 n n O3 HO3 GOL sing 183 n n # _atom_sites.entry_id 3VB7 _atom_sites.fract_transf_matrix[1][1] 0.019114 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00452 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010364 _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] 0.015191 _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 3 EDO A 1 401 1 EDO EDO . F 3 EDO B 1 401 2 EDO EDO . G 3 EDO B 1 402 3 EDO EDO . H 4 GOL B 1 403 4 GOL GOL . I 5 HOH A 1 501 6 HOH HOH . I 5 HOH A 2 502 7 HOH HOH . I 5 HOH A 3 503 8 HOH HOH . I 5 HOH A 4 504 11 HOH HOH . I 5 HOH A 5 505 14 HOH HOH . I 5 HOH A 6 506 17 HOH HOH . I 5 HOH A 7 507 19 HOH HOH . I 5 HOH A 8 508 21 HOH HOH . I 5 HOH A 9 509 22 HOH HOH . I 5 HOH A 10 510 23 HOH HOH . I 5 HOH A 11 511 26 HOH HOH . I 5 HOH A 12 512 28 HOH HOH . I 5 HOH A 13 513 29 HOH HOH . I 5 HOH A 14 514 35 HOH HOH . I 5 HOH A 15 515 36 HOH HOH . I 5 HOH A 16 516 37 HOH HOH . I 5 HOH A 17 517 38 HOH HOH . I 5 HOH A 18 518 39 HOH HOH . I 5 HOH A 19 519 42 HOH HOH . I 5 HOH A 20 520 44 HOH HOH . I 5 HOH A 21 521 49 HOH HOH . I 5 HOH A 22 522 51 HOH HOH . I 5 HOH A 23 523 53 HOH HOH . I 5 HOH A 24 524 57 HOH HOH . I 5 HOH A 25 525 61 HOH HOH . I 5 HOH A 26 526 63 HOH HOH . I 5 HOH A 27 527 72 HOH HOH . I 5 HOH A 28 528 73 HOH HOH . I 5 HOH A 29 529 78 HOH HOH . I 5 HOH A 30 530 82 HOH HOH . I 5 HOH A 31 531 83 HOH HOH . I 5 HOH A 32 532 85 HOH HOH . I 5 HOH A 33 533 86 HOH HOH . I 5 HOH A 34 534 88 HOH HOH . I 5 HOH A 35 535 89 HOH HOH . I 5 HOH A 36 536 91 HOH HOH . I 5 HOH A 37 537 92 HOH HOH . I 5 HOH A 38 538 95 HOH HOH . I 5 HOH A 39 539 100 HOH HOH . I 5 HOH A 40 540 105 HOH HOH . I 5 HOH A 41 541 107 HOH HOH . I 5 HOH A 42 542 111 HOH HOH . I 5 HOH A 43 543 114 HOH HOH . I 5 HOH A 44 544 117 HOH HOH . I 5 HOH A 45 545 121 HOH HOH . I 5 HOH A 46 546 123 HOH HOH . I 5 HOH A 47 547 126 HOH HOH . I 5 HOH A 48 548 129 HOH HOH . I 5 HOH A 49 549 132 HOH HOH . I 5 HOH A 50 550 133 HOH HOH . I 5 HOH A 51 551 141 HOH HOH . I 5 HOH A 52 552 142 HOH HOH . I 5 HOH A 53 553 144 HOH HOH . I 5 HOH A 54 554 145 HOH HOH . I 5 HOH A 55 555 146 HOH HOH . I 5 HOH A 56 556 148 HOH HOH . I 5 HOH A 57 557 149 HOH HOH . I 5 HOH A 58 558 150 HOH HOH . I 5 HOH A 59 559 154 HOH HOH . I 5 HOH A 60 560 155 HOH HOH . I 5 HOH A 61 561 158 HOH HOH . I 5 HOH A 62 562 161 HOH HOH . I 5 HOH A 63 563 163 HOH HOH . I 5 HOH A 64 564 164 HOH HOH . I 5 HOH A 65 565 166 HOH HOH . I 5 HOH A 66 566 170 HOH HOH . I 5 HOH A 67 567 174 HOH HOH . I 5 HOH A 68 568 177 HOH HOH . I 5 HOH A 69 569 178 HOH HOH . I 5 HOH A 70 570 182 HOH HOH . I 5 HOH A 71 571 185 HOH HOH . I 5 HOH A 72 572 188 HOH HOH . I 5 HOH A 73 573 190 HOH HOH . I 5 HOH A 74 574 194 HOH HOH . I 5 HOH A 75 575 202 HOH HOH . I 5 HOH A 76 576 206 HOH HOH . I 5 HOH A 77 577 208 HOH HOH . I 5 HOH A 78 578 209 HOH HOH . I 5 HOH A 79 579 210 HOH HOH . I 5 HOH A 80 580 211 HOH HOH . I 5 HOH A 81 581 213 HOH HOH . I 5 HOH A 82 582 214 HOH HOH . I 5 HOH A 83 583 215 HOH HOH . I 5 HOH A 84 584 216 HOH HOH . I 5 HOH A 85 585 219 HOH HOH . I 5 HOH A 86 586 225 HOH HOH . I 5 HOH A 87 587 227 HOH HOH . I 5 HOH A 88 588 235 HOH HOH . I 5 HOH A 89 589 236 HOH HOH . I 5 HOH A 90 590 238 HOH HOH . I 5 HOH A 91 591 240 HOH HOH . I 5 HOH A 92 592 250 HOH HOH . I 5 HOH A 93 593 251 HOH HOH . I 5 HOH A 94 594 253 HOH HOH . I 5 HOH A 95 595 260 HOH HOH . I 5 HOH A 96 596 262 HOH HOH . I 5 HOH A 97 597 265 HOH HOH . I 5 HOH A 98 598 266 HOH HOH . I 5 HOH A 99 599 267 HOH HOH . I 5 HOH A 100 600 269 HOH HOH . I 5 HOH A 101 601 271 HOH HOH . I 5 HOH A 102 602 272 HOH HOH . I 5 HOH A 103 603 275 HOH HOH . I 5 HOH A 104 604 276 HOH HOH . I 5 HOH A 105 605 282 HOH HOH . I 5 HOH A 106 606 286 HOH HOH . I 5 HOH A 107 607 291 HOH HOH . I 5 HOH A 108 608 292 HOH HOH . I 5 HOH A 109 609 293 HOH HOH . I 5 HOH A 110 610 297 HOH HOH . I 5 HOH A 111 611 300 HOH HOH . I 5 HOH A 112 612 303 HOH HOH . I 5 HOH A 113 613 304 HOH HOH . I 5 HOH A 114 614 305 HOH HOH . I 5 HOH A 115 615 306 HOH HOH . I 5 HOH A 116 616 307 HOH HOH . I 5 HOH A 117 617 309 HOH HOH . I 5 HOH A 118 618 310 HOH HOH . I 5 HOH A 119 619 315 HOH HOH . I 5 HOH A 120 620 320 HOH HOH . I 5 HOH A 121 621 323 HOH HOH . I 5 HOH A 122 622 331 HOH HOH . I 5 HOH A 123 623 332 HOH HOH . I 5 HOH A 124 624 334 HOH HOH . I 5 HOH A 125 625 335 HOH HOH . I 5 HOH A 126 626 337 HOH HOH . I 5 HOH A 127 627 338 HOH HOH . I 5 HOH A 128 628 339 HOH HOH . I 5 HOH A 129 629 340 HOH HOH . J 5 HOH B 1 501 3 HOH HOH . J 5 HOH B 2 502 5 HOH HOH . J 5 HOH B 3 503 9 HOH HOH . J 5 HOH B 4 504 10 HOH HOH . J 5 HOH B 5 505 12 HOH HOH . J 5 HOH B 6 506 13 HOH HOH . J 5 HOH B 7 507 15 HOH HOH . J 5 HOH B 8 508 16 HOH HOH . J 5 HOH B 9 509 18 HOH HOH . J 5 HOH B 10 510 20 HOH HOH . J 5 HOH B 11 511 24 HOH HOH . J 5 HOH B 12 512 25 HOH HOH . J 5 HOH B 13 513 27 HOH HOH . J 5 HOH B 14 514 30 HOH HOH . J 5 HOH B 15 515 32 HOH HOH . J 5 HOH B 16 516 34 HOH HOH . J 5 HOH B 17 517 40 HOH HOH . J 5 HOH B 18 518 41 HOH HOH . J 5 HOH B 19 519 43 HOH HOH . J 5 HOH B 20 520 45 HOH HOH . J 5 HOH B 21 521 46 HOH HOH . J 5 HOH B 22 522 48 HOH HOH . J 5 HOH B 23 523 54 HOH HOH . J 5 HOH B 24 524 55 HOH HOH . J 5 HOH B 25 525 56 HOH HOH . J 5 HOH B 26 526 58 HOH HOH . J 5 HOH B 27 527 59 HOH HOH . J 5 HOH B 28 528 60 HOH HOH . J 5 HOH B 29 529 62 HOH HOH . J 5 HOH B 30 530 64 HOH HOH . J 5 HOH B 31 531 65 HOH HOH . J 5 HOH B 32 532 66 HOH HOH . J 5 HOH B 33 533 67 HOH HOH . J 5 HOH B 34 534 68 HOH HOH . J 5 HOH B 35 535 69 HOH HOH . J 5 HOH B 36 536 70 HOH HOH . J 5 HOH B 37 537 71 HOH HOH . J 5 HOH B 38 538 74 HOH HOH . J 5 HOH B 39 539 75 HOH HOH . J 5 HOH B 40 540 76 HOH HOH . J 5 HOH B 41 541 77 HOH HOH . J 5 HOH B 42 542 79 HOH HOH . J 5 HOH B 43 543 80 HOH HOH . J 5 HOH B 44 544 90 HOH HOH . J 5 HOH B 45 545 93 HOH HOH . J 5 HOH B 46 546 94 HOH HOH . J 5 HOH B 47 547 96 HOH HOH . J 5 HOH B 48 548 97 HOH HOH . J 5 HOH B 49 549 98 HOH HOH . J 5 HOH B 50 550 101 HOH HOH . J 5 HOH B 51 551 102 HOH HOH . J 5 HOH B 52 552 103 HOH HOH . J 5 HOH B 53 553 104 HOH HOH . J 5 HOH B 54 554 106 HOH HOH . J 5 HOH B 55 555 108 HOH HOH . J 5 HOH B 56 556 110 HOH HOH . J 5 HOH B 57 557 113 HOH HOH . J 5 HOH B 58 558 119 HOH HOH . J 5 HOH B 59 559 124 HOH HOH . J 5 HOH B 60 560 127 HOH HOH . J 5 HOH B 61 561 128 HOH HOH . J 5 HOH B 62 562 130 HOH HOH . J 5 HOH B 63 563 134 HOH HOH . J 5 HOH B 64 564 135 HOH HOH . J 5 HOH B 65 565 137 HOH HOH . J 5 HOH B 66 566 138 HOH HOH . J 5 HOH B 67 567 140 HOH HOH . J 5 HOH B 68 568 143 HOH HOH . J 5 HOH B 69 569 152 HOH HOH . J 5 HOH B 70 570 153 HOH HOH . J 5 HOH B 71 571 157 HOH HOH . J 5 HOH B 72 572 159 HOH HOH . J 5 HOH B 73 573 162 HOH HOH . J 5 HOH B 74 574 167 HOH HOH . J 5 HOH B 75 575 169 HOH HOH . J 5 HOH B 76 576 171 HOH HOH . J 5 HOH B 77 577 173 HOH HOH . J 5 HOH B 78 578 175 HOH HOH . J 5 HOH B 79 579 176 HOH HOH . J 5 HOH B 80 580 180 HOH HOH . J 5 HOH B 81 581 181 HOH HOH . J 5 HOH B 82 582 183 HOH HOH . J 5 HOH B 83 583 184 HOH HOH . J 5 HOH B 84 584 186 HOH HOH . J 5 HOH B 85 585 191 HOH HOH . J 5 HOH B 86 586 192 HOH HOH . J 5 HOH B 87 587 195 HOH HOH . J 5 HOH B 88 588 196 HOH HOH . J 5 HOH B 89 589 197 HOH HOH . J 5 HOH B 90 590 198 HOH HOH . J 5 HOH B 91 591 201 HOH HOH . J 5 HOH B 92 592 203 HOH HOH . J 5 HOH B 93 593 204 HOH HOH . J 5 HOH B 94 594 205 HOH HOH . J 5 HOH B 95 595 207 HOH HOH . J 5 HOH B 96 596 212 HOH HOH . J 5 HOH B 97 597 217 HOH HOH . J 5 HOH B 98 598 218 HOH HOH . J 5 HOH B 99 599 220 HOH HOH . J 5 HOH B 100 600 222 HOH HOH . J 5 HOH B 101 601 223 HOH HOH . J 5 HOH B 102 602 224 HOH HOH . J 5 HOH B 103 603 229 HOH HOH . J 5 HOH B 104 604 231 HOH HOH . J 5 HOH B 105 605 232 HOH HOH . J 5 HOH B 106 606 233 HOH HOH . J 5 HOH B 107 607 237 HOH HOH . J 5 HOH B 108 608 241 HOH HOH . J 5 HOH B 109 609 245 HOH HOH . J 5 HOH B 110 610 247 HOH HOH . J 5 HOH B 111 611 248 HOH HOH . J 5 HOH B 112 612 252 HOH HOH . J 5 HOH B 113 613 257 HOH HOH . J 5 HOH B 114 614 258 HOH HOH . J 5 HOH B 115 615 263 HOH HOH . J 5 HOH B 116 616 268 HOH HOH . J 5 HOH B 117 617 270 HOH HOH . J 5 HOH B 118 618 274 HOH HOH . J 5 HOH B 119 619 281 HOH HOH . J 5 HOH B 120 620 283 HOH HOH . J 5 HOH B 121 621 284 HOH HOH . J 5 HOH B 122 622 285 HOH HOH . J 5 HOH B 123 623 287 HOH HOH . J 5 HOH B 124 624 288 HOH HOH . J 5 HOH B 125 625 289 HOH HOH . J 5 HOH B 126 626 290 HOH HOH . J 5 HOH B 127 627 294 HOH HOH . J 5 HOH B 128 628 295 HOH HOH . J 5 HOH B 129 629 296 HOH HOH . J 5 HOH B 130 630 298 HOH HOH . J 5 HOH B 131 631 299 HOH HOH . J 5 HOH B 132 632 301 HOH HOH . J 5 HOH B 133 633 302 HOH HOH . J 5 HOH B 134 634 308 HOH HOH . J 5 HOH B 135 635 311 HOH HOH . J 5 HOH B 136 636 312 HOH HOH . J 5 HOH B 137 637 313 HOH HOH . J 5 HOH B 138 638 314 HOH HOH . J 5 HOH B 139 639 316 HOH HOH . J 5 HOH B 140 640 317 HOH HOH . J 5 HOH B 141 641 321 HOH HOH . J 5 HOH B 142 642 322 HOH HOH . J 5 HOH B 143 643 324 HOH HOH . J 5 HOH B 144 644 325 HOH HOH . J 5 HOH B 145 645 326 HOH HOH . J 5 HOH B 146 646 327 HOH HOH . J 5 HOH B 147 647 328 HOH HOH . J 5 HOH B 148 648 329 HOH HOH . J 5 HOH B 149 649 330 HOH HOH . J 5 HOH B 150 650 333 HOH HOH . J 5 HOH B 151 651 341 HOH HOH . K 5 HOH E 1 101 318 HOH HOH . K 5 HOH E 2 102 319 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 C1 GOL . . . H 4 30.113 1.673 5.763 1 30.72 ? C1 GOL 403 B 1 HETATM 2 O O1 GOL . . . H 4 28.979 0.956 5.327 1 26.93 ? O1 GOL 403 B 1 HETATM 3 C C2 GOL . . . H 4 31.399 0.851 5.672 1 34.6 ? C2 GOL 403 B 1 HETATM 4 O O2 GOL . . . H 4 31.206 -0.511 6.041 1 32.79 ? O2 GOL 403 B 1 HETATM 5 C C3 GOL . . . H 4 31.999 1.004 4.279 1 39.12 ? C3 GOL 403 B 1 HETATM 6 O O3 GOL . . . H 4 33.306 0.465 4.262 1 48.76 ? O3 GOL 403 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 6 #