data_5B4V # _model_server_result.job_id RfyqyEIfyLxs5Zz57rDBnA _model_server_result.datetime_utc '2024-11-17 11:52:38' _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 5b4v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5B4V # _exptl.entry_id 5B4V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.088 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'METHYLMALONIC 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 90 _cell.angle_gamma 90 _cell.entry_id 5B4V _cell.length_a 62.77 _cell.length_b 62.77 _cell.length_c 119.31 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B4V _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 A O GLY 4 A GLY 4 1_555 G NA NA . A NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.057 ? metalc ? metalc2 A O LEU 64 A LEU 64 1_555 F NA NA . A NA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.103 ? metalc ? metalc3 A OD1 ASP 85 A ASP 85 1_555 G NA NA . A NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc4 A O ALA 112 A ALA 112 1_555 F NA NA . A NA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc5 A OXT ARG 260 A ARG 260 1_555 E NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc6 A OXT ARG 260 A ARG 260 1_555 E NA NA . A NA 304 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc7 E NA NA . A NA 304 1_555 H O HOH . A HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc8 E NA NA . A NA 304 1_555 H O HOH . A HOH 424 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc9 E NA NA . A NA 304 1_555 H O HOH . A HOH 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc10 E NA NA . A NA 304 1_555 H O HOH . A HOH 432 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc11 F NA NA . A NA 305 1_555 H O HOH . A HOH 457 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc12 F NA NA . A NA 305 1_555 H O HOH . A HOH 593 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? # _chem_comp.formula 'C4 H6 O4' _chem_comp.formula_weight 118.088 _chem_comp.id DXX _chem_comp.mon_nstd_flag . _chem_comp.name 'METHYLMALONIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 DXX sing 83 n n C1 OXT DXX doub 84 n n C1 CA DXX sing 85 n n O1 H1 DXX sing 86 n n CA CB DXX sing 87 n n CA C DXX sing 88 n n CA HA DXX sing 89 n n CB HB1 DXX sing 90 n n CB HB2 DXX sing 91 n n CB HB3 DXX sing 92 n n C O DXX doub 93 n n C O2 DXX sing 94 n n O2 HO2 DXX sing 95 n n # _atom_sites.entry_id 5B4V _atom_sites.fract_transf_matrix[1][1] 0.015931 _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] 0.015931 _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] 0.008382 _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 NAD A 1 301 301 NAD NAD . C 3 DXX A 1 302 302 DXX DXX . D 4 CL A 1 303 303 CL CL . E 5 NA A 1 304 304 NA NA . F 5 NA A 1 305 305 NA NA . G 5 NA A 1 306 306 NA NA . H 6 HOH A 1 401 761 HOH HOH . H 6 HOH A 2 402 757 HOH HOH . H 6 HOH A 3 403 546 HOH HOH . H 6 HOH A 4 404 504 HOH HOH . H 6 HOH A 5 405 628 HOH HOH . H 6 HOH A 6 406 551 HOH HOH . H 6 HOH A 7 407 449 HOH HOH . H 6 HOH A 8 408 752 HOH HOH . H 6 HOH A 9 409 482 HOH HOH . H 6 HOH A 10 410 605 HOH HOH . H 6 HOH A 11 411 497 HOH HOH . H 6 HOH A 12 412 569 HOH HOH . H 6 HOH A 13 413 536 HOH HOH . H 6 HOH A 14 414 429 HOH HOH . H 6 HOH A 15 415 580 HOH HOH . H 6 HOH A 16 416 491 HOH HOH . H 6 HOH A 17 417 448 HOH HOH . H 6 HOH A 18 418 788 HOH HOH . H 6 HOH A 19 419 517 HOH HOH . H 6 HOH A 20 420 570 HOH HOH . H 6 HOH A 21 421 543 HOH HOH . H 6 HOH A 22 422 426 HOH HOH . H 6 HOH A 23 423 457 HOH HOH . H 6 HOH A 24 424 476 HOH HOH . H 6 HOH A 25 425 408 HOH HOH . H 6 HOH A 26 426 499 HOH HOH . H 6 HOH A 27 427 516 HOH HOH . H 6 HOH A 28 428 438 HOH HOH . H 6 HOH A 29 429 474 HOH HOH . H 6 HOH A 30 430 422 HOH HOH . H 6 HOH A 31 431 772 HOH HOH . H 6 HOH A 32 432 723 HOH HOH . H 6 HOH A 33 433 545 HOH HOH . H 6 HOH A 34 434 565 HOH HOH . H 6 HOH A 35 435 485 HOH HOH . H 6 HOH A 36 436 704 HOH HOH . H 6 HOH A 37 437 585 HOH HOH . H 6 HOH A 38 438 598 HOH HOH . H 6 HOH A 39 439 603 HOH HOH . H 6 HOH A 40 440 505 HOH HOH . H 6 HOH A 41 441 592 HOH HOH . H 6 HOH A 42 442 521 HOH HOH . H 6 HOH A 43 443 453 HOH HOH . H 6 HOH A 44 444 518 HOH HOH . H 6 HOH A 45 445 492 HOH HOH . H 6 HOH A 46 446 402 HOH HOH . H 6 HOH A 47 447 477 HOH HOH . H 6 HOH A 48 448 663 HOH HOH . H 6 HOH A 49 449 424 HOH HOH . H 6 HOH A 50 450 434 HOH HOH . H 6 HOH A 51 451 412 HOH HOH . H 6 HOH A 52 452 478 HOH HOH . H 6 HOH A 53 453 594 HOH HOH . H 6 HOH A 54 454 530 HOH HOH . H 6 HOH A 55 455 472 HOH HOH . H 6 HOH A 56 456 646 HOH HOH . H 6 HOH A 57 457 447 HOH HOH . H 6 HOH A 58 458 533 HOH HOH . H 6 HOH A 59 459 731 HOH HOH . H 6 HOH A 60 460 791 HOH HOH . H 6 HOH A 61 461 428 HOH HOH . H 6 HOH A 62 462 614 HOH HOH . H 6 HOH A 63 463 420 HOH HOH . H 6 HOH A 64 464 458 HOH HOH . H 6 HOH A 65 465 469 HOH HOH . H 6 HOH A 66 466 508 HOH HOH . H 6 HOH A 67 467 431 HOH HOH . H 6 HOH A 68 468 410 HOH HOH . H 6 HOH A 69 469 403 HOH HOH . H 6 HOH A 70 470 587 HOH HOH . H 6 HOH A 71 471 496 HOH HOH . H 6 HOH A 72 472 407 HOH HOH . H 6 HOH A 73 473 421 HOH HOH . H 6 HOH A 74 474 762 HOH HOH . H 6 HOH A 75 475 528 HOH HOH . H 6 HOH A 76 476 432 HOH HOH . H 6 HOH A 77 477 463 HOH HOH . H 6 HOH A 78 478 413 HOH HOH . H 6 HOH A 79 479 756 HOH HOH . H 6 HOH A 80 480 577 HOH HOH . H 6 HOH A 81 481 473 HOH HOH . H 6 HOH A 82 482 460 HOH HOH . H 6 HOH A 83 483 532 HOH HOH . H 6 HOH A 84 484 445 HOH HOH . H 6 HOH A 85 485 405 HOH HOH . H 6 HOH A 86 486 435 HOH HOH . H 6 HOH A 87 487 419 HOH HOH . H 6 HOH A 88 488 522 HOH HOH . H 6 HOH A 89 489 520 HOH HOH . H 6 HOH A 90 490 406 HOH HOH . H 6 HOH A 91 491 575 HOH HOH . H 6 HOH A 92 492 523 HOH HOH . H 6 HOH A 93 493 526 HOH HOH . H 6 HOH A 94 494 409 HOH HOH . H 6 HOH A 95 495 415 HOH HOH . H 6 HOH A 96 496 524 HOH HOH . H 6 HOH A 97 497 535 HOH HOH . H 6 HOH A 98 498 540 HOH HOH . H 6 HOH A 99 499 537 HOH HOH . H 6 HOH A 100 500 401 HOH HOH . H 6 HOH A 101 501 558 HOH HOH . H 6 HOH A 102 502 427 HOH HOH . H 6 HOH A 103 503 425 HOH HOH . H 6 HOH A 104 504 423 HOH HOH . H 6 HOH A 105 505 643 HOH HOH . H 6 HOH A 106 506 488 HOH HOH . H 6 HOH A 107 507 442 HOH HOH . H 6 HOH A 108 508 513 HOH HOH . H 6 HOH A 109 509 404 HOH HOH . H 6 HOH A 110 510 430 HOH HOH . H 6 HOH A 111 511 441 HOH HOH . H 6 HOH A 112 512 759 HOH HOH . H 6 HOH A 113 513 572 HOH HOH . H 6 HOH A 114 514 600 HOH HOH . H 6 HOH A 115 515 464 HOH HOH . H 6 HOH A 116 516 470 HOH HOH . H 6 HOH A 117 517 586 HOH HOH . H 6 HOH A 118 518 708 HOH HOH . H 6 HOH A 119 519 527 HOH HOH . H 6 HOH A 120 520 583 HOH HOH . H 6 HOH A 121 521 411 HOH HOH . H 6 HOH A 122 522 417 HOH HOH . H 6 HOH A 123 523 446 HOH HOH . H 6 HOH A 124 524 519 HOH HOH . H 6 HOH A 125 525 750 HOH HOH . H 6 HOH A 126 526 705 HOH HOH . H 6 HOH A 127 527 494 HOH HOH . H 6 HOH A 128 528 755 HOH HOH . H 6 HOH A 129 529 615 HOH HOH . H 6 HOH A 130 530 437 HOH HOH . H 6 HOH A 131 531 490 HOH HOH . H 6 HOH A 132 532 414 HOH HOH . H 6 HOH A 133 533 768 HOH HOH . H 6 HOH A 134 534 529 HOH HOH . H 6 HOH A 135 535 475 HOH HOH . H 6 HOH A 136 536 455 HOH HOH . H 6 HOH A 137 537 456 HOH HOH . H 6 HOH A 138 538 439 HOH HOH . H 6 HOH A 139 539 578 HOH HOH . H 6 HOH A 140 540 602 HOH HOH . H 6 HOH A 141 541 451 HOH HOH . H 6 HOH A 142 542 489 HOH HOH . H 6 HOH A 143 543 604 HOH HOH . H 6 HOH A 144 544 418 HOH HOH . H 6 HOH A 145 545 501 HOH HOH . H 6 HOH A 146 546 534 HOH HOH . H 6 HOH A 147 547 550 HOH HOH . H 6 HOH A 148 548 444 HOH HOH . H 6 HOH A 149 549 443 HOH HOH . H 6 HOH A 150 550 648 HOH HOH . H 6 HOH A 151 551 670 HOH HOH . H 6 HOH A 152 552 531 HOH HOH . H 6 HOH A 153 553 498 HOH HOH . H 6 HOH A 154 554 436 HOH HOH . H 6 HOH A 155 555 452 HOH HOH . H 6 HOH A 156 556 657 HOH HOH . H 6 HOH A 157 557 468 HOH HOH . H 6 HOH A 158 558 440 HOH HOH . H 6 HOH A 159 559 707 HOH HOH . H 6 HOH A 160 560 796 HOH HOH . H 6 HOH A 161 561 564 HOH HOH . H 6 HOH A 162 562 510 HOH HOH . H 6 HOH A 163 563 433 HOH HOH . H 6 HOH A 164 564 795 HOH HOH . H 6 HOH A 165 565 461 HOH HOH . H 6 HOH A 166 566 732 HOH HOH . H 6 HOH A 167 567 645 HOH HOH . H 6 HOH A 168 568 416 HOH HOH . H 6 HOH A 169 569 466 HOH HOH . H 6 HOH A 170 570 576 HOH HOH . H 6 HOH A 171 571 769 HOH HOH . H 6 HOH A 172 572 465 HOH HOH . H 6 HOH A 173 573 642 HOH HOH . H 6 HOH A 174 574 459 HOH HOH . H 6 HOH A 175 575 601 HOH HOH . H 6 HOH A 176 576 462 HOH HOH . H 6 HOH A 177 577 560 HOH HOH . H 6 HOH A 178 578 611 HOH HOH . H 6 HOH A 179 579 480 HOH HOH . H 6 HOH A 180 580 548 HOH HOH . H 6 HOH A 181 581 710 HOH HOH . H 6 HOH A 182 582 721 HOH HOH . H 6 HOH A 183 583 778 HOH HOH . H 6 HOH A 184 584 703 HOH HOH . H 6 HOH A 185 585 568 HOH HOH . H 6 HOH A 186 586 554 HOH HOH . H 6 HOH A 187 587 557 HOH HOH . H 6 HOH A 188 588 784 HOH HOH . H 6 HOH A 189 589 573 HOH HOH . H 6 HOH A 190 590 481 HOH HOH . H 6 HOH A 191 591 525 HOH HOH . H 6 HOH A 192 592 797 HOH HOH . H 6 HOH A 193 593 454 HOH HOH . H 6 HOH A 194 594 635 HOH HOH . H 6 HOH A 195 595 561 HOH HOH . H 6 HOH A 196 596 722 HOH HOH . H 6 HOH A 197 597 479 HOH HOH . H 6 HOH A 198 598 794 HOH HOH . H 6 HOH A 199 599 779 HOH HOH . H 6 HOH A 200 600 730 HOH HOH . H 6 HOH A 201 601 571 HOH HOH . H 6 HOH A 202 602 495 HOH HOH . H 6 HOH A 203 603 487 HOH HOH . H 6 HOH A 204 604 467 HOH HOH . H 6 HOH A 205 605 774 HOH HOH . H 6 HOH A 206 606 770 HOH HOH . H 6 HOH A 207 607 792 HOH HOH . H 6 HOH A 208 608 727 HOH HOH . H 6 HOH A 209 609 751 HOH HOH . H 6 HOH A 210 610 450 HOH HOH . H 6 HOH A 211 611 486 HOH HOH . H 6 HOH A 212 612 738 HOH HOH . H 6 HOH A 213 613 538 HOH HOH . H 6 HOH A 214 614 624 HOH HOH . H 6 HOH A 215 615 562 HOH HOH . H 6 HOH A 216 616 694 HOH HOH . H 6 HOH A 217 617 582 HOH HOH . H 6 HOH A 218 618 500 HOH HOH . H 6 HOH A 219 619 509 HOH HOH . H 6 HOH A 220 620 766 HOH HOH . H 6 HOH A 221 621 553 HOH HOH . H 6 HOH A 222 622 613 HOH HOH . H 6 HOH A 223 623 608 HOH HOH . H 6 HOH A 224 624 512 HOH HOH . H 6 HOH A 225 625 567 HOH HOH . H 6 HOH A 226 626 765 HOH HOH . H 6 HOH A 227 627 584 HOH HOH . H 6 HOH A 228 628 503 HOH HOH . H 6 HOH A 229 629 612 HOH HOH . H 6 HOH A 230 630 588 HOH HOH . H 6 HOH A 231 631 626 HOH HOH . H 6 HOH A 232 632 771 HOH HOH . H 6 HOH A 233 633 742 HOH HOH . H 6 HOH A 234 634 502 HOH HOH . H 6 HOH A 235 635 706 HOH HOH . H 6 HOH A 236 636 493 HOH HOH . H 6 HOH A 237 637 544 HOH HOH . H 6 HOH A 238 638 627 HOH HOH . H 6 HOH A 239 639 599 HOH HOH . H 6 HOH A 240 640 556 HOH HOH . H 6 HOH A 241 641 637 HOH HOH . H 6 HOH A 242 642 506 HOH HOH . H 6 HOH A 243 643 623 HOH HOH . H 6 HOH A 244 644 507 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 DXX . . . C 3 -4.85 -14.795 12.154 1 21.28 ? C1 DXX 302 A 1 HETATM 2 O O1 DXX . . . C 3 -5.042 -15.128 13.342 1 16.81 ? O1 DXX 302 A 1 HETATM 3 O OXT DXX . . . C 3 -5.6 -14.019 11.541 1 22.82 ? OXT DXX 302 A 1 HETATM 4 C CA DXX . . . C 3 -3.582 -15.221 11.484 1 16.87 ? CA DXX 302 A 1 HETATM 5 C CB DXX . . . C 3 -3.729 -15.268 9.965 1 19.94 ? CB DXX 302 A 1 HETATM 6 C C DXX . . . C 3 -2.516 -14.26 11.866 1 15.49 ? C DXX 302 A 1 HETATM 7 O O DXX . . . C 3 -2.491 -13.133 11.307 1 15.18 ? O DXX 302 A 1 HETATM 8 O O2 DXX . . . C 3 -1.89 -14.536 12.904 1 15.63 ? O2 DXX 302 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 8 #