data_4L4Z # _model_server_result.job_id iH31MyGQhC5OcOeIh1JU1g _model_server_result.datetime_utc '2024-11-25 07:44:40' _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 4l4z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 4L4Z # _exptl.entry_id 4L4Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 230.11 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2,3,3-trihydroxy-4-oxopentyl dihydrogen 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 120 _cell.entry_id 4L4Z _cell.length_a 117.689 _cell.length_b 117.689 _cell.length_c 79.372 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L4Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 # _chem_comp.formula 'C5 H11 O8 P' _chem_comp.formula_weight 230.11 _chem_comp.id D5X _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2,3,3-trihydroxy-4-oxopentyl dihydrogen phosphate' _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 O3 C3 D5X sing 83 n n C5 O5 D5X sing 84 n n C5 C4 D5X sing 85 n n C3 C4 D5X sing 86 n n C3 O3' D5X sing 87 n n C3 C2 D5X sing 88 n n O5 P D5X sing 89 n n O2 C2 D5X doub 90 n n C4 O4 D5X sing 91 n n O2P P D5X doub 92 n n C2 C1 D5X sing 93 n n O3P P D5X sing 94 n n P O1P D5X sing 95 n n O3P H1 D5X sing 96 n n O1P H2 D5X sing 97 n n C5 H3 D5X sing 98 n n C5 H4 D5X sing 99 n n C4 H5 D5X sing 100 n n O4 H6 D5X sing 101 n n O3 H7 D5X sing 102 n n O3' H8 D5X sing 103 n n C1 H9 D5X sing 104 n n C1 H10 D5X sing 105 n n C1 H11 D5X sing 106 n n # _atom_sites.entry_id 4L4Z _atom_sites.fract_transf_matrix[1][1] 0.008497 _atom_sites.fract_transf_matrix[1][2] 0.004906 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009811 _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] 0.012599 _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 D5X A 1 501 501 D5X D5X . D 2 D5X B 1 401 502 D5X D5X . E 3 HOH A 1 601 2 HOH HOH . E 3 HOH A 2 602 4 HOH HOH . E 3 HOH A 3 603 6 HOH HOH . E 3 HOH A 4 604 9 HOH HOH . E 3 HOH A 5 605 10 HOH HOH . E 3 HOH A 6 606 12 HOH HOH . E 3 HOH A 7 607 15 HOH HOH . E 3 HOH A 8 608 19 HOH HOH . E 3 HOH A 9 609 20 HOH HOH . E 3 HOH A 10 610 24 HOH HOH . E 3 HOH A 11 611 25 HOH HOH . E 3 HOH A 12 612 29 HOH HOH . E 3 HOH A 13 613 30 HOH HOH . E 3 HOH A 14 614 31 HOH HOH . E 3 HOH A 15 615 33 HOH HOH . E 3 HOH A 16 616 35 HOH HOH . E 3 HOH A 17 617 36 HOH HOH . E 3 HOH A 18 618 43 HOH HOH . E 3 HOH A 19 619 50 HOH HOH . E 3 HOH A 20 620 51 HOH HOH . E 3 HOH A 21 621 52 HOH HOH . E 3 HOH A 22 622 56 HOH HOH . E 3 HOH A 23 623 58 HOH HOH . E 3 HOH A 24 624 60 HOH HOH . E 3 HOH A 25 625 61 HOH HOH . E 3 HOH A 26 626 62 HOH HOH . E 3 HOH A 27 627 64 HOH HOH . E 3 HOH A 28 628 66 HOH HOH . E 3 HOH A 29 629 67 HOH HOH . E 3 HOH A 30 630 68 HOH HOH . E 3 HOH A 31 631 69 HOH HOH . E 3 HOH A 32 632 70 HOH HOH . E 3 HOH A 33 633 73 HOH HOH . E 3 HOH A 34 634 75 HOH HOH . E 3 HOH A 35 635 77 HOH HOH . E 3 HOH A 36 636 79 HOH HOH . E 3 HOH A 37 637 81 HOH HOH . E 3 HOH A 38 638 82 HOH HOH . E 3 HOH A 39 639 88 HOH HOH . E 3 HOH A 40 640 90 HOH HOH . E 3 HOH A 41 641 92 HOH HOH . E 3 HOH A 42 642 93 HOH HOH . E 3 HOH A 43 643 96 HOH HOH . E 3 HOH A 44 644 97 HOH HOH . E 3 HOH A 45 645 99 HOH HOH . E 3 HOH A 46 646 102 HOH HOH . E 3 HOH A 47 647 105 HOH HOH . E 3 HOH A 48 648 106 HOH HOH . E 3 HOH A 49 649 107 HOH HOH . E 3 HOH A 50 650 108 HOH HOH . E 3 HOH A 51 651 112 HOH HOH . E 3 HOH A 52 652 114 HOH HOH . E 3 HOH A 53 653 116 HOH HOH . E 3 HOH A 54 654 118 HOH HOH . E 3 HOH A 55 655 119 HOH HOH . E 3 HOH A 56 656 120 HOH HOH . E 3 HOH A 57 657 121 HOH HOH . E 3 HOH A 58 658 122 HOH HOH . E 3 HOH A 59 659 123 HOH HOH . E 3 HOH A 60 660 124 HOH HOH . E 3 HOH A 61 661 140 HOH HOH . E 3 HOH A 62 662 141 HOH HOH . E 3 HOH A 63 663 142 HOH HOH . E 3 HOH A 64 664 143 HOH HOH . E 3 HOH A 65 665 144 HOH HOH . E 3 HOH A 66 666 145 HOH HOH . E 3 HOH A 67 667 154 HOH HOH . E 3 HOH A 68 668 155 HOH HOH . E 3 HOH A 69 669 156 HOH HOH . E 3 HOH A 70 670 157 HOH HOH . E 3 HOH A 71 671 158 HOH HOH . E 3 HOH A 72 672 162 HOH HOH . E 3 HOH A 73 673 171 HOH HOH . E 3 HOH A 74 674 172 HOH HOH . F 3 HOH B 1 501 1 HOH HOH . F 3 HOH B 2 502 3 HOH HOH . F 3 HOH B 3 503 5 HOH HOH . F 3 HOH B 4 504 7 HOH HOH . F 3 HOH B 5 505 8 HOH HOH . F 3 HOH B 6 506 11 HOH HOH . F 3 HOH B 7 507 13 HOH HOH . F 3 HOH B 8 508 14 HOH HOH . F 3 HOH B 9 509 16 HOH HOH . F 3 HOH B 10 510 17 HOH HOH . F 3 HOH B 11 511 18 HOH HOH . F 3 HOH B 12 512 21 HOH HOH . F 3 HOH B 13 513 22 HOH HOH . F 3 HOH B 14 514 23 HOH HOH . F 3 HOH B 15 515 26 HOH HOH . F 3 HOH B 16 516 27 HOH HOH . F 3 HOH B 17 517 28 HOH HOH . F 3 HOH B 18 518 32 HOH HOH . F 3 HOH B 19 519 34 HOH HOH . F 3 HOH B 20 520 37 HOH HOH . F 3 HOH B 21 521 38 HOH HOH . F 3 HOH B 22 522 39 HOH HOH . F 3 HOH B 23 523 40 HOH HOH . F 3 HOH B 24 524 41 HOH HOH . F 3 HOH B 25 525 42 HOH HOH . F 3 HOH B 26 526 44 HOH HOH . F 3 HOH B 27 527 45 HOH HOH . F 3 HOH B 28 528 46 HOH HOH . F 3 HOH B 29 529 47 HOH HOH . F 3 HOH B 30 530 48 HOH HOH . F 3 HOH B 31 531 49 HOH HOH . F 3 HOH B 32 532 53 HOH HOH . F 3 HOH B 33 533 54 HOH HOH . F 3 HOH B 34 534 55 HOH HOH . F 3 HOH B 35 535 57 HOH HOH . F 3 HOH B 36 536 59 HOH HOH . F 3 HOH B 37 537 63 HOH HOH . F 3 HOH B 38 538 65 HOH HOH . F 3 HOH B 39 539 71 HOH HOH . F 3 HOH B 40 540 72 HOH HOH . F 3 HOH B 41 541 74 HOH HOH . F 3 HOH B 42 542 76 HOH HOH . F 3 HOH B 43 543 78 HOH HOH . F 3 HOH B 44 544 80 HOH HOH . F 3 HOH B 45 545 83 HOH HOH . F 3 HOH B 46 546 84 HOH HOH . F 3 HOH B 47 547 85 HOH HOH . F 3 HOH B 48 548 86 HOH HOH . F 3 HOH B 49 549 87 HOH HOH . F 3 HOH B 50 550 89 HOH HOH . F 3 HOH B 51 551 91 HOH HOH . F 3 HOH B 52 552 94 HOH HOH . F 3 HOH B 53 553 95 HOH HOH . F 3 HOH B 54 554 98 HOH HOH . F 3 HOH B 55 555 100 HOH HOH . F 3 HOH B 56 556 101 HOH HOH . F 3 HOH B 57 557 103 HOH HOH . F 3 HOH B 58 558 104 HOH HOH . F 3 HOH B 59 559 109 HOH HOH . F 3 HOH B 60 560 110 HOH HOH . F 3 HOH B 61 561 111 HOH HOH . F 3 HOH B 62 562 113 HOH HOH . F 3 HOH B 63 563 115 HOH HOH . F 3 HOH B 64 564 117 HOH HOH . F 3 HOH B 65 565 125 HOH HOH . F 3 HOH B 66 566 126 HOH HOH . F 3 HOH B 67 567 127 HOH HOH . F 3 HOH B 68 568 128 HOH HOH . F 3 HOH B 69 569 129 HOH HOH . F 3 HOH B 70 570 130 HOH HOH . F 3 HOH B 71 571 131 HOH HOH . F 3 HOH B 72 572 132 HOH HOH . F 3 HOH B 73 573 133 HOH HOH . F 3 HOH B 74 574 134 HOH HOH . F 3 HOH B 75 575 135 HOH HOH . F 3 HOH B 76 576 136 HOH HOH . F 3 HOH B 77 577 137 HOH HOH . F 3 HOH B 78 578 138 HOH HOH . F 3 HOH B 79 579 139 HOH HOH . F 3 HOH B 80 580 146 HOH HOH . F 3 HOH B 81 581 147 HOH HOH . F 3 HOH B 82 582 148 HOH HOH . F 3 HOH B 83 583 149 HOH HOH . F 3 HOH B 84 584 150 HOH HOH . F 3 HOH B 85 585 151 HOH HOH . F 3 HOH B 86 586 152 HOH HOH . F 3 HOH B 87 587 153 HOH HOH . F 3 HOH B 88 588 159 HOH HOH . F 3 HOH B 89 589 160 HOH HOH . F 3 HOH B 90 590 161 HOH HOH . F 3 HOH B 91 591 163 HOH HOH . F 3 HOH B 92 592 164 HOH HOH . F 3 HOH B 93 593 165 HOH HOH . F 3 HOH B 94 594 166 HOH HOH . F 3 HOH B 95 595 167 HOH HOH . F 3 HOH B 96 596 168 HOH HOH . F 3 HOH B 97 597 169 HOH HOH . F 3 HOH B 98 598 170 HOH HOH . F 3 HOH B 99 599 173 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 O O3P D5X . . . D 2 -43.204 -12.807 12.748 1 23.79 ? O3P D5X 401 B 1 HETATM 2 P P D5X . . . D 2 -43.13 -11.184 12.714 1 29.94 ? P D5X 401 B 1 HETATM 3 O O2P D5X . . . D 2 -44.461 -10.566 13.249 1 28.16 ? O2P D5X 401 B 1 HETATM 4 O O1P D5X . . . D 2 -42.8 -10.528 11.355 1 29.21 ? O1P D5X 401 B 1 HETATM 5 O O5 D5X . . . D 2 -42.062 -10.607 13.802 1 33.98 ? O5 D5X 401 B 1 HETATM 6 C C5 D5X . . . D 2 -40.687 -11.015 13.809 1 41.24 ? C5 D5X 401 B 1 HETATM 7 C C4 D5X . . . D 2 -39.785 -9.966 13.1 1 42.84 ? C4 D5X 401 B 1 HETATM 8 O O4 D5X . . . D 2 -39.945 -10.128 11.686 1 48.77 ? O4 D5X 401 B 1 HETATM 9 C C3 D5X . . . D 2 -38.318 -10.17 13.469 1 44.64 ? C3 D5X 401 B 1 HETATM 10 O O3 D5X . . . D 2 -37.935 -11.499 13.089 1 37.1 ? O3 D5X 401 B 1 HETATM 11 O O3' D5X . . . D 2 -38.174 -10.013 14.877 1 40.41 ? O3' D5X 401 B 1 HETATM 12 C C2 D5X . . . D 2 -37.385 -9.149 12.739 1 55.14 ? C2 D5X 401 B 1 HETATM 13 O O2 D5X . . . D 2 -37.014 -8.08 13.243 1 59.9 ? O2 D5X 401 B 1 HETATM 14 C C1 D5X . . . D 2 -36.859 -9.558 11.344 1 57.27 ? C1 D5X 401 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #