data_4L5J # _model_server_result.job_id bigoRbpr40gA3clgX2Uacg _model_server_result.datetime_utc '2024-10-28 02:21:35' _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 4l5j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 4L5J # _exptl.entry_id 4L5J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 230.11 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 5-O-phosphono-alpha-D-ribofuranose _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 118.01 _cell.angle_gamma 90 _cell.entry_id 4L5J _cell.length_a 189.33 _cell.length_b 80.611 _cell.length_c 118.701 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L5J _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA octameric 8 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L 1 1 A,B,C,D,E,F,G,H,I,J,K,L 2 1,2 # 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C5 H11 O8 P' _chem_comp.formula_weight 230.11 _chem_comp.id HSX _chem_comp.mon_nstd_flag n _chem_comp.name 5-O-phosphono-alpha-D-ribofuranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms 5-O-phosphono-alpha-D-ribose;5-O-phosphono-D-ribose;5-O-phosphono-ribose # 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 O4 C1 HSX sing 152 n n C1 O1 HSX sing 153 n n C1 C2 HSX sing 154 n n C1 H1 HSX sing 155 n n O4 C4 HSX sing 156 n n C3 C2 HSX sing 157 n n C2 O2 HSX sing 158 n n C2 H2 HSX sing 159 n n O2 HO2 HSX sing 160 n n C4 C3 HSX sing 161 n n C3 O3 HSX sing 162 n n C3 H3 HSX sing 163 n n O3 HO3 HSX sing 164 n n C5 C4 HSX sing 165 n n C4 H4 HSX sing 166 n n O5 C5 HSX sing 167 n n C5 H51 HSX sing 168 n n C5 H52 HSX sing 169 n n P' O5 HSX sing 170 n n O1X P' HSX doub 171 n n O3X P' HSX sing 172 n n P' O2X HSX sing 173 n n O2X HO2X HSX sing 174 n n O3X HO3X HSX sing 175 n n O1 HO1 HSX sing 176 n n # _pdbx_chem_comp_identifier.comp_id HSX _pdbx_chem_comp_identifier.identifier a-D-Ribf5PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 4L5J _atom_sites.fract_transf_matrix[1][1] 0.005282 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002809 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012405 _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] 0.009542 _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 2 HSX A 1 501 501 HSX PRA . F 2 HSX B 1 401 502 HSX PRA . G 2 HSX C 1 401 503 HSX PRA . H 2 HSX D 1 401 504 HSX PRA . I 3 HOH A 1 601 7 HOH HOH . I 3 HOH A 2 602 8 HOH HOH . I 3 HOH A 3 603 15 HOH HOH . I 3 HOH A 4 604 16 HOH HOH . I 3 HOH A 5 605 18 HOH HOH . I 3 HOH A 6 606 21 HOH HOH . I 3 HOH A 7 607 26 HOH HOH . I 3 HOH A 8 608 29 HOH HOH . I 3 HOH A 9 609 31 HOH HOH . I 3 HOH A 10 610 32 HOH HOH . I 3 HOH A 11 611 34 HOH HOH . I 3 HOH A 12 612 35 HOH HOH . I 3 HOH A 13 613 36 HOH HOH . I 3 HOH A 14 614 39 HOH HOH . I 3 HOH A 15 615 40 HOH HOH . I 3 HOH A 16 616 57 HOH HOH . I 3 HOH A 17 617 61 HOH HOH . I 3 HOH A 18 618 67 HOH HOH . I 3 HOH A 19 619 69 HOH HOH . I 3 HOH A 20 620 72 HOH HOH . I 3 HOH A 21 621 80 HOH HOH . I 3 HOH A 22 622 94 HOH HOH . I 3 HOH A 23 623 97 HOH HOH . I 3 HOH A 24 624 102 HOH HOH . I 3 HOH A 25 625 107 HOH HOH . I 3 HOH A 26 626 110 HOH HOH . I 3 HOH A 27 627 113 HOH HOH . I 3 HOH A 28 628 114 HOH HOH . I 3 HOH A 29 629 115 HOH HOH . I 3 HOH A 30 630 117 HOH HOH . I 3 HOH A 31 631 123 HOH HOH . I 3 HOH A 32 632 128 HOH HOH . I 3 HOH A 33 633 131 HOH HOH . I 3 HOH A 34 634 137 HOH HOH . I 3 HOH A 35 635 142 HOH HOH . I 3 HOH A 36 636 144 HOH HOH . I 3 HOH A 37 637 147 HOH HOH . I 3 HOH A 38 638 151 HOH HOH . I 3 HOH A 39 639 152 HOH HOH . I 3 HOH A 40 640 154 HOH HOH . I 3 HOH A 41 641 160 HOH HOH . I 3 HOH A 42 642 167 HOH HOH . I 3 HOH A 43 643 178 HOH HOH . I 3 HOH A 44 644 182 HOH HOH . I 3 HOH A 45 645 183 HOH HOH . I 3 HOH A 46 646 186 HOH HOH . I 3 HOH A 47 647 198 HOH HOH . I 3 HOH A 48 648 199 HOH HOH . I 3 HOH A 49 649 203 HOH HOH . I 3 HOH A 50 650 211 HOH HOH . I 3 HOH A 51 651 213 HOH HOH . I 3 HOH A 52 652 225 HOH HOH . I 3 HOH A 53 653 227 HOH HOH . I 3 HOH A 54 654 228 HOH HOH . I 3 HOH A 55 655 230 HOH HOH . I 3 HOH A 56 656 78 HOH HOH . J 3 HOH B 1 501 3 HOH HOH . J 3 HOH B 2 502 13 HOH HOH . J 3 HOH B 3 503 14 HOH HOH . J 3 HOH B 4 504 19 HOH HOH . J 3 HOH B 5 505 23 HOH HOH . J 3 HOH B 6 506 24 HOH HOH . J 3 HOH B 7 507 37 HOH HOH . J 3 HOH B 8 508 42 HOH HOH . J 3 HOH B 9 509 43 HOH HOH . J 3 HOH B 10 510 45 HOH HOH . J 3 HOH B 11 511 49 HOH HOH . J 3 HOH B 12 512 54 HOH HOH . J 3 HOH B 13 513 55 HOH HOH . J 3 HOH B 14 514 62 HOH HOH . J 3 HOH B 15 515 63 HOH HOH . J 3 HOH B 16 516 64 HOH HOH . J 3 HOH B 17 517 68 HOH HOH . J 3 HOH B 18 518 71 HOH HOH . J 3 HOH B 19 519 74 HOH HOH . J 3 HOH B 20 520 76 HOH HOH . J 3 HOH B 21 521 77 HOH HOH . J 3 HOH B 22 522 79 HOH HOH . J 3 HOH B 23 523 83 HOH HOH . J 3 HOH B 24 524 85 HOH HOH . J 3 HOH B 25 525 87 HOH HOH . J 3 HOH B 26 526 88 HOH HOH . J 3 HOH B 27 527 89 HOH HOH . J 3 HOH B 28 528 99 HOH HOH . J 3 HOH B 29 529 100 HOH HOH . J 3 HOH B 30 530 101 HOH HOH . J 3 HOH B 31 531 103 HOH HOH . J 3 HOH B 32 532 105 HOH HOH . J 3 HOH B 33 533 106 HOH HOH . J 3 HOH B 34 534 109 HOH HOH . J 3 HOH B 35 535 116 HOH HOH . J 3 HOH B 36 536 122 HOH HOH . J 3 HOH B 37 537 129 HOH HOH . J 3 HOH B 38 538 132 HOH HOH . J 3 HOH B 39 539 134 HOH HOH . J 3 HOH B 40 540 135 HOH HOH . J 3 HOH B 41 541 139 HOH HOH . J 3 HOH B 42 542 150 HOH HOH . J 3 HOH B 43 543 155 HOH HOH . J 3 HOH B 44 544 159 HOH HOH . J 3 HOH B 45 545 161 HOH HOH . J 3 HOH B 46 546 162 HOH HOH . J 3 HOH B 47 547 164 HOH HOH . J 3 HOH B 48 548 171 HOH HOH . J 3 HOH B 49 549 173 HOH HOH . J 3 HOH B 50 550 176 HOH HOH . J 3 HOH B 51 551 180 HOH HOH . J 3 HOH B 52 552 184 HOH HOH . J 3 HOH B 53 553 187 HOH HOH . J 3 HOH B 54 554 188 HOH HOH . J 3 HOH B 55 555 190 HOH HOH . J 3 HOH B 56 556 192 HOH HOH . J 3 HOH B 57 557 201 HOH HOH . J 3 HOH B 58 558 204 HOH HOH . J 3 HOH B 59 559 206 HOH HOH . J 3 HOH B 60 560 207 HOH HOH . J 3 HOH B 61 561 208 HOH HOH . J 3 HOH B 62 562 218 HOH HOH . J 3 HOH B 63 563 219 HOH HOH . J 3 HOH B 64 564 220 HOH HOH . J 3 HOH B 65 565 229 HOH HOH . J 3 HOH B 66 566 234 HOH HOH . J 3 HOH B 67 567 130 HOH HOH . K 3 HOH C 1 501 1 HOH HOH . K 3 HOH C 2 502 5 HOH HOH . K 3 HOH C 3 503 6 HOH HOH . K 3 HOH C 4 504 9 HOH HOH . K 3 HOH C 5 505 11 HOH HOH . K 3 HOH C 6 506 17 HOH HOH . K 3 HOH C 7 507 30 HOH HOH . K 3 HOH C 8 508 33 HOH HOH . K 3 HOH C 9 509 38 HOH HOH . K 3 HOH C 10 510 47 HOH HOH . K 3 HOH C 11 511 52 HOH HOH . K 3 HOH C 12 512 56 HOH HOH . K 3 HOH C 13 513 59 HOH HOH . K 3 HOH C 14 514 70 HOH HOH . K 3 HOH C 15 515 81 HOH HOH . K 3 HOH C 16 516 90 HOH HOH . K 3 HOH C 17 517 91 HOH HOH . K 3 HOH C 18 518 92 HOH HOH . K 3 HOH C 19 519 93 HOH HOH . K 3 HOH C 20 520 96 HOH HOH . K 3 HOH C 21 521 108 HOH HOH . K 3 HOH C 22 522 111 HOH HOH . K 3 HOH C 23 523 112 HOH HOH . K 3 HOH C 24 524 119 HOH HOH . K 3 HOH C 25 525 124 HOH HOH . K 3 HOH C 26 526 125 HOH HOH . K 3 HOH C 27 527 127 HOH HOH . K 3 HOH C 28 528 133 HOH HOH . K 3 HOH C 29 529 136 HOH HOH . K 3 HOH C 30 530 140 HOH HOH . K 3 HOH C 31 531 145 HOH HOH . K 3 HOH C 32 532 146 HOH HOH . K 3 HOH C 33 533 148 HOH HOH . K 3 HOH C 34 534 153 HOH HOH . K 3 HOH C 35 535 156 HOH HOH . K 3 HOH C 36 536 163 HOH HOH . K 3 HOH C 37 537 166 HOH HOH . K 3 HOH C 38 538 169 HOH HOH . K 3 HOH C 39 539 172 HOH HOH . K 3 HOH C 40 540 175 HOH HOH . K 3 HOH C 41 541 181 HOH HOH . K 3 HOH C 42 542 185 HOH HOH . K 3 HOH C 43 543 189 HOH HOH . K 3 HOH C 44 544 191 HOH HOH . K 3 HOH C 45 545 197 HOH HOH . K 3 HOH C 46 546 205 HOH HOH . K 3 HOH C 47 547 209 HOH HOH . K 3 HOH C 48 548 210 HOH HOH . K 3 HOH C 49 549 216 HOH HOH . K 3 HOH C 50 550 217 HOH HOH . K 3 HOH C 51 551 223 HOH HOH . K 3 HOH C 52 552 231 HOH HOH . K 3 HOH C 53 553 233 HOH HOH . K 3 HOH C 54 554 235 HOH HOH . K 3 HOH C 55 555 236 HOH HOH . L 3 HOH D 1 501 2 HOH HOH . L 3 HOH D 2 502 4 HOH HOH . L 3 HOH D 3 503 10 HOH HOH . L 3 HOH D 4 504 12 HOH HOH . L 3 HOH D 5 505 20 HOH HOH . L 3 HOH D 6 506 22 HOH HOH . L 3 HOH D 7 507 25 HOH HOH . L 3 HOH D 8 508 27 HOH HOH . L 3 HOH D 9 509 28 HOH HOH . L 3 HOH D 10 510 41 HOH HOH . L 3 HOH D 11 511 44 HOH HOH . L 3 HOH D 12 512 46 HOH HOH . L 3 HOH D 13 513 48 HOH HOH . L 3 HOH D 14 514 50 HOH HOH . L 3 HOH D 15 515 51 HOH HOH . L 3 HOH D 16 516 53 HOH HOH . L 3 HOH D 17 517 58 HOH HOH . L 3 HOH D 18 518 60 HOH HOH . L 3 HOH D 19 519 65 HOH HOH . L 3 HOH D 20 520 66 HOH HOH . L 3 HOH D 21 521 73 HOH HOH . L 3 HOH D 22 522 75 HOH HOH . L 3 HOH D 23 523 82 HOH HOH . L 3 HOH D 24 524 84 HOH HOH . L 3 HOH D 25 525 86 HOH HOH . L 3 HOH D 26 526 95 HOH HOH . L 3 HOH D 27 527 98 HOH HOH . L 3 HOH D 28 528 104 HOH HOH . L 3 HOH D 29 529 118 HOH HOH . L 3 HOH D 30 530 120 HOH HOH . L 3 HOH D 31 531 121 HOH HOH . L 3 HOH D 32 532 126 HOH HOH . L 3 HOH D 33 533 138 HOH HOH . L 3 HOH D 34 534 141 HOH HOH . L 3 HOH D 35 535 143 HOH HOH . L 3 HOH D 36 536 149 HOH HOH . L 3 HOH D 37 537 157 HOH HOH . L 3 HOH D 38 538 158 HOH HOH . L 3 HOH D 39 539 165 HOH HOH . L 3 HOH D 40 540 168 HOH HOH . L 3 HOH D 41 541 170 HOH HOH . L 3 HOH D 42 542 174 HOH HOH . L 3 HOH D 43 543 177 HOH HOH . L 3 HOH D 44 544 179 HOH HOH . L 3 HOH D 45 545 193 HOH HOH . L 3 HOH D 46 546 194 HOH HOH . L 3 HOH D 47 547 195 HOH HOH . L 3 HOH D 48 548 196 HOH HOH . L 3 HOH D 49 549 200 HOH HOH . L 3 HOH D 50 550 202 HOH HOH . L 3 HOH D 51 551 212 HOH HOH . L 3 HOH D 52 552 214 HOH HOH . L 3 HOH D 53 553 215 HOH HOH . L 3 HOH D 54 554 221 HOH HOH . L 3 HOH D 55 555 222 HOH HOH . L 3 HOH D 56 556 224 HOH HOH . L 3 HOH D 57 557 226 HOH HOH . L 3 HOH D 58 558 232 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 HSX . . . E 2 6.627 28.927 27.179 1 68.04 ? C1 HSX 501 A 1 HETATM 2 O O4 HSX . . . E 2 6.303 27.589 26.759 1 67.26 ? O4 HSX 501 A 1 HETATM 3 C C2 HSX . . . E 2 5.353 29.313 27.901 1 68.17 ? C2 HSX 501 A 1 HETATM 4 O O2 HSX . . . E 2 5.272 28.603 29.146 1 68.15 ? O2 HSX 501 A 1 HETATM 5 C C3 HSX . . . E 2 4.29 28.785 26.957 1 67.78 ? C3 HSX 501 A 1 HETATM 6 O O3 HSX . . . E 2 3.242 28.166 27.717 1 70.31 ? O3 HSX 501 A 1 HETATM 7 C C4 HSX . . . E 2 5.025 27.742 26.118 1 64.81 ? C4 HSX 501 A 1 HETATM 8 C C5 HSX . . . E 2 5.218 28.306 24.711 1 60.17 ? C5 HSX 501 A 1 HETATM 9 O O5 HSX . . . E 2 6.152 27.492 24.008 1 56.74 ? O5 HSX 501 A 1 HETATM 10 P P' HSX . . . E 2 5.925 27.199 22.45 1 53.96 ? P' HSX 501 A 1 HETATM 11 O O1X HSX . . . E 2 4.703 28.104 21.925 1 53.97 ? O1X HSX 501 A 1 HETATM 12 O O2X HSX . . . E 2 5.558 25.649 22.257 1 54.45 ? O2X HSX 501 A 1 HETATM 13 O O3X HSX . . . E 2 7.271 27.526 21.637 1 54.09 ? O3X HSX 501 A 1 HETATM 14 O O1 HSX . . . E 2 7.76 28.924 28.071 1 67.02 ? O1 HSX 501 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 211 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #