data_6E2U # _model_server_result.job_id 9fvffhQ6OhB_b0mWD5PThg _model_server_result.datetime_utc '2024-10-19 00:52:25' _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 6e2u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6E2U # _exptl.entry_id 6E2U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.117 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC 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 6E2U _cell.length_a 80.037 _cell.length_b 97.036 _cell.length_c 46.018 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6E2U _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 OG SER 130 A SER 106 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc2 B O1A DP6 . A DP6 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc3 C O2G ACP . A ACP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc4 C O2B ACP . A ACP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc5 C O2A ACP . A ACP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? # _chem_comp.formula 'C6 H14 O10 P2' _chem_comp.formula_weight 308.117 _chem_comp.id DP6 _chem_comp.mon_nstd_flag . _chem_comp.name '(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC 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 C3A C3 DP6 sing 134 n n C3A H3A1 DP6 sing 135 n n C3A H3A2 DP6 sing 136 n n C3A H3A3 DP6 sing 137 n n O1A PA DP6 doub 138 n n O2A PA DP6 sing 139 n n O2A HO2A DP6 sing 140 n n O3A C3 DP6 sing 141 n n O3A HO3A DP6 sing 142 n n O1B PB DP6 doub 143 n n O2B PB DP6 sing 144 n n O2B HO2B DP6 sing 145 n n O3B PB DP6 sing 146 n n O3B HO3B DP6 sing 147 n n PB O6 DP6 sing 148 n n O6 PA DP6 sing 149 n n PA O5 DP6 sing 150 n n O5 C5 DP6 sing 151 n n C5 C4 DP6 sing 152 n n C5 H51 DP6 sing 153 n n C5 H52 DP6 sing 154 n n C4 C3 DP6 sing 155 n n C4 H41 DP6 sing 156 n n C4 H42 DP6 sing 157 n n C3 C2 DP6 sing 158 n n C2 C1 DP6 sing 159 n n C2 H21 DP6 sing 160 n n C2 H22 DP6 sing 161 n n C1 O1 DP6 doub 162 n n C1 O2 DP6 sing 163 n n O2 HO2 DP6 sing 164 n n # _atom_sites.entry_id 6E2U _atom_sites.fract_transf_matrix[1][1] 0.012494 _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] 0.010305 _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] 0.021731 _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 DP6 A 1 401 401 DP6 DP6 . C 3 ACP A 1 402 402 ACP ACP . D 4 MG A 1 403 403 MG MG . E 5 HOH A 1 501 501 HOH HOH . E 5 HOH A 2 502 502 HOH HOH . E 5 HOH A 3 503 503 HOH HOH . E 5 HOH A 4 504 504 HOH HOH . E 5 HOH A 5 505 505 HOH HOH . E 5 HOH A 6 506 506 HOH HOH . E 5 HOH A 7 507 507 HOH HOH . E 5 HOH A 8 508 508 HOH HOH . E 5 HOH A 9 509 509 HOH HOH . E 5 HOH A 10 510 510 HOH HOH . E 5 HOH A 11 511 511 HOH HOH . E 5 HOH A 12 512 512 HOH HOH . E 5 HOH A 13 513 513 HOH HOH . E 5 HOH A 14 514 514 HOH HOH . E 5 HOH A 15 515 515 HOH HOH . E 5 HOH A 16 516 516 HOH HOH . E 5 HOH A 17 517 517 HOH HOH . E 5 HOH A 18 518 518 HOH HOH . E 5 HOH A 19 519 519 HOH HOH . E 5 HOH A 20 520 520 HOH HOH . E 5 HOH A 21 521 521 HOH HOH . E 5 HOH A 22 522 522 HOH HOH . E 5 HOH A 23 523 523 HOH HOH . E 5 HOH A 24 524 524 HOH HOH . E 5 HOH A 25 525 525 HOH HOH . E 5 HOH A 26 526 526 HOH HOH . E 5 HOH A 27 527 527 HOH HOH . E 5 HOH A 28 528 528 HOH HOH . E 5 HOH A 29 529 529 HOH HOH . E 5 HOH A 30 530 530 HOH HOH . E 5 HOH A 31 531 531 HOH HOH . E 5 HOH A 32 532 532 HOH HOH . E 5 HOH A 33 533 533 HOH HOH . E 5 HOH A 34 534 534 HOH HOH . E 5 HOH A 35 535 535 HOH HOH . E 5 HOH A 36 536 536 HOH HOH . E 5 HOH A 37 537 537 HOH HOH . E 5 HOH A 38 538 538 HOH HOH . E 5 HOH A 39 539 539 HOH HOH . E 5 HOH A 40 540 540 HOH HOH . E 5 HOH A 41 541 541 HOH HOH . E 5 HOH A 42 542 542 HOH HOH . E 5 HOH A 43 543 543 HOH HOH . E 5 HOH A 44 544 544 HOH HOH . E 5 HOH A 45 545 545 HOH HOH . E 5 HOH A 46 546 546 HOH HOH . E 5 HOH A 47 547 547 HOH HOH . E 5 HOH A 48 548 548 HOH HOH . E 5 HOH A 49 549 549 HOH HOH . E 5 HOH A 50 550 550 HOH HOH . E 5 HOH A 51 551 551 HOH HOH . E 5 HOH A 52 552 552 HOH HOH . E 5 HOH A 53 553 553 HOH HOH . E 5 HOH A 54 554 554 HOH HOH . E 5 HOH A 55 555 555 HOH HOH . E 5 HOH A 56 556 556 HOH HOH . E 5 HOH A 57 557 557 HOH HOH . E 5 HOH A 58 558 558 HOH HOH . E 5 HOH A 59 559 559 HOH HOH . E 5 HOH A 60 560 560 HOH HOH . E 5 HOH A 61 561 561 HOH HOH . E 5 HOH A 62 562 562 HOH HOH . E 5 HOH A 63 563 563 HOH HOH . E 5 HOH A 64 564 564 HOH HOH . E 5 HOH A 65 565 565 HOH HOH . E 5 HOH A 66 566 566 HOH HOH . E 5 HOH A 67 567 567 HOH HOH . E 5 HOH A 68 568 568 HOH HOH . E 5 HOH A 69 569 569 HOH HOH . E 5 HOH A 70 570 570 HOH HOH . E 5 HOH A 71 571 571 HOH HOH . E 5 HOH A 72 572 572 HOH HOH . E 5 HOH A 73 573 573 HOH HOH . E 5 HOH A 74 574 574 HOH HOH . E 5 HOH A 75 575 575 HOH HOH . E 5 HOH A 76 576 576 HOH HOH . E 5 HOH A 77 577 577 HOH HOH . E 5 HOH A 78 578 578 HOH HOH . E 5 HOH A 79 579 579 HOH HOH . E 5 HOH A 80 580 580 HOH HOH . E 5 HOH A 81 581 581 HOH HOH . E 5 HOH A 82 582 582 HOH HOH . E 5 HOH A 83 583 583 HOH HOH . E 5 HOH A 84 584 584 HOH HOH . E 5 HOH A 85 585 585 HOH HOH . E 5 HOH A 86 586 586 HOH HOH . E 5 HOH A 87 587 587 HOH HOH . E 5 HOH A 88 588 588 HOH HOH . E 5 HOH A 89 589 589 HOH HOH . E 5 HOH A 90 590 590 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 C3A DP6 . . . B 2 12.658 7.526 16.455 1 28.88 ? C3A DP6 401 A 1 HETATM 2 O O1A DP6 . . . B 2 15.297 13.299 16.546 1 24.7 ? O1A DP6 401 A 1 HETATM 3 O O2A DP6 . . . B 2 16.625 12.27 18.487 1 24.65 ? O2A DP6 401 A 1 HETATM 4 O O3A DP6 . . . B 2 14.818 8.041 15.803 1 20.61 ? O3A DP6 401 A 1 HETATM 5 O O1B DP6 . . . B 2 16.089 15.708 18.975 1 23.23 ? O1B DP6 401 A 1 HETATM 6 O O2B DP6 . . . B 2 14.009 15.636 20.317 1 21.61 ? O2B DP6 401 A 1 HETATM 7 O O3B DP6 . . . B 2 16.015 14.203 20.911 1 22.79 ? O3B DP6 401 A 1 HETATM 8 P PB DP6 . . . B 2 15.198 14.879 19.84 1 23.98 ? PB DP6 401 A 1 HETATM 9 O O6 DP6 . . . B 2 14.65 13.745 18.935 1 23.66 ? O6 DP6 401 A 1 HETATM 10 P PA DP6 . . . B 2 15.33 12.734 17.93 1 23.95 ? PA DP6 401 A 1 HETATM 11 O O5 DP6 . . . B 2 14.402 11.485 17.882 1 29.72 ? O5 DP6 401 A 1 HETATM 12 C C5 DP6 . . . B 2 14.72 10.316 17.128 1 29.41 ? C5 DP6 401 A 1 HETATM 13 C C4 DP6 . . . B 2 14.021 9.137 17.766 1 28.53 ? C4 DP6 401 A 1 HETATM 14 C C3 DP6 . . . B 2 14.038 7.826 16.966 1 22.8 ? C3 DP6 401 A 1 HETATM 15 C C2 DP6 . . . B 2 14.54 6.66 17.775 1 19.82 ? C2 DP6 401 A 1 HETATM 16 C C1 DP6 . . . B 2 16.004 6.767 18.214 1 23.03 ? C1 DP6 401 A 1 HETATM 17 O O1 DP6 . . . B 2 16.819 7.35 17.471 1 21.92 ? O1 DP6 401 A 1 HETATM 18 O O2 DP6 . . . B 2 16.358 6.292 19.287 1 22.83 ? O2 DP6 401 A 1 HETATM 19 H H3A1 DP6 . . . B 2 12.26 8.303 16.032 1 34.69 ? H3A1 DP6 401 A 1 HETATM 20 H H3A2 DP6 . . . B 2 12.646 6.805 15.806 1 34.69 ? H3A2 DP6 401 A 1 HETATM 21 H H3A3 DP6 . . . B 2 12.06 7.261 17.171 1 34.69 ? H3A3 DP6 401 A 1 HETATM 22 H HO3A DP6 . . . B 2 14.975 7.281 15.456 1 24.77 ? HO3A DP6 401 A 1 HETATM 23 H H51 DP6 . . . B 2 14.462 10.396 16.197 1 35.32 ? H51 DP6 401 A 1 HETATM 24 H H52 DP6 . . . B 2 15.678 10.162 17.115 1 35.32 ? H52 DP6 401 A 1 HETATM 25 H H41 DP6 . . . B 2 14.402 8.979 18.644 1 34.27 ? H41 DP6 401 A 1 HETATM 26 H H42 DP6 . . . B 2 13.099 9.38 17.946 1 34.27 ? H42 DP6 401 A 1 HETATM 27 H H21 DP6 . . . B 2 14.023 6.557 18.59 1 23.82 ? H21 DP6 401 A 1 HETATM 28 H H22 DP6 . . . B 2 14.403 5.841 17.273 1 23.82 ? H22 DP6 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #