data_4DWB # _model_server_result.job_id H2OUuFPu933cAaZDgG1kkg _model_server_result.datetime_utc '2024-11-28 00:14:39' _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 4dwb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4DWB # _exptl.entry_id 4DWB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 246.092 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE' _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 120 _cell.entry_id 4DWB _cell.length_a 57.871 _cell.length_b 57.871 _cell.length_c 392.442 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DWB _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 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,F,G,H,I,J,K _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' 10_665 -y+1,-x+1,-z+5/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 28.9355 50.117756 327.035 # _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 OD1 ASP 98 A ASP 98 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc2 A OD2 ASP 98 A ASP 98 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc3 A OD2 ASP 102 A ASP 102 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc4 A OD2 ASP 102 A ASP 102 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc5 A O ILE 129 A ILE 129 1_555 F NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc6 A OD2 ASP 250 A ASP 250 1_555 I MG MG . A MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc7 F NA NA . A NA 505 1_555 K O HOH . A HOH 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.084 ? metalc ? metalc8 G MG MG . A MG 506 1_555 J O14 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc9 G MG MG . A MG 506 1_555 K O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc10 G MG MG . A MG 506 1_555 K O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc11 G MG MG . A MG 506 1_555 K O HOH . A HOH 623 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc12 H MG MG . A MG 507 1_555 J O14 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc13 H MG MG . A MG 507 1_555 J O13 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc14 H MG MG . A MG 507 1_555 K O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc15 H MG MG . A MG 507 1_555 K O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc16 I MG MG . A MG 508 1_555 J O15 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.82 ? metalc ? metalc17 I MG MG . A MG 508 1_555 J O11 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc18 I MG MG . A MG 508 1_555 K O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc19 I MG MG . A MG 508 1_555 K O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc20 I MG MG . A MG 508 1_555 K O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? # _chem_comp.formula 'C5 H12 O7 P2' _chem_comp.formula_weight 246.092 _chem_comp.id IPE _chem_comp.mon_nstd_flag . _chem_comp.name '3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ISOPENTENYL PYROPHOSPHATE' # 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 IPE sing 213 n n C1 C2 IPE sing 214 n n C1 H11 IPE sing 215 n n C1 H12 IPE sing 216 n n O1 PA IPE sing 217 n n C2 C3 IPE sing 218 n n C2 H21 IPE sing 219 n n C2 H22 IPE sing 220 n n C3 C4 IPE doub 221 n n C3 C5 IPE sing 222 n n C4 H41 IPE sing 223 n n C4 H42 IPE sing 224 n n C5 H51 IPE sing 225 n n C5 H52 IPE sing 226 n n C5 H53 IPE sing 227 n n PA O1A IPE doub 228 n n PA O2A IPE sing 229 n n PA O3A IPE sing 230 n n O2A H2A IPE sing 231 n n O3A PB IPE sing 232 n n PB O1B IPE sing 233 n n PB O2B IPE doub 234 n n PB O3B IPE sing 235 n n O1B H1B IPE sing 236 n n O3B H3B IPE sing 237 n n # _atom_sites.entry_id 4DWB _atom_sites.fract_transf_matrix[1][1] 0.01728 _atom_sites.fract_transf_matrix[1][2] 0.009977 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019953 _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] 0.002548 _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 IPE A 1 501 501 IPE IPR . C 3 SO4 A 1 502 1 SO4 SO4 . D 3 SO4 A 1 503 2 SO4 SO4 . E 4 ACT A 1 504 3 ACT ACT . F 5 NA A 1 505 4 NA NA . G 6 MG A 1 506 401 MG MG . H 6 MG A 1 507 402 MG MG . I 6 MG A 1 508 403 MG MG . J 7 0M7 A 1 509 500 0M7 BR6 . K 8 HOH A 1 601 1 HOH HOH . K 8 HOH A 2 602 2 HOH HOH . K 8 HOH A 3 603 3 HOH HOH . K 8 HOH A 4 604 4 HOH HOH . K 8 HOH A 5 605 5 HOH HOH . K 8 HOH A 6 606 6 HOH HOH . K 8 HOH A 7 607 7 HOH HOH . K 8 HOH A 8 608 11 HOH HOH . K 8 HOH A 9 609 12 HOH HOH . K 8 HOH A 10 610 13 HOH HOH . K 8 HOH A 11 611 14 HOH HOH . K 8 HOH A 12 612 15 HOH HOH . K 8 HOH A 13 613 16 HOH HOH . K 8 HOH A 14 614 17 HOH HOH . K 8 HOH A 15 615 18 HOH HOH . K 8 HOH A 16 616 19 HOH HOH . K 8 HOH A 17 617 21 HOH HOH . K 8 HOH A 18 618 23 HOH HOH . K 8 HOH A 19 619 24 HOH HOH . K 8 HOH A 20 620 25 HOH HOH . K 8 HOH A 21 621 26 HOH HOH . K 8 HOH A 22 622 27 HOH HOH . K 8 HOH A 23 623 28 HOH HOH . K 8 HOH A 24 624 30 HOH HOH . K 8 HOH A 25 625 32 HOH HOH . K 8 HOH A 26 626 33 HOH HOH . K 8 HOH A 27 627 34 HOH HOH . K 8 HOH A 28 628 35 HOH HOH . K 8 HOH A 29 629 36 HOH HOH . K 8 HOH A 30 630 37 HOH HOH . K 8 HOH A 31 631 38 HOH HOH . K 8 HOH A 32 632 39 HOH HOH . K 8 HOH A 33 633 40 HOH HOH . K 8 HOH A 34 634 41 HOH HOH . K 8 HOH A 35 635 43 HOH HOH . K 8 HOH A 36 636 44 HOH HOH . K 8 HOH A 37 637 45 HOH HOH . K 8 HOH A 38 638 46 HOH HOH . K 8 HOH A 39 639 47 HOH HOH . K 8 HOH A 40 640 48 HOH HOH . K 8 HOH A 41 641 49 HOH HOH . K 8 HOH A 42 642 51 HOH HOH . K 8 HOH A 43 643 52 HOH HOH . K 8 HOH A 44 644 53 HOH HOH . K 8 HOH A 45 645 54 HOH HOH . K 8 HOH A 46 646 55 HOH HOH . K 8 HOH A 47 647 56 HOH HOH . K 8 HOH A 48 648 57 HOH HOH . K 8 HOH A 49 649 58 HOH HOH . K 8 HOH A 50 650 60 HOH HOH . K 8 HOH A 51 651 61 HOH HOH . K 8 HOH A 52 652 62 HOH HOH . K 8 HOH A 53 653 64 HOH HOH . K 8 HOH A 54 654 65 HOH HOH . K 8 HOH A 55 655 66 HOH HOH . K 8 HOH A 56 656 67 HOH HOH . K 8 HOH A 57 657 68 HOH HOH . K 8 HOH A 58 658 69 HOH HOH . K 8 HOH A 59 659 70 HOH HOH . K 8 HOH A 60 660 71 HOH HOH . K 8 HOH A 61 661 72 HOH HOH . K 8 HOH A 62 662 73 HOH HOH . K 8 HOH A 63 663 74 HOH HOH . K 8 HOH A 64 664 75 HOH HOH . K 8 HOH A 65 665 76 HOH HOH . K 8 HOH A 66 666 77 HOH HOH . K 8 HOH A 67 667 79 HOH HOH . K 8 HOH A 68 668 80 HOH HOH . K 8 HOH A 69 669 82 HOH HOH . K 8 HOH A 70 670 83 HOH HOH . K 8 HOH A 71 671 84 HOH HOH . K 8 HOH A 72 672 85 HOH HOH . K 8 HOH A 73 673 86 HOH HOH . K 8 HOH A 74 674 87 HOH HOH . K 8 HOH A 75 675 88 HOH HOH . K 8 HOH A 76 676 89 HOH HOH . K 8 HOH A 77 677 90 HOH HOH . K 8 HOH A 78 678 91 HOH HOH . K 8 HOH A 79 679 92 HOH HOH . K 8 HOH A 80 680 93 HOH HOH . K 8 HOH A 81 681 94 HOH HOH . K 8 HOH A 82 682 95 HOH HOH . K 8 HOH A 83 683 96 HOH HOH . K 8 HOH A 84 684 97 HOH HOH . K 8 HOH A 85 685 98 HOH HOH . K 8 HOH A 86 686 99 HOH HOH . K 8 HOH A 87 687 100 HOH HOH . K 8 HOH A 88 688 101 HOH HOH . K 8 HOH A 89 689 102 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 IPE . . . B 2 7.166 12.311 177.668 1 66.06 ? C1 IPE 501 A 1 HETATM 2 O O1 IPE . . . B 2 6.217 11.67 176.801 1 64.28 ? O1 IPE 501 A 1 HETATM 3 C C2 IPE . . . B 2 8.447 12.694 176.92 1 65.27 ? C2 IPE 501 A 1 HETATM 4 C C3 IPE . . . B 2 8.515 14.179 176.648 1 64.38 ? C3 IPE 501 A 1 HETATM 5 C C4 IPE . . . B 2 8.496 14.592 175.394 1 64.1 ? C4 IPE 501 A 1 HETATM 6 C C5 IPE . . . B 2 8.615 15.181 177.772 1 64.89 ? C5 IPE 501 A 1 HETATM 7 P PA IPE . . . B 2 5.434 12.477 175.637 1 62.33 ? PA IPE 501 A 1 HETATM 8 O O1A IPE . . . B 2 6.133 12.094 174.329 1 61.6 ? O1A IPE 501 A 1 HETATM 9 O O2A IPE . . . B 2 5.461 13.926 176.084 1 60.78 ? O2A IPE 501 A 1 HETATM 10 O O3A IPE . . . B 2 3.859 11.956 175.611 1 50.5 ? O3A IPE 501 A 1 HETATM 11 P PB IPE . . . B 2 2.919 11.543 174.313 1 44.17 ? PB IPE 501 A 1 HETATM 12 O O1B IPE . . . B 2 2.966 10.046 174.172 1 38.79 ? O1B IPE 501 A 1 HETATM 13 O O2B IPE . . . B 2 3.501 12.313 173.123 1 42.42 ? O2B IPE 501 A 1 HETATM 14 O O3B IPE . . . B 2 1.556 11.99 174.722 1 41.85 ? O3B IPE 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #