data_6J06 # _model_server_result.job_id BPoZR3lSVS02y63LFfpocQ _model_server_result.datetime_utc '2024-10-20 20:51:14' _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 6j06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6J06 # _exptl.entry_id 6J06 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 352.214 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2E)-3-(hydroxymethyl)-4-(4-methylphenyl)but-2-en-1-yl trihydrogen diphosphate' _entity.pdbx_number_of_molecules 3 _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 6J06 _cell.length_a 112.929 _cell.length_b 211.588 _cell.length_c 56.269 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6J06 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,H,I,J,V 1 1 B,K,L,M,N,O,P,Q,W 2 1 C,R,S,T,U,X 3 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 D N N ? 2 K N N ? 2 R N 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 B OE1 GLU 63 B GLU 358 1_555 Q CA CA . B CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc2 B O SER 64 B SER 359 1_555 Q CA CA . B CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? # _chem_comp.formula 'C12 H18 O8 P2' _chem_comp.formula_weight 352.214 _chem_comp.id 99C _chem_comp.mon_nstd_flag . _chem_comp.name '(2E)-3-(hydroxymethyl)-4-(4-methylphenyl)but-2-en-1-yl trihydrogen diphosphate' _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 O1 C1 99C sing 1 n n O8 P2 99C doub 2 n n O5 P1 99C doub 3 n n C1 C2 99C sing 4 n n O2 P1 99C sing 5 n n O2 C12 99C sing 6 n n C3 C2 99C doub 7 e n C3 C12 99C sing 8 n n C2 C4 99C sing 9 n n P1 O3 99C sing 10 n n P1 O4 99C sing 11 n n P2 O6 99C sing 12 n n P2 O3 99C sing 13 n n P2 O7 99C sing 14 n n C4 C5 99C sing 15 n n C10 C5 99C doub 16 n y C10 C9 99C sing 17 n y C5 C6 99C sing 18 n y C9 C8 99C doub 19 n y C6 C7 99C doub 20 n y C8 C7 99C sing 21 n y C8 C11 99C sing 22 n n O1 H1 99C sing 23 n n C1 H2 99C sing 24 n n C1 H3 99C sing 25 n n C3 H4 99C sing 26 n n C4 H5 99C sing 27 n n C4 H6 99C sing 28 n n C6 H7 99C sing 29 n n C7 H8 99C sing 30 n n C9 H9 99C sing 31 n n C10 H10 99C sing 32 n n C11 H11 99C sing 33 n n C11 H12 99C sing 34 n n C11 H13 99C sing 35 n n C12 H14 99C sing 36 n n C12 H15 99C sing 37 n n O4 H16 99C sing 38 n n O6 H17 99C sing 39 n n O7 H18 99C sing 40 n n # _atom_sites.entry_id 6J06 _atom_sites.fract_transf_matrix[1][1] 0.008855 _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] 0.004726 _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] 0.017772 _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 D 2 99C A 1 501 501 99C 99C . E 3 SO4 A 1 502 502 SO4 SO4 . F 3 SO4 A 1 503 503 SO4 SO4 . G 3 SO4 A 1 504 504 SO4 SO4 . H 3 SO4 A 1 505 505 SO4 SO4 . I 3 SO4 A 1 506 506 SO4 SO4 . J 4 FLC A 1 507 507 FLC FLC . K 2 99C B 1 501 501 99C 99C . L 3 SO4 B 1 502 502 SO4 SO4 . M 3 SO4 B 1 503 503 SO4 SO4 . N 3 SO4 B 1 504 504 SO4 SO4 . O 3 SO4 B 1 505 505 SO4 SO4 . P 3 SO4 B 1 506 506 SO4 SO4 . Q 5 CA B 1 507 507 CA CA . R 2 99C C 1 501 501 99C 99C . S 3 SO4 C 1 502 502 SO4 SO4 . T 3 SO4 C 1 503 503 SO4 SO4 . U 3 SO4 C 1 504 504 SO4 SO4 . V 6 HOH A 1 601 601 HOH HOH . V 6 HOH A 2 602 602 HOH HOH . V 6 HOH A 3 603 603 HOH HOH . V 6 HOH A 4 604 604 HOH HOH . V 6 HOH A 5 605 605 HOH HOH . V 6 HOH A 6 606 606 HOH HOH . V 6 HOH A 7 607 607 HOH HOH . V 6 HOH A 8 608 608 HOH HOH . V 6 HOH A 9 609 609 HOH HOH . V 6 HOH A 10 610 610 HOH HOH . V 6 HOH A 11 611 611 HOH HOH . V 6 HOH A 12 612 612 HOH HOH . V 6 HOH A 13 613 613 HOH HOH . V 6 HOH A 14 614 614 HOH HOH . V 6 HOH A 15 615 615 HOH HOH . V 6 HOH A 16 616 616 HOH HOH . V 6 HOH A 17 617 617 HOH HOH . V 6 HOH A 18 618 618 HOH HOH . V 6 HOH A 19 619 619 HOH HOH . V 6 HOH A 20 620 620 HOH HOH . V 6 HOH A 21 621 621 HOH HOH . V 6 HOH A 22 622 622 HOH HOH . V 6 HOH A 23 623 623 HOH HOH . V 6 HOH A 24 624 624 HOH HOH . V 6 HOH A 25 625 625 HOH HOH . V 6 HOH A 26 626 626 HOH HOH . V 6 HOH A 27 627 627 HOH HOH . V 6 HOH A 28 628 628 HOH HOH . V 6 HOH A 29 629 629 HOH HOH . V 6 HOH A 30 630 630 HOH HOH . V 6 HOH A 31 631 631 HOH HOH . V 6 HOH A 32 632 632 HOH HOH . V 6 HOH A 33 633 633 HOH HOH . V 6 HOH A 34 634 634 HOH HOH . V 6 HOH A 35 635 635 HOH HOH . V 6 HOH A 36 636 636 HOH HOH . V 6 HOH A 37 637 637 HOH HOH . V 6 HOH A 38 638 638 HOH HOH . V 6 HOH A 39 639 639 HOH HOH . V 6 HOH A 40 640 640 HOH HOH . V 6 HOH A 41 641 641 HOH HOH . V 6 HOH A 42 642 642 HOH HOH . V 6 HOH A 43 643 643 HOH HOH . V 6 HOH A 44 644 644 HOH HOH . V 6 HOH A 45 645 645 HOH HOH . V 6 HOH A 46 646 646 HOH HOH . V 6 HOH A 47 647 647 HOH HOH . V 6 HOH A 48 648 648 HOH HOH . V 6 HOH A 49 649 649 HOH HOH . V 6 HOH A 50 650 650 HOH HOH . V 6 HOH A 51 651 651 HOH HOH . V 6 HOH A 52 652 652 HOH HOH . V 6 HOH A 53 653 653 HOH HOH . V 6 HOH A 54 654 654 HOH HOH . V 6 HOH A 55 655 655 HOH HOH . V 6 HOH A 56 656 656 HOH HOH . V 6 HOH A 57 657 657 HOH HOH . V 6 HOH A 58 658 658 HOH HOH . V 6 HOH A 59 659 659 HOH HOH . V 6 HOH A 60 660 660 HOH HOH . V 6 HOH A 61 661 661 HOH HOH . V 6 HOH A 62 662 662 HOH HOH . V 6 HOH A 63 663 663 HOH HOH . V 6 HOH A 64 664 664 HOH HOH . V 6 HOH A 65 665 665 HOH HOH . V 6 HOH A 66 666 666 HOH HOH . V 6 HOH A 67 667 667 HOH HOH . V 6 HOH A 68 668 668 HOH HOH . V 6 HOH A 69 669 669 HOH HOH . V 6 HOH A 70 670 670 HOH HOH . V 6 HOH A 71 671 671 HOH HOH . V 6 HOH A 72 672 672 HOH HOH . V 6 HOH A 73 673 673 HOH HOH . V 6 HOH A 74 674 674 HOH HOH . V 6 HOH A 75 675 675 HOH HOH . V 6 HOH A 76 676 676 HOH HOH . V 6 HOH A 77 677 677 HOH HOH . V 6 HOH A 78 678 678 HOH HOH . V 6 HOH A 79 679 679 HOH HOH . V 6 HOH A 80 680 680 HOH HOH . V 6 HOH A 81 681 681 HOH HOH . V 6 HOH A 82 682 682 HOH HOH . V 6 HOH A 83 683 683 HOH HOH . V 6 HOH A 84 684 684 HOH HOH . V 6 HOH A 85 685 685 HOH HOH . V 6 HOH A 86 686 686 HOH HOH . V 6 HOH A 87 687 687 HOH HOH . V 6 HOH A 88 688 688 HOH HOH . V 6 HOH A 89 689 689 HOH HOH . V 6 HOH A 90 690 690 HOH HOH . V 6 HOH A 91 691 691 HOH HOH . V 6 HOH A 92 692 692 HOH HOH . V 6 HOH A 93 693 693 HOH HOH . W 6 HOH B 1 601 601 HOH HOH . W 6 HOH B 2 602 602 HOH HOH . W 6 HOH B 3 603 603 HOH HOH . W 6 HOH B 4 604 604 HOH HOH . W 6 HOH B 5 605 605 HOH HOH . W 6 HOH B 6 606 606 HOH HOH . W 6 HOH B 7 607 607 HOH HOH . W 6 HOH B 8 608 608 HOH HOH . W 6 HOH B 9 609 609 HOH HOH . W 6 HOH B 10 610 610 HOH HOH . W 6 HOH B 11 611 611 HOH HOH . W 6 HOH B 12 612 612 HOH HOH . W 6 HOH B 13 613 613 HOH HOH . W 6 HOH B 14 614 614 HOH HOH . W 6 HOH B 15 615 615 HOH HOH . W 6 HOH B 16 616 616 HOH HOH . W 6 HOH B 17 617 617 HOH HOH . W 6 HOH B 18 618 618 HOH HOH . W 6 HOH B 19 619 619 HOH HOH . W 6 HOH B 20 620 620 HOH HOH . W 6 HOH B 21 621 621 HOH HOH . W 6 HOH B 22 622 622 HOH HOH . W 6 HOH B 23 623 623 HOH HOH . W 6 HOH B 24 624 624 HOH HOH . W 6 HOH B 25 625 625 HOH HOH . W 6 HOH B 26 626 626 HOH HOH . W 6 HOH B 27 627 627 HOH HOH . W 6 HOH B 28 628 628 HOH HOH . W 6 HOH B 29 629 629 HOH HOH . W 6 HOH B 30 630 630 HOH HOH . W 6 HOH B 31 631 631 HOH HOH . W 6 HOH B 32 632 632 HOH HOH . W 6 HOH B 33 633 633 HOH HOH . W 6 HOH B 34 634 634 HOH HOH . W 6 HOH B 35 635 635 HOH HOH . W 6 HOH B 36 636 636 HOH HOH . W 6 HOH B 37 637 637 HOH HOH . W 6 HOH B 38 638 638 HOH HOH . W 6 HOH B 39 639 639 HOH HOH . W 6 HOH B 40 640 640 HOH HOH . W 6 HOH B 41 641 641 HOH HOH . W 6 HOH B 42 642 642 HOH HOH . W 6 HOH B 43 643 643 HOH HOH . W 6 HOH B 44 644 644 HOH HOH . W 6 HOH B 45 645 645 HOH HOH . W 6 HOH B 46 646 646 HOH HOH . W 6 HOH B 47 647 647 HOH HOH . W 6 HOH B 48 648 648 HOH HOH . W 6 HOH B 49 649 649 HOH HOH . W 6 HOH B 50 650 650 HOH HOH . W 6 HOH B 51 651 651 HOH HOH . W 6 HOH B 52 652 652 HOH HOH . W 6 HOH B 53 653 653 HOH HOH . W 6 HOH B 54 654 654 HOH HOH . W 6 HOH B 55 655 655 HOH HOH . W 6 HOH B 56 656 656 HOH HOH . W 6 HOH B 57 657 657 HOH HOH . W 6 HOH B 58 658 658 HOH HOH . W 6 HOH B 59 659 659 HOH HOH . W 6 HOH B 60 660 660 HOH HOH . W 6 HOH B 61 661 661 HOH HOH . W 6 HOH B 62 662 662 HOH HOH . W 6 HOH B 63 663 663 HOH HOH . W 6 HOH B 64 664 664 HOH HOH . W 6 HOH B 65 665 665 HOH HOH . X 6 HOH C 1 601 601 HOH HOH . X 6 HOH C 2 602 602 HOH HOH . X 6 HOH C 3 603 603 HOH HOH . X 6 HOH C 4 604 604 HOH HOH . X 6 HOH C 5 605 605 HOH HOH . X 6 HOH C 6 606 606 HOH HOH . X 6 HOH C 7 607 607 HOH HOH . X 6 HOH C 8 608 608 HOH HOH . X 6 HOH C 9 609 609 HOH HOH . X 6 HOH C 10 610 610 HOH HOH . X 6 HOH C 11 611 611 HOH HOH . X 6 HOH C 12 612 612 HOH HOH . X 6 HOH C 13 613 613 HOH HOH . X 6 HOH C 14 614 614 HOH HOH . X 6 HOH C 15 615 615 HOH HOH . X 6 HOH C 16 616 616 HOH HOH . X 6 HOH C 17 617 617 HOH HOH . X 6 HOH C 18 618 618 HOH HOH . X 6 HOH C 19 619 619 HOH HOH . X 6 HOH C 20 620 620 HOH HOH . X 6 HOH C 21 621 621 HOH HOH . X 6 HOH C 22 622 622 HOH HOH . X 6 HOH C 23 623 623 HOH HOH . X 6 HOH C 24 624 624 HOH HOH . X 6 HOH C 25 625 625 HOH HOH . X 6 HOH C 26 626 626 HOH HOH . X 6 HOH C 27 627 627 HOH HOH . X 6 HOH C 28 628 628 HOH HOH . X 6 HOH C 29 629 629 HOH HOH . X 6 HOH C 30 630 630 HOH HOH . X 6 HOH C 31 631 631 HOH HOH . X 6 HOH C 32 632 632 HOH HOH . X 6 HOH C 33 633 633 HOH HOH . X 6 HOH C 34 634 634 HOH HOH . X 6 HOH C 35 635 635 HOH HOH . X 6 HOH C 36 636 636 HOH HOH . X 6 HOH C 37 637 637 HOH HOH . X 6 HOH C 38 638 638 HOH HOH . X 6 HOH C 39 639 639 HOH HOH . X 6 HOH C 40 640 640 HOH HOH . X 6 HOH C 41 641 641 HOH HOH . X 6 HOH C 42 642 642 HOH HOH . X 6 HOH C 43 643 643 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 O1 99C . . . D 2 31.071 231.376 28.7 1 38.81 ? O1 99C 501 A 1 HETATM 2 C C1 99C . . . D 2 30.307 231.839 29.759 1 45.25 ? C1 99C 501 A 1 HETATM 3 C C2 99C . . . D 2 29.486 230.745 30.424 1 43.77 ? C2 99C 501 A 1 HETATM 4 C C3 99C . . . D 2 29.857 229.481 30.318 1 45.12 ? C3 99C 501 A 1 HETATM 5 C C4 99C . . . D 2 28.295 231.195 31.27 1 46.31 ? C4 99C 501 A 1 HETATM 6 C C5 99C . . . D 2 28.893 231.757 32.539 1 40.15 ? C5 99C 501 A 1 HETATM 7 C C6 99C . . . D 2 28.918 230.997 33.695 1 40.49 ? C6 99C 501 A 1 HETATM 8 C C7 99C . . . D 2 29.553 231.491 34.832 1 45.15 ? C7 99C 501 A 1 HETATM 9 C C8 99C . . . D 2 30.088 232.777 34.812 1 52.26 ? C8 99C 501 A 1 HETATM 10 C C9 99C . . . D 2 30.004 233.557 33.672 1 49.43 ? C9 99C 501 A 1 HETATM 11 C C10 99C . . . D 2 29.408 233.04 32.529 1 47.16 ? C10 99C 501 A 1 HETATM 12 C C11 99C . . . D 2 30.727 233.36 36.075 1 95.37 ? C11 99C 501 A 1 HETATM 13 C C12 99C . . . D 2 29.164 228.31 31.034 1 36.17 ? C12 99C 501 A 1 HETATM 14 O O2 99C . . . D 2 28.39 227.552 30.16 1 42.71 ? O2 99C 501 A 1 HETATM 15 P P1 99C . . . D 2 27.578 226.246 30.759 1 41.64 ? P1 99C 501 A 1 HETATM 16 O O3 99C . . . D 2 28.694 225.449 31.611 1 50.31 ? O3 99C 501 A 1 HETATM 17 O O4 99C . . . D 2 26.523 226.657 31.737 1 49.07 ? O4 99C 501 A 1 HETATM 18 O O5 99C . . . D 2 27.09 225.296 29.682 1 41.79 ? O5 99C 501 A 1 HETATM 19 P P2 99C . . . D 2 29.904 224.622 30.894 1 43.03 ? P2 99C 501 A 1 HETATM 20 O O6 99C . . . D 2 29.506 223.223 31.023 1 39.63 ? O6 99C 501 A 1 HETATM 21 O O7 99C . . . D 2 31.091 224.867 31.705 1 36.97 ? O7 99C 501 A 1 HETATM 22 O O8 99C . . . D 2 30.167 224.953 29.316 1 41.59 ? O8 99C 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #