data_5KX5 # _model_server_result.job_id cXuNhJd3ald1BDESSVPTDQ _model_server_result.datetime_utc '2024-11-05 05:41:16' _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 5kx5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":401}' # _entry.id 5KX5 # _exptl.entry_id 5KX5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-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 90 _cell.entry_id 5KX5 _cell.length_a 104.79 _cell.length_b 153.9 _cell.length_c 185.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KX5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA _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 # _struct_asym.details ? _struct_asym.entity_id 10 _struct_asym.id W _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 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.08 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc10 X O HOH . A HOH 601 1_555 V CA CA . E CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc11 B OE2 GLU 111 B GLU 113 1_555 L CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.196 ? metalc ? metalc12 B OG SER 296 B SER 298 1_555 N MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? metalc ? metalc13 N MG MG . B MG 505 1_555 Y O HOH . B HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc14 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc15 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc16 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc17 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.097 ? metalc ? metalc18 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc19 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc20 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc21 D OE1 GLN 11 D GLN 11 1_555 T MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc22 R O1A GDP . D GDP 501 1_555 T MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc23 T MG MG . D MG 503 1_555 AA O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-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 PB O1B ADP doub 113 n n PB O2B ADP sing 114 n n PB O3B ADP sing 115 n n PB O3A ADP sing 116 n n O2B HOB2 ADP sing 117 n n O3B HOB3 ADP sing 118 n n PA O1A ADP doub 119 n n PA O2A ADP sing 120 n n PA O3A ADP sing 121 n n PA O5' ADP sing 122 n n O2A HOA2 ADP sing 123 n n O5' C5' ADP sing 124 n n C5' C4' ADP sing 125 n n C5' "H5'1" ADP sing 126 n n C5' "H5'2" ADP sing 127 n n C4' O4' ADP sing 128 n n C4' C3' ADP sing 129 n n C4' H4' ADP sing 130 n n O4' C1' ADP sing 131 n n C3' O3' ADP sing 132 n n C3' C2' ADP sing 133 n n C3' H3' ADP sing 134 n n O3' HO3' ADP sing 135 n n C2' O2' ADP sing 136 n n C2' C1' ADP sing 137 n n C2' H2' ADP sing 138 n n O2' HO2' ADP sing 139 n n C1' N9 ADP sing 140 n n C1' H1' ADP sing 141 n n N9 C8 ADP sing 142 n y N9 C4 ADP sing 143 n y C8 N7 ADP doub 144 n y C8 H8 ADP sing 145 n n N7 C5 ADP sing 146 n y C5 C6 ADP sing 147 n y C5 C4 ADP doub 148 n y C6 N6 ADP sing 149 n n C6 N1 ADP doub 150 n y N6 HN61 ADP sing 151 n n N6 HN62 ADP sing 152 n n N1 C2 ADP sing 153 n y C2 N3 ADP doub 154 n y C2 H2 ADP sing 155 n n N3 C4 ADP sing 156 n y # _atom_sites.entry_id 5KX5 _atom_sites.fract_transf_matrix[1][1] 0.009543 _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] 0.006498 _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] 0.0054 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GDP B 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 7 CA B 1 503 503 CA CA . M 9 6YK B 1 504 3 6YK PFE . N 6 MG B 1 505 1 MG MG . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 503 CA CA . R 8 GDP D 1 501 600 GDP GDP . S 6 MG D 1 502 601 MG MG . T 6 MG D 1 503 602 MG MG . U 9 6YK D 1 504 4 6YK PFE . V 7 CA E 1 201 505 CA CA . W 10 ADP F 1 401 703 ADP ADP . X 11 HOH A 1 601 33 HOH HOH . X 11 HOH A 2 602 89 HOH HOH . X 11 HOH A 3 603 49 HOH HOH . X 11 HOH A 4 604 27 HOH HOH . X 11 HOH A 5 605 81 HOH HOH . X 11 HOH A 6 606 79 HOH HOH . X 11 HOH A 7 607 41 HOH HOH . X 11 HOH A 8 608 32 HOH HOH . X 11 HOH A 9 609 90 HOH HOH . X 11 HOH A 10 610 63 HOH HOH . X 11 HOH A 11 611 50 HOH HOH . X 11 HOH A 12 612 105 HOH HOH . X 11 HOH A 13 613 80 HOH HOH . X 11 HOH A 14 614 48 HOH HOH . X 11 HOH A 15 615 40 HOH HOH . X 11 HOH A 16 616 39 HOH HOH . X 11 HOH A 17 617 110 HOH HOH . X 11 HOH A 18 618 29 HOH HOH . X 11 HOH A 19 619 58 HOH HOH . X 11 HOH A 20 620 82 HOH HOH . X 11 HOH A 21 621 64 HOH HOH . X 11 HOH A 22 622 106 HOH HOH . Y 11 HOH B 1 601 66 HOH HOH . Y 11 HOH B 2 602 1 HOH HOH . Y 11 HOH B 3 603 60 HOH HOH . Y 11 HOH B 4 604 84 HOH HOH . Y 11 HOH B 5 605 5 HOH HOH . Y 11 HOH B 6 606 52 HOH HOH . Y 11 HOH B 7 607 61 HOH HOH . Y 11 HOH B 8 608 2 HOH HOH . Y 11 HOH B 9 609 62 HOH HOH . Y 11 HOH B 10 610 78 HOH HOH . Y 11 HOH B 11 611 76 HOH HOH . Y 11 HOH B 12 612 55 HOH HOH . Y 11 HOH B 13 613 12 HOH HOH . Y 11 HOH B 14 614 11 HOH HOH . Y 11 HOH B 15 615 88 HOH HOH . Y 11 HOH B 16 616 103 HOH HOH . Y 11 HOH B 17 617 104 HOH HOH . Y 11 HOH B 18 618 25 HOH HOH . Y 11 HOH B 19 619 87 HOH HOH . Y 11 HOH B 20 620 72 HOH HOH . Y 11 HOH B 21 621 6 HOH HOH . Y 11 HOH B 22 622 85 HOH HOH . Y 11 HOH B 23 623 75 HOH HOH . Y 11 HOH B 24 624 20 HOH HOH . Y 11 HOH B 25 625 14 HOH HOH . Y 11 HOH B 26 626 100 HOH HOH . Y 11 HOH B 27 627 13 HOH HOH . Y 11 HOH B 28 628 71 HOH HOH . Y 11 HOH B 29 629 4 HOH HOH . Y 11 HOH B 30 630 67 HOH HOH . Y 11 HOH B 31 631 44 HOH HOH . Y 11 HOH B 32 632 77 HOH HOH . Y 11 HOH B 33 633 74 HOH HOH . Z 11 HOH C 1 601 121 HOH HOH . Z 11 HOH C 2 602 114 HOH HOH . Z 11 HOH C 3 603 10 HOH HOH . Z 11 HOH C 4 604 113 HOH HOH . Z 11 HOH C 5 605 24 HOH HOH . Z 11 HOH C 6 606 73 HOH HOH . Z 11 HOH C 7 607 8 HOH HOH . Z 11 HOH C 8 608 46 HOH HOH . Z 11 HOH C 9 609 119 HOH HOH . Z 11 HOH C 10 610 47 HOH HOH . Z 11 HOH C 11 611 36 HOH HOH . Z 11 HOH C 12 612 56 HOH HOH . Z 11 HOH C 13 613 18 HOH HOH . Z 11 HOH C 14 614 53 HOH HOH . Z 11 HOH C 15 615 21 HOH HOH . Z 11 HOH C 16 616 86 HOH HOH . Z 11 HOH C 17 617 120 HOH HOH . Z 11 HOH C 18 618 23 HOH HOH . Z 11 HOH C 19 619 54 HOH HOH . Z 11 HOH C 20 620 68 HOH HOH . Z 11 HOH C 21 621 101 HOH HOH . Z 11 HOH C 22 622 115 HOH HOH . Z 11 HOH C 23 623 37 HOH HOH . Z 11 HOH C 24 624 118 HOH HOH . Z 11 HOH C 25 625 65 HOH HOH . Z 11 HOH C 26 626 116 HOH HOH . Z 11 HOH C 27 627 22 HOH HOH . Z 11 HOH C 28 628 117 HOH HOH . Z 11 HOH C 29 629 70 HOH HOH . Z 11 HOH C 30 630 9 HOH HOH . Z 11 HOH C 31 631 3 HOH HOH . Z 11 HOH C 32 632 112 HOH HOH . Z 11 HOH C 33 633 19 HOH HOH . Z 11 HOH C 34 634 45 HOH HOH . Z 11 HOH C 35 635 7 HOH HOH . Z 11 HOH C 36 636 16 HOH HOH . Z 11 HOH C 37 637 34 HOH HOH . Z 11 HOH C 38 638 69 HOH HOH . Z 11 HOH C 39 639 43 HOH HOH . Z 11 HOH C 40 640 83 HOH HOH . Z 11 HOH C 41 641 17 HOH HOH . AA 11 HOH D 1 601 38 HOH HOH . AA 11 HOH D 2 602 42 HOH HOH . AA 11 HOH D 3 603 111 HOH HOH . AA 11 HOH D 4 604 109 HOH HOH . AA 11 HOH D 5 605 31 HOH HOH . AA 11 HOH D 6 606 108 HOH HOH . AA 11 HOH D 7 607 28 HOH HOH . BA 11 HOH E 1 301 15 HOH HOH . BA 11 HOH E 2 302 26 HOH HOH . BA 11 HOH E 3 303 57 HOH HOH . BA 11 HOH E 4 304 102 HOH HOH . CA 11 HOH F 1 501 95 HOH HOH . CA 11 HOH F 2 502 122 HOH HOH . CA 11 HOH F 3 503 99 HOH HOH . CA 11 HOH F 4 504 92 HOH HOH . CA 11 HOH F 5 505 94 HOH HOH . CA 11 HOH F 6 506 96 HOH HOH . CA 11 HOH F 7 507 93 HOH HOH . CA 11 HOH F 8 508 91 HOH HOH . CA 11 HOH F 9 509 51 HOH HOH . CA 11 HOH F 10 510 107 HOH HOH . CA 11 HOH F 11 511 97 HOH HOH . CA 11 HOH F 12 512 98 HOH HOH . CA 11 HOH F 13 513 35 HOH HOH . CA 11 HOH F 14 514 30 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 P PB ADP . . . W 10 10.864 46.676 95.514 1 121.37 ? PB ADP 401 F 1 HETATM 2 O O1B ADP . . . W 10 11.366 47.817 94.593 1 121.75 ? O1B ADP 401 F 1 HETATM 3 O O2B ADP . . . W 10 9.451 46.207 95.156 1 122.02 ? O2B ADP 401 F 1 HETATM 4 O O3B ADP . . . W 10 11.899 45.548 95.366 1 121.12 ? O3B ADP 401 F 1 HETATM 5 P PA ADP . . . W 10 9.996 47.865 98.099 1 115.02 ? PA ADP 401 F 1 HETATM 6 O O1A ADP . . . W 10 8.602 48.027 97.441 1 115.78 ? O1A ADP 401 F 1 HETATM 7 O O2A ADP . . . W 10 10.536 49.179 98.524 1 112.87 ? O2A ADP 401 F 1 HETATM 8 O O3A ADP . . . W 10 10.972 47.192 97.025 1 118.39 ? O3A ADP 401 F 1 HETATM 9 O O5' ADP . . . W 10 9.784 46.977 99.435 1 112.36 ? O5' ADP 401 F 1 HETATM 10 C C5' ADP . . . W 10 9.165 45.673 99.462 1 109.44 ? C5' ADP 401 F 1 HETATM 11 C C4' ADP . . . W 10 8.369 45.468 100.728 1 106.36 ? C4' ADP 401 F 1 HETATM 12 O O4' ADP . . . W 10 9.15 45.852 101.877 1 104.22 ? O4' ADP 401 F 1 HETATM 13 C C3' ADP . . . W 10 7.083 46.274 100.847 1 106.13 ? C3' ADP 401 F 1 HETATM 14 O O3' ADP . . . W 10 6.028 45.645 100.128 1 108.17 ? O3' ADP 401 F 1 HETATM 15 C C2' ADP . . . W 10 6.865 46.319 102.364 1 103.35 ? C2' ADP 401 F 1 HETATM 16 O O2' ADP . . . W 10 6.197 45.183 102.902 1 102.82 ? O2' ADP 401 F 1 HETATM 17 C C1' ADP . . . W 10 8.301 46.361 102.892 1 101.83 ? C1' ADP 401 F 1 HETATM 18 N N9 ADP . . . W 10 8.769 47.687 103.288 1 98.92 ? N9 ADP 401 F 1 HETATM 19 C C8 ADP . . . W 10 9.6 48.518 102.58 1 98.07 ? C8 ADP 401 F 1 HETATM 20 N N7 ADP . . . W 10 9.97 49.591 103.238 1 98.04 ? N7 ADP 401 F 1 HETATM 21 C C5 ADP . . . W 10 9.328 49.465 104.461 1 97.13 ? C5 ADP 401 F 1 HETATM 22 C C6 ADP . . . W 10 9.331 50.265 105.625 1 94.45 ? C6 ADP 401 F 1 HETATM 23 N N6 ADP . . . W 10 9.987 51.424 105.729 1 91.94 ? N6 ADP 401 F 1 HETATM 24 N N1 ADP . . . W 10 8.6 49.839 106.684 1 95.22 ? N1 ADP 401 F 1 HETATM 25 C C2 ADP . . . W 10 7.899 48.704 106.57 1 95.72 ? C2 ADP 401 F 1 HETATM 26 N N3 ADP . . . W 10 7.818 47.871 105.527 1 96.51 ? N3 ADP 401 F 1 HETATM 27 C C4 ADP . . . W 10 8.569 48.305 104.5 1 97.72 ? C4 ADP 401 F 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 27 #