data_4DW1 # _model_server_result.job_id ON0JrjSFC-ab1gMdYa4b2Q _model_server_result.datetime_utc '2025-01-31 15:54:43' _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 4dw1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":508}' # _entry.id 4DW1 # _exptl.entry_id 4DW1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 4DW1 _cell.length_a 128.791 _cell.length_b 128.791 _cell.length_c 252.074 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DW1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 2 6 3 MAN BMA C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 501 NAG 2 n B NAG 2 B 2 NAG A 502 NAG 2 n B BMA 3 B 3 BMA A 503 BMA 2 n B MAN 4 B 4 MAN A 505 MAN 2 n B MAN 5 B 5 MAN A 506 MAN 2 n B MAN 6 B 6 MAN A 504 MAN # 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 disulf ? disulf1 A SG CYS 94 A CYS 119 1_555 A SG CYS 143 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf2 A SG CYS 104 A CYS 129 1_555 A SG CYS 127 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 110 A CYS 135 1_555 A SG CYS 137 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 195 A CYS 220 1_555 A SG CYS 205 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf5 A SG CYS 239 A CYS 264 1_555 A SG CYS 248 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 88 A ASN 113 1_555 C C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale2 A ND2 ASN 188 A ASN 213 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale5 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale6 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 B O3 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 4DW1 _atom_sites.fract_transf_matrix[1][1] 0.007765 _atom_sites.fract_transf_matrix[1][2] 0.004483 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008966 _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] 0.003967 _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 C 3 NAG A 1 507 511 NAG NAG . D 4 ATP A 1 508 1 ATP ATP . E 5 GOL A 1 509 1 GOL GOL . F 5 GOL A 1 510 2 GOL GOL . G 6 HOH A 1 601 1 HOH HOH . G 6 HOH A 2 602 2 HOH HOH . G 6 HOH A 3 603 3 HOH HOH . G 6 HOH A 4 604 4 HOH HOH . G 6 HOH A 5 605 5 HOH HOH . G 6 HOH A 6 606 6 HOH HOH . G 6 HOH A 7 607 7 HOH HOH . G 6 HOH A 8 608 8 HOH HOH . G 6 HOH A 9 609 9 HOH HOH . G 6 HOH A 10 610 10 HOH HOH . G 6 HOH A 11 611 11 HOH HOH . G 6 HOH A 12 612 12 HOH HOH . G 6 HOH A 13 613 13 HOH HOH . G 6 HOH A 14 614 14 HOH HOH . G 6 HOH A 15 615 15 HOH HOH . G 6 HOH A 16 616 16 HOH HOH . G 6 HOH A 17 617 17 HOH HOH . G 6 HOH A 18 618 18 HOH HOH . G 6 HOH A 19 619 19 HOH HOH . G 6 HOH A 20 620 20 HOH HOH . G 6 HOH A 21 621 21 HOH HOH . G 6 HOH A 22 622 22 HOH HOH . G 6 HOH A 23 623 23 HOH HOH . G 6 HOH A 24 624 24 HOH HOH . G 6 HOH A 25 625 25 HOH HOH . G 6 HOH A 26 626 26 HOH HOH . G 6 HOH A 27 627 27 HOH HOH . G 6 HOH A 28 628 28 HOH HOH . G 6 HOH A 29 629 29 HOH HOH . G 6 HOH A 30 630 30 HOH HOH . G 6 HOH A 31 631 31 HOH HOH . G 6 HOH A 32 632 32 HOH HOH . G 6 HOH A 33 633 33 HOH HOH . G 6 HOH A 34 634 34 HOH HOH . G 6 HOH A 35 635 35 HOH HOH . G 6 HOH A 36 636 36 HOH HOH . G 6 HOH A 37 637 37 HOH HOH . G 6 HOH A 38 638 38 HOH HOH . G 6 HOH A 39 639 39 HOH HOH . G 6 HOH A 40 640 40 HOH HOH . G 6 HOH A 41 641 41 HOH HOH . G 6 HOH A 42 642 42 HOH HOH . G 6 HOH A 43 643 43 HOH HOH . G 6 HOH A 44 644 44 HOH HOH . G 6 HOH A 45 645 45 HOH HOH . G 6 HOH A 46 646 46 HOH HOH . G 6 HOH A 47 647 47 HOH HOH . G 6 HOH A 48 648 48 HOH HOH . G 6 HOH A 49 649 49 HOH HOH . G 6 HOH A 50 650 50 HOH HOH . G 6 HOH A 51 651 51 HOH HOH . G 6 HOH A 52 652 52 HOH HOH . G 6 HOH A 53 653 53 HOH HOH . G 6 HOH A 54 654 54 HOH HOH . G 6 HOH A 55 655 55 HOH HOH . G 6 HOH A 56 656 56 HOH HOH . G 6 HOH A 57 657 57 HOH HOH . G 6 HOH A 58 658 58 HOH HOH . G 6 HOH A 59 659 59 HOH HOH . G 6 HOH A 60 660 60 HOH HOH . G 6 HOH A 61 661 61 HOH HOH . G 6 HOH A 62 662 62 HOH HOH . G 6 HOH A 63 663 63 HOH HOH . G 6 HOH A 64 664 64 HOH HOH . G 6 HOH A 65 665 65 HOH HOH . G 6 HOH A 66 666 66 HOH HOH . G 6 HOH A 67 667 67 HOH HOH . G 6 HOH A 68 668 68 HOH HOH . G 6 HOH A 69 669 69 HOH HOH . G 6 HOH A 70 670 70 HOH HOH . G 6 HOH A 71 671 71 HOH HOH . G 6 HOH A 72 672 72 HOH HOH . G 6 HOH A 73 673 73 HOH HOH . G 6 HOH A 74 674 74 HOH HOH . G 6 HOH A 75 675 75 HOH HOH . G 6 HOH A 76 676 76 HOH HOH . G 6 HOH A 77 677 77 HOH HOH . G 6 HOH A 78 678 78 HOH HOH . G 6 HOH A 79 679 82 HOH HOH . G 6 HOH A 80 680 83 HOH HOH . G 6 HOH A 81 681 84 HOH HOH . G 6 HOH A 82 682 85 HOH HOH . G 6 HOH A 83 683 86 HOH HOH . G 6 HOH A 84 684 87 HOH HOH . G 6 HOH A 85 685 88 HOH HOH . G 6 HOH A 86 686 89 HOH HOH . G 6 HOH A 87 687 90 HOH HOH . G 6 HOH A 88 688 91 HOH HOH . G 6 HOH A 89 689 92 HOH HOH . G 6 HOH A 90 690 93 HOH HOH . G 6 HOH A 91 691 94 HOH HOH . G 6 HOH A 92 692 95 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 PG ATP . . . D 4 -20.962 -0.896 46.95 1 65.97 ? PG ATP 508 A 1 HETATM 2 O O1G ATP . . . D 4 -21.023 -1.98 45.886 1 58.07 ? O1G ATP 508 A 1 HETATM 3 O O2G ATP . . . D 4 -19.61 -0.248 47.151 1 65.62 ? O2G ATP 508 A 1 HETATM 4 O O3G ATP . . . D 4 -22.095 0.106 46.795 1 71.53 ? O3G ATP 508 A 1 HETATM 5 P PB ATP . . . D 4 -21.145 -3.097 48.775 1 67.56 ? PB ATP 508 A 1 HETATM 6 O O1B ATP . . . D 4 -19.746 -3.592 48.582 1 71.88 ? O1B ATP 508 A 1 HETATM 7 O O2B ATP . . . D 4 -22.258 -3.787 48.019 1 74.06 ? O2B ATP 508 A 1 HETATM 8 O O3B ATP . . . D 4 -21.24 -1.529 48.415 1 61.92 ? O3B ATP 508 A 1 HETATM 9 P PA ATP . . . D 4 -20.606 -2.404 51.511 1 66.72 ? PA ATP 508 A 1 HETATM 10 O O1A ATP . . . D 4 -19.357 -1.851 50.884 1 66.32 ? O1A ATP 508 A 1 HETATM 11 O O2A ATP . . . D 4 -20.506 -3.43 52.608 1 73.57 ? O2A ATP 508 A 1 HETATM 12 O O3A ATP . . . D 4 -21.537 -3.029 50.345 1 63.51 ? O3A ATP 508 A 1 HETATM 13 O O5' ATP . . . D 4 -21.497 -1.175 52.03 1 64.05 ? O5' ATP 508 A 1 HETATM 14 C C5' ATP . . . D 4 -22.815 -1.374 52.546 1 66.42 ? C5' ATP 508 A 1 HETATM 15 C C4' ATP . . . D 4 -23.747 -0.289 52.01 1 64.92 ? C4' ATP 508 A 1 HETATM 16 O O4' ATP . . . D 4 -23.193 0.998 52.275 1 58.73 ? O4' ATP 508 A 1 HETATM 17 C C3' ATP . . . D 4 -23.876 -0.403 50.5 1 68.74 ? C3' ATP 508 A 1 HETATM 18 O O3' ATP . . . D 4 -25.223 -0.124 50.108 1 63.25 ? O3' ATP 508 A 1 HETATM 19 C C2' ATP . . . D 4 -22.945 0.671 49.98 1 63.62 ? C2' ATP 508 A 1 HETATM 20 O O2' ATP . . . D 4 -23.356 1.22 48.742 1 63.48 ? O2' ATP 508 A 1 HETATM 21 C C1' ATP . . . D 4 -22.985 1.721 51.06 1 61.03 ? C1' ATP 508 A 1 HETATM 22 N N9 ATP . . . D 4 -21.684 2.429 51.121 1 68.01 ? N9 ATP 508 A 1 HETATM 23 C C8 ATP . . . D 4 -20.471 1.843 51.275 1 64.63 ? C8 ATP 508 A 1 HETATM 24 N N7 ATP . . . D 4 -19.482 2.775 51.304 1 63.96 ? N7 ATP 508 A 1 HETATM 25 C C5 ATP . . . D 4 -20.055 3.984 51.156 1 62.7 ? C5 ATP 508 A 1 HETATM 26 C C6 ATP . . . D 4 -19.589 5.388 51.099 1 60.16 ? C6 ATP 508 A 1 HETATM 27 N N6 ATP . . . D 4 -18.282 5.705 51.202 1 62.74 ? N6 ATP 508 A 1 HETATM 28 N N1 ATP . . . D 4 -20.528 6.353 50.951 1 67.41 ? N1 ATP 508 A 1 HETATM 29 C C2 ATP . . . D 4 -21.847 6.067 50.844 1 64.51 ? C2 ATP 508 A 1 HETATM 30 N N3 ATP . . . D 4 -22.335 4.814 50.886 1 62.87 ? N3 ATP 508 A 1 HETATM 31 C C4 ATP . . . D 4 -21.509 3.752 51.038 1 64.58 ? C4 ATP 508 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #