data_3VEY # _model_server_result.job_id fs1k6-0CED5UuHNpCQ4KrA _model_server_result.datetime_utc '2024-12-12 09:02:27' _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 3vey # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 3VEY # _exptl.entry_id 3VEY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 3VEY _cell.length_a 80.387 _cell.length_b 80.387 _cell.length_c 324.334 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VEY _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 O MET 228 A MET 238 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc2 A O VAL 231 A VAL 241 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? metalc ? metalc3 A O VAL 234 A VAL 244 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc4 A O GLY 236 A GLY 246 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 S1G AGS doub 35 n n PG O2G AGS sing 36 n n PG O3G AGS sing 37 n n PG O3B AGS sing 38 n n PB O1B AGS doub 39 n n PB O2B AGS sing 40 n n PB O3B AGS sing 41 n n PB O3A AGS sing 42 n n PA O1A AGS doub 43 n n PA O2A AGS sing 44 n n PA O3A AGS sing 45 n n PA O5' AGS sing 46 n n O5' C5' AGS sing 47 n n C5' C4' AGS sing 48 n n C4' O4' AGS sing 49 n n C4' C3' AGS sing 50 n n O4' C1' AGS sing 51 n n C3' O3' AGS sing 52 n n C3' C2' AGS sing 53 n n C2' O2' AGS sing 54 n n C2' C1' AGS sing 55 n n C1' N9 AGS sing 56 n n N9 C8 AGS sing 57 n y N9 C4 AGS sing 58 n y C8 N7 AGS doub 59 n y N7 C5 AGS sing 60 n y C5 C6 AGS sing 61 n y C5 C4 AGS doub 62 n y C6 N6 AGS sing 63 n n C6 N1 AGS doub 64 n y N1 C2 AGS sing 65 n y C2 N3 AGS doub 66 n y N3 C4 AGS sing 67 n y O2G HOG2 AGS sing 68 n n O3G H21 AGS sing 69 n n O2B HOB2 AGS sing 70 n n O2A HOA2 AGS sing 71 n n C5' "H5'1" AGS sing 72 n n C5' "H5'2" AGS sing 73 n n C4' H4' AGS sing 74 n n C3' H3' AGS sing 75 n n O3' HO3' AGS sing 76 n n C2' H2' AGS sing 77 n n O2' HO2' AGS sing 78 n n C1' H1' AGS sing 79 n n C8 H8 AGS sing 80 n n N6 HN61 AGS sing 81 n n N6 HN62 AGS sing 82 n n C2 H2 AGS sing 83 n n # _atom_sites.entry_id 3VEY _atom_sites.fract_transf_matrix[1][1] 0.01244 _atom_sites.fract_transf_matrix[1][2] 0.007182 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014364 _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] 0.003083 _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 GLC A 1 501 500 GLC GLC . C 3 NA A 1 502 600 NA NA . D 4 AGS A 1 503 604 AGS AGS . E 5 0H5 A 1 504 501 0H5 0H5 . F 6 HOH A 1 601 1 HOH HOH . F 6 HOH A 2 602 2 HOH HOH . F 6 HOH A 3 603 3 HOH HOH . F 6 HOH A 4 604 4 HOH HOH . F 6 HOH A 5 605 5 HOH HOH . F 6 HOH A 6 606 6 HOH HOH . F 6 HOH A 7 607 7 HOH HOH . F 6 HOH A 8 608 8 HOH HOH . F 6 HOH A 9 609 9 HOH HOH . F 6 HOH A 10 610 10 HOH HOH . F 6 HOH A 11 611 11 HOH HOH . F 6 HOH A 12 612 12 HOH HOH . F 6 HOH A 13 613 13 HOH HOH . F 6 HOH A 14 614 14 HOH HOH . F 6 HOH A 15 615 15 HOH HOH . F 6 HOH A 16 616 16 HOH HOH . F 6 HOH A 17 617 17 HOH HOH . F 6 HOH A 18 618 18 HOH HOH . F 6 HOH A 19 619 19 HOH HOH . F 6 HOH A 20 620 20 HOH HOH . F 6 HOH A 21 621 21 HOH HOH . F 6 HOH A 22 622 22 HOH HOH . F 6 HOH A 23 623 23 HOH HOH . F 6 HOH A 24 624 24 HOH HOH . F 6 HOH A 25 625 25 HOH HOH . F 6 HOH A 26 626 26 HOH HOH . F 6 HOH A 27 627 27 HOH HOH . F 6 HOH A 28 628 28 HOH HOH . F 6 HOH A 29 629 29 HOH HOH . F 6 HOH A 30 630 30 HOH HOH . F 6 HOH A 31 631 31 HOH HOH . F 6 HOH A 32 632 32 HOH HOH . F 6 HOH A 33 633 33 HOH HOH . F 6 HOH A 34 634 34 HOH HOH . F 6 HOH A 35 635 35 HOH HOH . F 6 HOH A 36 636 36 HOH HOH . F 6 HOH A 37 637 37 HOH HOH . F 6 HOH A 38 638 38 HOH HOH . F 6 HOH A 39 639 39 HOH HOH . F 6 HOH A 40 640 40 HOH HOH . F 6 HOH A 41 641 41 HOH HOH . F 6 HOH A 42 642 42 HOH HOH . F 6 HOH A 43 643 43 HOH HOH . F 6 HOH A 44 644 44 HOH HOH . F 6 HOH A 45 645 45 HOH HOH . F 6 HOH A 46 646 46 HOH HOH . F 6 HOH A 47 647 47 HOH HOH . F 6 HOH A 48 648 48 HOH HOH . F 6 HOH A 49 649 49 HOH HOH . F 6 HOH A 50 650 50 HOH HOH . F 6 HOH A 51 651 51 HOH HOH . F 6 HOH A 52 652 52 HOH HOH . F 6 HOH A 53 653 53 HOH HOH . F 6 HOH A 54 654 54 HOH HOH . F 6 HOH A 55 655 55 HOH HOH . F 6 HOH A 56 656 56 HOH HOH . F 6 HOH A 57 657 57 HOH HOH . F 6 HOH A 58 658 58 HOH HOH . F 6 HOH A 59 659 59 HOH HOH . F 6 HOH A 60 660 60 HOH HOH . F 6 HOH A 61 661 61 HOH HOH . F 6 HOH A 62 662 63 HOH HOH . F 6 HOH A 63 663 64 HOH HOH . F 6 HOH A 64 664 65 HOH HOH . F 6 HOH A 65 665 66 HOH HOH . F 6 HOH A 66 666 67 HOH HOH . F 6 HOH A 67 667 68 HOH HOH . F 6 HOH A 68 668 69 HOH HOH . F 6 HOH A 69 669 70 HOH HOH . F 6 HOH A 70 670 71 HOH HOH . F 6 HOH A 71 671 72 HOH HOH . F 6 HOH A 72 672 73 HOH HOH . F 6 HOH A 73 673 74 HOH HOH . F 6 HOH A 74 674 75 HOH HOH . F 6 HOH A 75 675 76 HOH HOH . F 6 HOH A 76 676 77 HOH HOH . F 6 HOH A 77 677 78 HOH HOH . F 6 HOH A 78 678 79 HOH HOH . F 6 HOH A 79 679 80 HOH HOH . F 6 HOH A 80 680 81 HOH HOH . F 6 HOH A 81 681 82 HOH HOH . F 6 HOH A 82 682 83 HOH HOH . F 6 HOH A 83 683 84 HOH HOH . F 6 HOH A 84 684 85 HOH HOH . F 6 HOH A 85 685 86 HOH HOH . F 6 HOH A 86 686 87 HOH HOH . F 6 HOH A 87 687 88 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 AGS . . . D 4 24.972 4.851 73.017 1 135.92 ? PG AGS 503 A 1 HETATM 2 S S1G AGS . . . D 4 26.286 6.562 72.765 1 137.97 ? S1G AGS 503 A 1 HETATM 3 O O2G AGS . . . D 4 25.842 3.691 73.675 1 124.07 ? O2G AGS 503 A 1 HETATM 4 O O3G AGS . . . D 4 24.464 4.211 71.764 1 122.04 ? O3G AGS 503 A 1 HETATM 5 P PB AGS . . . D 4 24.021 5.447 75.514 1 114.07 ? PB AGS 503 A 1 HETATM 6 O O1B AGS . . . D 4 24.35 6.882 75.734 1 112.75 ? O1B AGS 503 A 1 HETATM 7 O O2B AGS . . . D 4 22.733 5.052 76.429 1 111.61 ? O2B AGS 503 A 1 HETATM 8 O O3B AGS . . . D 4 23.669 5.245 73.942 1 129.95 ? O3B AGS 503 A 1 HETATM 9 P PA AGS . . . D 4 25.523 3.899 77.309 1 92.52 ? PA AGS 503 A 1 HETATM 10 O O1A AGS . . . D 4 27.001 3.802 77.39 1 84.69 ? O1A AGS 503 A 1 HETATM 11 O O2A AGS . . . D 4 24.928 4.741 78.576 1 101.32 ? O2A AGS 503 A 1 HETATM 12 O O3A AGS . . . D 4 25.353 4.604 75.878 1 92.88 ? O3A AGS 503 A 1 HETATM 13 O O5' AGS . . . D 4 24.893 2.417 77.215 1 82.97 ? O5' AGS 503 A 1 HETATM 14 C C5' AGS . . . D 4 23.635 2.217 77.886 1 82.64 ? C5' AGS 503 A 1 HETATM 15 C C4' AGS . . . D 4 23.229 0.796 77.466 1 84.43 ? C4' AGS 503 A 1 HETATM 16 O O4' AGS . . . D 4 24.117 -0.201 78.005 1 81.78 ? O4' AGS 503 A 1 HETATM 17 C C3' AGS . . . D 4 21.793 0.35 77.778 1 87.1 ? C3' AGS 503 A 1 HETATM 18 O O3' AGS . . . D 4 21.321 -0.378 76.649 1 85.59 ? O3' AGS 503 A 1 HETATM 19 C C2' AGS . . . D 4 21.953 -0.547 79.043 1 81.63 ? C2' AGS 503 A 1 HETATM 20 O O2' AGS . . . D 4 21.012 -1.631 79.088 1 92.38 ? O2' AGS 503 A 1 HETATM 21 C C1' AGS . . . D 4 23.431 -1.025 78.969 1 91.06 ? C1' AGS 503 A 1 HETATM 22 N N9 AGS . . . D 4 24.11 -1.128 80.287 1 73.07 ? N9 AGS 503 A 1 HETATM 23 C C8 AGS . . . D 4 23.822 -0.419 81.429 1 73.29 ? C8 AGS 503 A 1 HETATM 24 N N7 AGS . . . D 4 24.596 -0.799 82.417 1 71.41 ? N7 AGS 503 A 1 HETATM 25 C C5 AGS . . . D 4 25.435 -1.776 82.003 1 75.76 ? C5 AGS 503 A 1 HETATM 26 C C6 AGS . . . D 4 26.475 -2.541 82.615 1 80.67 ? C6 AGS 503 A 1 HETATM 27 N N6 AGS . . . D 4 26.819 -2.399 83.959 1 53.75 ? N6 AGS 503 A 1 HETATM 28 N N1 AGS . . . D 4 27.132 -3.431 81.848 1 58.76 ? N1 AGS 503 A 1 HETATM 29 C C2 AGS . . . D 4 26.83 -3.658 80.545 1 75.86 ? C2 AGS 503 A 1 HETATM 30 N N3 AGS . . . D 4 25.869 -2.951 79.927 1 58.5 ? N3 AGS 503 A 1 HETATM 31 C C4 AGS . . . D 4 25.139 -2.011 80.614 1 74.81 ? C4 AGS 503 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #