data_5VKR # _model_server_result.job_id Dgszl6A-5Xkr6gtPs5XRpQ _model_server_result.datetime_utc '2024-10-18 16:30:02' _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 5vkr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5VKR # _exptl.entry_id 5VKR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _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 5VKR _cell.length_a 55.37 _cell.length_b 74.27 _cell.length_c 180.95 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VKR _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 90.475 # _struct_asym.details ? _struct_asym.entity_id 3 _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 SG CYS 46 A CYS 46 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc2 A NE2 HIS 67 A HIS 67 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc3 A SG CYS 97 A CYS 97 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc4 A SG CYS 100 A CYS 100 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc5 A SG CYS 103 A CYS 103 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc6 A SG CYS 111 A CYS 111 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc7 A SG CYS 174 A CYS 174 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc8 B ZN ZN . A ZN 401 1_555 E O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _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 N1 C2 APR sing 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 5VKR _atom_sites.fract_transf_matrix[1][1] 0.01806 _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] 0.013464 _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] 0.005526 _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 ZN A 1 401 375 ZN ZN . C 2 ZN A 1 402 376 ZN ZN . D 3 APR A 1 403 377 APR APR . E 4 HOH A 1 501 437 HOH HOH . E 4 HOH A 2 502 442 HOH HOH . E 4 HOH A 3 503 443 HOH HOH . E 4 HOH A 4 504 445 HOH HOH . E 4 HOH A 5 505 423 HOH HOH . E 4 HOH A 6 506 438 HOH HOH . E 4 HOH A 7 507 429 HOH HOH . E 4 HOH A 8 508 433 HOH HOH . E 4 HOH A 9 509 420 HOH HOH . E 4 HOH A 10 510 424 HOH HOH . E 4 HOH A 11 511 436 HOH HOH . E 4 HOH A 12 512 425 HOH HOH . E 4 HOH A 13 513 411 HOH HOH . E 4 HOH A 14 514 422 HOH HOH . E 4 HOH A 15 515 412 HOH HOH . E 4 HOH A 16 516 428 HOH HOH . E 4 HOH A 17 517 421 HOH HOH . E 4 HOH A 18 518 408 HOH HOH . E 4 HOH A 19 519 415 HOH HOH . E 4 HOH A 20 520 441 HOH HOH . E 4 HOH A 21 521 403 HOH HOH . E 4 HOH A 22 522 409 HOH HOH . E 4 HOH A 23 523 407 HOH HOH . E 4 HOH A 24 524 418 HOH HOH . E 4 HOH A 25 525 434 HOH HOH . E 4 HOH A 26 526 431 HOH HOH . E 4 HOH A 27 527 404 HOH HOH . E 4 HOH A 28 528 435 HOH HOH . E 4 HOH A 29 529 406 HOH HOH . E 4 HOH A 30 530 413 HOH HOH . E 4 HOH A 31 531 426 HOH HOH . E 4 HOH A 32 532 414 HOH HOH . E 4 HOH A 33 533 419 HOH HOH . E 4 HOH A 34 534 432 HOH HOH . E 4 HOH A 35 535 416 HOH HOH . E 4 HOH A 36 536 402 HOH HOH . E 4 HOH A 37 537 401 HOH HOH . E 4 HOH A 38 538 427 HOH HOH . E 4 HOH A 39 539 417 HOH HOH . E 4 HOH A 40 540 410 HOH HOH . E 4 HOH A 41 541 439 HOH HOH . E 4 HOH A 42 542 440 HOH HOH . E 4 HOH A 43 543 444 HOH HOH . E 4 HOH A 44 544 430 HOH HOH . E 4 HOH A 45 545 405 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 N N1 APR . . . D 3 16.512 3.897 36.643 0.6 47.96 ? N1 APR 403 A 1 HETATM 2 C C2 APR . . . D 3 16.933 5.043 36.063 0.6 43.34 ? C2 APR 403 A 1 HETATM 3 N N3 APR . . . D 3 16.831 5.186 34.715 0.6 44.13 ? N3 APR 403 A 1 HETATM 4 C C4 APR . . . D 3 16.281 4.235 33.877 0.6 47.19 ? C4 APR 403 A 1 HETATM 5 C C5 APR . . . D 3 15.8 2.97 34.454 0.6 47.86 ? C5 APR 403 A 1 HETATM 6 C C6 APR . . . D 3 15.971 2.873 35.919 0.6 49.71 ? C6 APR 403 A 1 HETATM 7 N N6 APR . . . D 3 15.554 1.751 36.499 0.6 63.83 ? N6 APR 403 A 1 HETATM 8 N N7 APR . . . D 3 15.299 2.219 33.444 0.6 47.48 ? N7 APR 403 A 1 HETATM 9 C C8 APR . . . D 3 15.452 2.908 32.284 0.6 47.56 ? C8 APR 403 A 1 HETATM 10 N N9 APR . . . D 3 16.035 4.121 32.562 0.6 51.91 ? N9 APR 403 A 1 HETATM 11 C C1' APR . . . D 3 16.366 5.245 31.642 0.6 49.51 ? C1' APR 403 A 1 HETATM 12 C C2' APR . . . D 3 16.976 4.921 30.292 0.6 49 ? C2' APR 403 A 1 HETATM 13 O O2' APR . . . D 3 18.389 4.689 30.405 0.6 54.33 ? O2' APR 403 A 1 HETATM 14 C C3' APR . . . D 3 16.651 6.201 29.522 0.6 52.1 ? C3' APR 403 A 1 HETATM 15 O O3' APR . . . D 3 17.677 7.215 29.571 0.6 52.78 ? O3' APR 403 A 1 HETATM 16 O O4' APR . . . D 3 15.176 5.987 31.372 0.6 49.48 ? O4' APR 403 A 1 HETATM 17 C C4' APR . . . D 3 15.39 6.745 30.198 0.6 53.68 ? C4' APR 403 A 1 HETATM 18 C C5' APR . . . D 3 14.182 6.617 29.285 0.6 52.14 ? C5' APR 403 A 1 HETATM 19 O O5' APR . . . D 3 14.391 7.636 28.301 0.6 53.86 ? O5' APR 403 A 1 HETATM 20 P PA APR . . . D 3 13.672 7.548 26.889 0.6 54.13 ? PA APR 403 A 1 HETATM 21 O O1A APR . . . D 3 13.365 6.069 26.831 0.6 52.6 ? O1A APR 403 A 1 HETATM 22 O O2A APR . . . D 3 14.444 8.293 25.798 0.6 55.96 ? O2A APR 403 A 1 HETATM 23 O O3A APR . . . D 3 12.269 8.3 27.011 0.6 62.43 ? O3A APR 403 A 1 HETATM 24 P PB APR . . . D 3 11.763 9.837 26.778 0.6 65.64 ? PB APR 403 A 1 HETATM 25 O O1B APR . . . D 3 11.419 10.196 25.342 0.6 54.61 ? O1B APR 403 A 1 HETATM 26 O O2B APR . . . D 3 12.524 10.846 27.573 0.6 51.03 ? O2B APR 403 A 1 HETATM 27 O O5D APR . . . D 3 10.411 9.47 27.579 0.6 73.23 ? O5D APR 403 A 1 HETATM 28 C C5D APR . . . D 3 10.106 8.171 28.126 0.6 76.05 ? C5D APR 403 A 1 HETATM 29 O O4D APR . . . D 3 8.56 7.936 29.934 0.6 82.56 ? O4D APR 403 A 1 HETATM 30 O O1D APR . . . D 3 7.949 9.234 31.859 0.6 84.78 ? O1D APR 403 A 1 HETATM 31 C C1D APR . . . D 3 7.712 8.965 30.463 0.6 81.66 ? C1D APR 403 A 1 HETATM 32 O O2D APR . . . D 3 7.046 11.253 29.601 0.6 66.02 ? O2D APR 403 A 1 HETATM 33 C C2D APR . . . D 3 7.981 10.157 29.536 0.6 76.44 ? C2D APR 403 A 1 HETATM 34 O O3D APR . . . D 3 6.628 9.188 27.747 0.6 88.66 ? O3D APR 403 A 1 HETATM 35 C C3D APR . . . D 3 7.954 9.455 28.198 0.6 76.36 ? C3D APR 403 A 1 HETATM 36 C C4D APR . . . D 3 8.65 8.135 28.515 0.6 79.72 ? C4D APR 403 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #