data_4YVZ # _model_server_result.job_id 2FVYiGfr_N5S6IEdY49KEg _model_server_result.datetime_utc '2024-11-19 08:24:27' _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 4yvz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 4YVZ # _exptl.entry_id 4YVZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-DEOXYADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 4YVZ _cell.length_a 107.49 _cell.length_b 107.49 _cell.length_c 168.79 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YVZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details Octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -107.49 0 3 'crystal symmetry operation' 3_445 -y-1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 -53.745 -53.745 0 4 'crystal symmetry operation' 4_545 y+1/2,-x-1/2,z 0 1 0 -1 0 0 0 0 1 53.745 -53.745 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F 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 A OD2 ASP 95 A ASP 75 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc2 A O GLU 249 A GLU 229 1_555 D MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc3 A OD1 ASP 252 A ASP 232 1_555 D MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc4 C MN MN . A MN 401 1_555 E O3G 3AT . A 3AT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc5 C MN MN . A MN 401 1_555 E O2B 3AT . A 3AT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc6 C MN MN . A MN 401 1_555 E O1A 3AT . A 3AT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc7 C MN MN . A MN 401 1_555 I O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc8 C MN MN . A MN 401 1_555 J O HOH . B HOH 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc9 B OD2 ASP 95 B ASP 75 1_555 G MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc10 B O GLU 249 B GLU 229 1_555 H MN MN . B MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc11 B OD1 ASP 252 B ASP 232 1_555 H MN MN . B MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc12 B OD2 ASP 252 B ASP 232 1_555 H MN MN . B MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc13 B OD1 ASP 253 B ASP 233 1_555 H MN MN . B MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc14 F O1G 3AT . B 3AT 401 1_555 G MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc15 F O1B 3AT . B 3AT 401 1_555 G MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc16 F O2A 3AT . B 3AT 401 1_555 G MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc17 G MN MN . B MN 402 1_555 J O HOH . B HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc18 G MN MN . B MN 402 1_555 J O HOH . B HOH 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id 3AT _chem_comp.mon_nstd_flag . _chem_comp.name "3'-DEOXYADENOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'CORDYCEPIN TRIPHOSPHATE' # 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 3AT doub 1 n n PG O2G 3AT sing 2 n n PG O3G 3AT sing 3 n n PG O3B 3AT sing 4 n n O2G HOG2 3AT sing 5 n n O3G HOG3 3AT sing 6 n n PB O1B 3AT doub 7 n n PB O2B 3AT sing 8 n n PB O3B 3AT sing 9 n n PB O3A 3AT sing 10 n n O2B HOB2 3AT sing 11 n n PA O1A 3AT doub 12 n n PA O2A 3AT sing 13 n n PA O3A 3AT sing 14 n n PA O5' 3AT sing 15 n n O2A HOA2 3AT sing 16 n n O5' C5' 3AT sing 17 n n C5' C4' 3AT sing 18 n n C5' "H5'1" 3AT sing 19 n n C5' "H5'2" 3AT sing 20 n n C4' O4' 3AT sing 21 n n C4' C3' 3AT sing 22 n n C4' H4' 3AT sing 23 n n O4' C1' 3AT sing 24 n n C3' C2' 3AT sing 25 n n C3' "H3'1" 3AT sing 26 n n C3' "H3'2" 3AT sing 27 n n C2' O2' 3AT sing 28 n n C2' C1' 3AT sing 29 n n C2' "H2'1" 3AT sing 30 n n O2' HO2' 3AT sing 31 n n C1' N9 3AT sing 32 n n C1' H1' 3AT sing 33 n n N9 C8 3AT sing 34 n y N9 C4 3AT sing 35 n y C8 N7 3AT doub 36 n y C8 H8 3AT sing 37 n n N7 C5 3AT sing 38 n y C5 C6 3AT sing 39 n y C5 C4 3AT doub 40 n y C6 N6 3AT sing 41 n n C6 N1 3AT doub 42 n y N6 HN61 3AT sing 43 n n N6 HN62 3AT sing 44 n n N1 C2 3AT sing 45 n y C2 N3 3AT doub 46 n y C2 H2 3AT sing 47 n n N3 C4 3AT sing 48 n y # _atom_sites.entry_id 4YVZ _atom_sites.fract_transf_matrix[1][1] 0.009303 _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] 0.009303 _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] 0.005925 _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 2 MN A 1 401 1 MN MN . D 2 MN A 1 402 3 MN MN . E 3 3AT A 1 403 1 3AT 3AT . F 3 3AT B 1 401 2 3AT 3AT . G 2 MN B 1 402 2 MN MN . H 2 MN B 1 403 4 MN MN . I 4 HOH A 1 501 7 HOH HOH . I 4 HOH A 2 502 45 HOH HOH . I 4 HOH A 3 503 28 HOH HOH . I 4 HOH A 4 504 51 HOH HOH . I 4 HOH A 5 505 5 HOH HOH . I 4 HOH A 6 506 105 HOH HOH . I 4 HOH A 7 507 85 HOH HOH . I 4 HOH A 8 508 89 HOH HOH . I 4 HOH A 9 509 88 HOH HOH . I 4 HOH A 10 510 2 HOH HOH . I 4 HOH A 11 511 102 HOH HOH . I 4 HOH A 12 512 10 HOH HOH . I 4 HOH A 13 513 4 HOH HOH . I 4 HOH A 14 514 69 HOH HOH . I 4 HOH A 15 515 71 HOH HOH . I 4 HOH A 16 516 74 HOH HOH . I 4 HOH A 17 517 8 HOH HOH . I 4 HOH A 18 518 1 HOH HOH . I 4 HOH A 19 519 37 HOH HOH . I 4 HOH A 20 520 107 HOH HOH . I 4 HOH A 21 521 17 HOH HOH . I 4 HOH A 22 522 92 HOH HOH . I 4 HOH A 23 523 56 HOH HOH . I 4 HOH A 24 524 108 HOH HOH . I 4 HOH A 25 525 6 HOH HOH . I 4 HOH A 26 526 42 HOH HOH . I 4 HOH A 27 527 76 HOH HOH . I 4 HOH A 28 528 49 HOH HOH . I 4 HOH A 29 529 82 HOH HOH . I 4 HOH A 30 530 109 HOH HOH . I 4 HOH A 31 531 41 HOH HOH . I 4 HOH A 32 532 98 HOH HOH . I 4 HOH A 33 533 66 HOH HOH . I 4 HOH A 34 534 9 HOH HOH . I 4 HOH A 35 535 93 HOH HOH . I 4 HOH A 36 536 44 HOH HOH . I 4 HOH A 37 537 20 HOH HOH . I 4 HOH A 38 538 81 HOH HOH . I 4 HOH A 39 539 3 HOH HOH . I 4 HOH A 40 540 53 HOH HOH . I 4 HOH A 41 541 30 HOH HOH . I 4 HOH A 42 542 87 HOH HOH . I 4 HOH A 43 543 19 HOH HOH . I 4 HOH A 44 544 83 HOH HOH . I 4 HOH A 45 545 110 HOH HOH . I 4 HOH A 46 546 18 HOH HOH . I 4 HOH A 47 547 72 HOH HOH . I 4 HOH A 48 548 111 HOH HOH . I 4 HOH A 49 549 38 HOH HOH . J 4 HOH B 1 501 84 HOH HOH . J 4 HOH B 2 502 47 HOH HOH . J 4 HOH B 3 503 55 HOH HOH . J 4 HOH B 4 504 22 HOH HOH . J 4 HOH B 5 505 11 HOH HOH . J 4 HOH B 6 506 14 HOH HOH . J 4 HOH B 7 507 86 HOH HOH . J 4 HOH B 8 508 94 HOH HOH . J 4 HOH B 9 509 78 HOH HOH . J 4 HOH B 10 510 13 HOH HOH . J 4 HOH B 11 511 12 HOH HOH . J 4 HOH B 12 512 59 HOH HOH . J 4 HOH B 13 513 36 HOH HOH . J 4 HOH B 14 514 95 HOH HOH . J 4 HOH B 15 515 39 HOH HOH . J 4 HOH B 16 516 70 HOH HOH . J 4 HOH B 17 517 29 HOH HOH . J 4 HOH B 18 518 62 HOH HOH . J 4 HOH B 19 519 33 HOH HOH . J 4 HOH B 20 520 24 HOH HOH . J 4 HOH B 21 521 46 HOH HOH . J 4 HOH B 22 522 48 HOH HOH . J 4 HOH B 23 523 61 HOH HOH . J 4 HOH B 24 524 68 HOH HOH . J 4 HOH B 25 525 43 HOH HOH . J 4 HOH B 26 526 23 HOH HOH . J 4 HOH B 27 527 79 HOH HOH . J 4 HOH B 28 528 103 HOH HOH . J 4 HOH B 29 529 75 HOH HOH . J 4 HOH B 30 530 25 HOH HOH . J 4 HOH B 31 531 96 HOH HOH . J 4 HOH B 32 532 58 HOH HOH . J 4 HOH B 33 533 64 HOH HOH . J 4 HOH B 34 534 15 HOH HOH . J 4 HOH B 35 535 40 HOH HOH . J 4 HOH B 36 536 54 HOH HOH . J 4 HOH B 37 537 77 HOH HOH . J 4 HOH B 38 538 60 HOH HOH . J 4 HOH B 39 539 106 HOH HOH . J 4 HOH B 40 540 34 HOH HOH . J 4 HOH B 41 541 100 HOH HOH . J 4 HOH B 42 542 97 HOH HOH . J 4 HOH B 43 543 101 HOH HOH . J 4 HOH B 44 544 67 HOH HOH . J 4 HOH B 45 545 91 HOH HOH . J 4 HOH B 46 546 73 HOH HOH . J 4 HOH B 47 547 35 HOH HOH . J 4 HOH B 48 548 32 HOH HOH . J 4 HOH B 49 549 26 HOH HOH . J 4 HOH B 50 550 16 HOH HOH . J 4 HOH B 51 551 31 HOH HOH . J 4 HOH B 52 552 50 HOH HOH . J 4 HOH B 53 553 52 HOH HOH . J 4 HOH B 54 554 57 HOH HOH . J 4 HOH B 55 555 80 HOH HOH . J 4 HOH B 56 556 99 HOH HOH . J 4 HOH B 57 557 27 HOH HOH . J 4 HOH B 58 558 90 HOH HOH . J 4 HOH B 59 559 21 HOH HOH . J 4 HOH B 60 560 63 HOH HOH . J 4 HOH B 61 561 104 HOH HOH . J 4 HOH B 62 562 65 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 3AT . . . F 3 11.751 -41.732 50.606 1 32.63 ? PG 3AT 401 B 1 HETATM 2 O O1G 3AT . . . F 3 11.714 -42.692 49.459 1 50.85 ? O1G 3AT 401 B 1 HETATM 3 O O2G 3AT . . . F 3 12.39 -42.35 51.83 1 40.66 ? O2G 3AT 401 B 1 HETATM 4 O O3G 3AT . . . F 3 10.331 -41.316 50.886 1 32.43 ? O3G 3AT 401 B 1 HETATM 5 P PB 3AT . . . F 3 14.059 -40.361 49.79 1 33.31 ? PB 3AT 401 B 1 HETATM 6 O O1B 3AT . . . F 3 14.586 -41.718 49.537 1 33.58 ? O1B 3AT 401 B 1 HETATM 7 O O2B 3AT . . . F 3 14.915 -39.65 50.79 1 33.72 ? O2B 3AT 401 B 1 HETATM 8 O O3B 3AT . . . F 3 12.564 -40.425 50.25 1 32.94 ? O3B 3AT 401 B 1 HETATM 9 P PA 3AT . . . F 3 13.569 -39.998 47.023 1 33.1 ? PA 3AT 401 B 1 HETATM 10 O O1A 3AT . . . F 3 14.807 -39.979 46.191 1 33.42 ? O1A 3AT 401 B 1 HETATM 11 O O2A 3AT . . . F 3 12.991 -41.363 47.03 1 32.79 ? O2A 3AT 401 B 1 HETATM 12 O O3A 3AT . . . F 3 14.053 -39.55 48.448 1 33.36 ? O3A 3AT 401 B 1 HETATM 13 O O5' 3AT . . . F 3 12.496 -38.968 46.485 1 34.16 ? O5' 3AT 401 B 1 HETATM 14 C C5' 3AT . . . F 3 11.141 -39.103 46.833 1 32.7 ? C5' 3AT 401 B 1 HETATM 15 C C4' 3AT . . . F 3 10.329 -37.874 46.592 1 32.79 ? C4' 3AT 401 B 1 HETATM 16 O O4' 3AT . . . F 3 10.726 -36.873 47.349 1 33.12 ? O4' 3AT 401 B 1 HETATM 17 C C3' 3AT . . . F 3 10.384 -37.308 45.047 1 32.87 ? C3' 3AT 401 B 1 HETATM 18 C C2' 3AT . . . F 3 9.942 -36.095 45.15 1 33.11 ? C2' 3AT 401 B 1 HETATM 19 O O2' 3AT . . . F 3 8.462 -36.023 45.024 1 39.97 ? O2' 3AT 401 B 1 HETATM 20 C C1' 3AT . . . F 3 10.365 -35.588 46.598 1 33.37 ? C1' 3AT 401 B 1 HETATM 21 N N9 3AT . . . F 3 11.414 -34.809 46.516 1 34.27 ? N9 3AT 401 B 1 HETATM 22 C C8 3AT . . . F 3 12.728 -35.153 46.495 1 33.95 ? C8 3AT 401 B 1 HETATM 23 N N7 3AT . . . F 3 13.471 -34.046 46.407 1 34.49 ? N7 3AT 401 B 1 HETATM 24 C C5 3AT . . . F 3 12.615 -33.004 46.351 1 35 ? C5 3AT 401 B 1 HETATM 25 C C6 3AT . . . F 3 12.862 -31.644 46.236 1 37.45 ? C6 3AT 401 B 1 HETATM 26 N N6 3AT . . . F 3 14.031 -30.866 46.136 1 35.86 ? N6 3AT 401 B 1 HETATM 27 N N1 3AT . . . F 3 11.84 -30.768 46.202 1 35.38 ? N1 3AT 401 B 1 HETATM 28 C C2 3AT . . . F 3 10.558 -31.225 46.283 1 34.94 ? C2 3AT 401 B 1 HETATM 29 N N3 3AT . . . F 3 10.314 -32.566 46.387 1 34.36 ? N3 3AT 401 B 1 HETATM 30 C C4 3AT . . . F 3 11.346 -33.458 46.42 1 34.21 ? C4 3AT 401 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #