data_4D9P # _model_server_result.job_id VLmGpuj1z6EQX6x3Pi15fg _model_server_result.datetime_utc '2024-11-23 19:38:43' _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 4d9p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":306}' # _entry.id 4D9P # _exptl.entry_id 4D9P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 279.252 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3R)-3-(7-amino-1-methyl-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)butanoic acid' _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 120 _cell.entry_id 4D9P _cell.length_a 99.667 _cell.length_b 99.667 _cell.length_c 261.081 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D9P _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,O 1 1,2 B,I,J,K,L,M,N,P 2 1,3 A,C,D,E,F,G,H,O 3 1,2 B,I,J,K,L,M,N,P 3 4,5 # 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' 4_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 -49.8335 86.314154 0 3 'crystal symmetry operation' 4_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -99.667 0 0 4 'crystal symmetry operation' 2_564 -y,x-y+1,z-1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -49.8335 86.314154 -87.027 5 'crystal symmetry operation' 5_554 y,-x+y,z-1/3 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 -87.027 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 N N N # _chem_comp.formula 'C11 H13 N5 O4' _chem_comp.formula_weight 279.252 _chem_comp.id Z17 _chem_comp.mon_nstd_flag . _chem_comp.name '(3R)-3-(7-amino-1-methyl-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)butanoic acid' _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 O2 C2 Z17 doub 380 n n C2 O4 Z17 sing 381 n n C2 C1 Z17 sing 382 n n C1 C11 Z17 sing 383 n n C11 C6 Z17 sing 384 n n C11 C5 Z17 sing 385 n n N3 C5 Z17 doub 386 n n N3 N5 Z17 sing 387 n n C5 C3 Z17 sing 388 n n C4 N5 Z17 sing 389 n n N5 C8 Z17 sing 390 n n C3 O1 Z17 doub 391 n n C3 C9 Z17 sing 392 n n C8 C9 Z17 doub 393 n n C8 N4 Z17 sing 394 n n C9 C10 Z17 sing 395 n n N4 C7 Z17 doub 396 n n C10 O3 Z17 doub 397 n n C10 N2 Z17 sing 398 n n C7 N2 Z17 sing 399 n n C7 N1 Z17 sing 400 n n C1 H1 Z17 sing 401 n n C1 H2 Z17 sing 402 n n N1 H3 Z17 sing 403 n n N1 H4 Z17 sing 404 n n N2 H5 Z17 sing 405 n n C4 H6 Z17 sing 406 n n C4 H7 Z17 sing 407 n n C4 H8 Z17 sing 408 n n C6 H9 Z17 sing 409 n n C6 H10 Z17 sing 410 n n C6 H11 Z17 sing 411 n n O4 H13 Z17 sing 412 n n C11 H14 Z17 sing 413 n n # _atom_sites.entry_id 4D9P _atom_sites.fract_transf_matrix[1][1] 0.010033 _atom_sites.fract_transf_matrix[1][2] 0.005793 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011586 _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] 0.00383 _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 SO4 A 1 301 2 SO4 SO4 . D 2 SO4 A 1 302 5 SO4 SO4 . E 2 SO4 A 1 303 8 SO4 SO4 . F 2 SO4 A 1 304 9 SO4 SO4 . G 2 SO4 A 1 305 10 SO4 SO4 . H 3 Z17 A 1 306 1 Z17 Z17 . I 2 SO4 B 1 301 1 SO4 SO4 . J 2 SO4 B 1 302 3 SO4 SO4 . K 2 SO4 B 1 303 4 SO4 SO4 . L 2 SO4 B 1 304 6 SO4 SO4 . M 2 SO4 B 1 305 7 SO4 SO4 . N 3 Z17 B 1 306 1 Z17 Z17 . O 4 HOH A 1 401 2 HOH HOH . O 4 HOH A 2 402 4 HOH HOH . O 4 HOH A 3 403 5 HOH HOH . O 4 HOH A 4 404 7 HOH HOH . O 4 HOH A 5 405 9 HOH HOH . O 4 HOH A 6 406 10 HOH HOH . O 4 HOH A 7 407 11 HOH HOH . O 4 HOH A 8 408 13 HOH HOH . O 4 HOH A 9 409 14 HOH HOH . O 4 HOH A 10 410 16 HOH HOH . O 4 HOH A 11 411 18 HOH HOH . O 4 HOH A 12 412 21 HOH HOH . O 4 HOH A 13 413 23 HOH HOH . O 4 HOH A 14 414 24 HOH HOH . O 4 HOH A 15 415 25 HOH HOH . O 4 HOH A 16 416 26 HOH HOH . O 4 HOH A 17 417 28 HOH HOH . O 4 HOH A 18 418 32 HOH HOH . O 4 HOH A 19 419 33 HOH HOH . O 4 HOH A 20 420 37 HOH HOH . O 4 HOH A 21 421 38 HOH HOH . O 4 HOH A 22 422 4 HOH HOH . O 4 HOH A 23 423 5 HOH HOH . O 4 HOH A 24 424 6 HOH HOH . O 4 HOH A 25 425 9 HOH HOH . O 4 HOH A 26 426 12 HOH HOH . O 4 HOH A 27 427 13 HOH HOH . P 4 HOH B 1 401 1 HOH HOH . P 4 HOH B 2 402 3 HOH HOH . P 4 HOH B 3 403 6 HOH HOH . P 4 HOH B 4 404 8 HOH HOH . P 4 HOH B 5 405 12 HOH HOH . P 4 HOH B 6 406 17 HOH HOH . P 4 HOH B 7 407 19 HOH HOH . P 4 HOH B 8 408 20 HOH HOH . P 4 HOH B 9 409 27 HOH HOH . P 4 HOH B 10 410 29 HOH HOH . P 4 HOH B 11 411 30 HOH HOH . P 4 HOH B 12 412 31 HOH HOH . P 4 HOH B 13 413 34 HOH HOH . P 4 HOH B 14 414 35 HOH HOH . P 4 HOH B 15 415 36 HOH HOH . P 4 HOH B 16 416 39 HOH HOH . P 4 HOH B 17 417 1 HOH HOH . P 4 HOH B 18 418 2 HOH HOH . P 4 HOH B 19 419 3 HOH HOH . P 4 HOH B 20 420 7 HOH HOH . P 4 HOH B 21 421 8 HOH HOH . P 4 HOH B 22 422 10 HOH HOH . P 4 HOH B 23 423 1 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 C C1 Z17 . . . H 3 -11.864 26.725 9.538 1 53.71 ? C1 Z17 306 A 1 HETATM 2 C C2 Z17 . . . H 3 -13.248 26.613 10.1 1 54.11 ? C2 Z17 306 A 1 HETATM 3 C C3 Z17 . . . H 3 -13.286 27.29 5.988 1 48.01 ? C3 Z17 306 A 1 HETATM 4 N N1 Z17 . . . H 3 -16.69 24.397 2.371 1 48.8 ? N1 Z17 306 A 1 HETATM 5 N N2 Z17 . . . H 3 -15.588 26.557 3.014 1 47.32 ? N2 Z17 306 A 1 HETATM 6 C C4 Z17 . . . H 3 -14.145 23.288 6.582 1 48.12 ? C4 Z17 306 A 1 HETATM 7 C C5 Z17 . . . H 3 -12.726 26.546 7.14 1 49.79 ? C5 Z17 306 A 1 HETATM 8 C C6 Z17 . . . H 3 -10.388 27.079 7.691 1 53.09 ? C6 Z17 306 A 1 HETATM 9 O O1 Z17 . . . H 3 -12.996 28.613 5.832 1 46.31 ? O1 Z17 306 A 1 HETATM 10 N N3 Z17 . . . H 3 -13.038 25.287 7.256 1 50.48 ? N3 Z17 306 A 1 HETATM 11 O O2 Z17 . . . H 3 -13.624 25.477 10.514 1 53.12 ? O2 Z17 306 A 1 HETATM 12 C C7 Z17 . . . H 3 -15.856 25.152 3.249 1 47.21 ? C7 Z17 306 A 1 HETATM 13 O O3 Z17 . . . H 3 -14.519 28.593 3.609 1 48.77 ? O3 Z17 306 A 1 HETATM 14 N N4 Z17 . . . H 3 -15.28 24.562 4.36 1 46.57 ? N4 Z17 306 A 1 HETATM 15 O O4 Z17 . . . H 3 -14.019 27.622 10.127 1 52.73 ? O4 Z17 306 A 1 HETATM 16 C C8 Z17 . . . H 3 -14.465 25.28 5.204 1 48.65 ? C8 Z17 306 A 1 HETATM 17 C C9 Z17 . . . H 3 -14.175 26.614 5.004 1 48.19 ? C9 Z17 306 A 1 HETATM 18 N N5 Z17 . . . H 3 -13.857 24.673 6.36 1 49.13 ? N5 Z17 306 A 1 HETATM 19 C C10 Z17 . . . H 3 -14.759 27.272 3.867 1 46.98 ? C10 Z17 306 A 1 HETATM 20 C C11 Z17 . . . H 3 -11.814 27.24 8.127 1 52.51 ? C11 Z17 306 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #