data_7U1D # _model_server_result.job_id euejR2BP4WyDiMZyPW9bwg _model_server_result.datetime_utc '2024-11-24 06:09:32' _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 7u1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":706}' # _entry.id 7U1D # _exptl.entry_id 7U1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 412.296 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3Z)-4-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}-3-MERCAPTOPENT-3-EN-1-YL TRIHYDROGEN DIPHOSPHATE' _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 7U1D _cell.length_a 178.479 _cell.length_b 178.479 _cell.length_c 184.169 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7U1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _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,F,G,H,I,J,K _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' 12_544 x,x-y-1,-z-1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 89.2395 -154.567348 -61.389667 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _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 covale ? covale1 A C PRO 254 A PRO 339 1_555 A N CSD 255 A CSD 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C CSD 255 A CSD 340 1_555 A N ASP 256 A ASP 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A O ILE 316 A ILE 401 1_555 I MG MG . A MG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc2 A O ILE 316 A ILE 401 1_555 I MG MG . A MG 708 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc3 A OD1 ASP 453 A ASP 538 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc4 A O MET 458 A MET 543 1_555 H MG MG . A MG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc5 A O MET 458 A MET 543 1_555 H MG MG . A MG 707 12_544 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc6 A OE1 GLN 461 A GLN 546 1_555 H MG MG . A MG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc7 A OE1 GLN 461 A GLN 546 1_555 H MG MG . A MG 707 12_544 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc8 A OD1 ASN 480 A ASN 565 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc9 A O HIS 482 A HIS 567 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc10 B MG MG . A MG 701 1_555 G O1A TP9 . A TP9 706 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.009 ? metalc ? metalc11 B MG MG . A MG 701 1_555 G O3B TP9 . A TP9 706 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.218 ? # _chem_comp.formula 'C11 H18 N4 O7 P2 S -2' _chem_comp.formula_weight 412.296 _chem_comp.id TP9 _chem_comp.mon_nstd_flag . _chem_comp.name '(3Z)-4-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}-3-MERCAPTOPENT-3-EN-1-YL TRIHYDROGEN DIPHOSPHATE' _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' C6' TP9 sing 495 n y N1' C2' TP9 doub 496 n y C2' N3' TP9 sing 497 n y C2' CM2 TP9 sing 498 n n CM2 HM21 TP9 sing 499 n n CM2 HM22 TP9 sing 500 n n CM2 HM23 TP9 sing 501 n n N3' C4' TP9 doub 502 n y C4' C5' TP9 sing 503 n y C4' N4' TP9 sing 504 n n N4' "H4'1" TP9 sing 505 n n N4' "H4'2" TP9 sing 506 n n C5' C7' TP9 sing 507 n n C5' C6' TP9 doub 508 n y C6' H6' TP9 sing 509 n n C7' N3 TP9 sing 510 n n C7' "H7'1" TP9 sing 511 n n C7' "H7'2" TP9 sing 512 n n N3 C4 TP9 sing 513 n n N3 HN3 TP9 sing 514 n n S1 C5 TP9 sing 515 n n S1 HS1 TP9 sing 516 n n C5 C6 TP9 sing 517 n n C5 C4 TP9 doub 518 z n C4 CM4 TP9 sing 519 n n CM4 HM41 TP9 sing 520 n n CM4 HM42 TP9 sing 521 n n CM4 HM43 TP9 sing 522 n n C6 C7 TP9 sing 523 n n C6 H61 TP9 sing 524 n n C6 H62 TP9 sing 525 n n C7 O7 TP9 sing 526 n n C7 H71 TP9 sing 527 n n C7 H72 TP9 sing 528 n n O7 PA TP9 sing 529 n n PA O3A TP9 sing 530 n n PA O1A TP9 sing 531 n n PA O2A TP9 doub 532 n n O3A PB TP9 sing 533 n n PB O1B TP9 sing 534 n n PB O2B TP9 sing 535 n n PB O3B TP9 doub 536 n n O1B H1B TP9 sing 537 n n # _atom_sites.entry_id 7U1D _atom_sites.fract_transf_matrix[1][1] 0.005603 _atom_sites.fract_transf_matrix[1][2] 0.003235 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00647 _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] 0.00543 _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 MG A 1 701 701 MG MG . C 3 FAD A 1 702 702 FAD FAD . D 4 CIE A 1 703 801 CIE CIE . E 5 NHE A 1 704 901 NHE NHE . F 6 F50 A 1 705 1001 F50 PER . G 7 TP9 A 1 706 1101 TP9 TP9 . H 2 MG A 1 707 1 MG MG . I 2 MG A 1 708 2 MG MG . J 8 SO4 A 1 709 1 SO4 SO4 . K 8 SO4 A 1 710 2 SO4 SO4 . # 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' TP9 . A . G 7 71.01 -71.05 -23.983 0.89 65.95 ? N1' TP9 706 A 1 HETATM 2 C C2' TP9 . A . G 7 70.294 -70.189 -23.289 0.89 70.19 ? C2' TP9 706 A 1 HETATM 3 C CM2 TP9 . A . G 7 69.693 -68.979 -24 0.89 72.99 ? CM2 TP9 706 A 1 HETATM 4 N N3' TP9 . A . G 7 70.085 -70.348 -21.996 0.89 68.3 ? N3' TP9 706 A 1 HETATM 5 C C4' TP9 . A . G 7 70.588 -71.383 -21.344 0.89 71.99 ? C4' TP9 706 A 1 HETATM 6 N N4' TP9 . A . G 7 70.347 -71.541 -19.921 0.89 70.06 ? N4' TP9 706 A 1 HETATM 7 C C5' TP9 . A . G 7 71.35 -72.308 -22.05 0.89 76.72 ? C5' TP9 706 A 1 HETATM 8 C C6' TP9 . A . G 7 71.549 -72.112 -23.41 0.89 74.13 ? C6' TP9 706 A 1 HETATM 9 C C7' TP9 . A . G 7 71.957 -73.528 -21.356 0.89 77.34 ? C7' TP9 706 A 1 HETATM 10 N N3 TP9 . A . G 7 72.793 -73.136 -20.236 0.89 81.18 ? N3 TP9 706 A 1 HETATM 11 S S1 TP9 . A . G 7 73.941 -71.877 -17.865 0.89 100.41 ? S1 TP9 706 A 1 HETATM 12 C C5 TP9 . A . G 7 74.787 -72.086 -19.458 0.89 75.54 ? C5 TP9 706 A 1 HETATM 13 C C4 TP9 . A . G 7 74.15 -72.672 -20.45 0.89 86.06 ? C4 TP9 706 A 1 HETATM 14 C CM4 TP9 . A . G 7 74.832 -72.865 -21.805 0.89 74.8 ? CM4 TP9 706 A 1 HETATM 15 C C6 TP9 . A . G 7 76.217 -71.578 -19.636 0.89 79.96 ? C6 TP9 706 A 1 HETATM 16 C C7 TP9 . A . G 7 76.449 -70.238 -18.936 0.89 69.78 ? C7 TP9 706 A 1 HETATM 17 O O7 TP9 . A . G 7 77.615 -69.646 -19.439 0.89 75.38 ? O7 TP9 706 A 1 HETATM 18 P PA TP9 . A . G 7 77.966 -68.102 -18.97 0.89 77.31 ? PA TP9 706 A 1 HETATM 19 O O1A TP9 . A . G 7 79.343 -67.718 -19.454 0.89 79.9 -1 O1A TP9 706 A 1 HETATM 20 O O2A TP9 . A . G 7 76.946 -67.148 -19.543 0.89 72.02 ? O2A TP9 706 A 1 HETATM 21 O O3A TP9 . A . G 7 77.932 -68.023 -17.325 0.89 75.78 ? O3A TP9 706 A 1 HETATM 22 P PB TP9 . A . G 7 78.895 -68.964 -16.378 0.89 76.13 ? PB TP9 706 A 1 HETATM 23 O O1B TP9 . A . G 7 79.187 -68.246 -15.08 0.89 78.37 -1 O1B TP9 706 A 1 HETATM 24 O O2B TP9 . A . G 7 78.192 -70.27 -16.099 0.89 66.36 -1 O2B TP9 706 A 1 HETATM 25 O O3B TP9 . A . G 7 80.187 -69.235 -17.11 0.89 84.81 ? O3B TP9 706 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #