data_3N0Y # _model_server_result.job_id D0VSnbetxe6bqsxy4tGFzg _model_server_result.datetime_utc '2024-11-07 09:58:58' _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 3n0y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":181}' # _entry.id 3N0Y # _exptl.entry_id 3N0Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 99.19 _cell.angle_gamma 90 _cell.entry_id 3N0Y _cell.length_a 64.349 _cell.length_b 38.063 _cell.length_c 81.217 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N0Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 OE1 GLU 12 A GLU 12 1_555 D MN MN . A MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc2 A OE1 GLU 136 A GLU 136 1_555 D MN MN . A MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc3 A OE2 GLU 136 A GLU 136 1_555 D MN MN . A MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc4 C O1B APC . A APC 181 1_555 D MN MN . A MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc5 C O1A APC . A APC 181 1_555 D MN MN . A MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc6 B OE1 GLU 12 B GLU 12 1_555 F MN MN . B MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc7 B OE2 GLU 136 B GLU 136 1_555 F MN MN . B MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc8 B OE1 GLU 136 B GLU 136 1_555 F MN MN . B MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc9 E O1B APC . B APC 181 1_555 F MN MN . B MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc10 E O1G APC . B APC 181 1_555 F MN MN . B MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc11 E O1A APC . B APC 181 1_555 F MN MN . B MN 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-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 APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 3N0Y _atom_sites.fract_transf_matrix[1][1] 0.01554 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002513 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026272 _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] 0.012473 _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 APC A 1 181 181 APC APC . D 3 MN A 1 182 182 MN MN . E 2 APC B 1 181 181 APC APC . F 3 MN B 1 182 182 MN MN . G 4 HOH A 1 301 301 HOH HOH . G 4 HOH A 2 306 306 HOH HOH . G 4 HOH A 3 307 307 HOH HOH . G 4 HOH A 4 308 308 HOH HOH . G 4 HOH A 5 309 309 HOH HOH . G 4 HOH A 6 312 312 HOH HOH . G 4 HOH A 7 313 313 HOH HOH . G 4 HOH A 8 315 315 HOH HOH . G 4 HOH A 9 317 317 HOH HOH . G 4 HOH A 10 321 321 HOH HOH . G 4 HOH A 11 328 328 HOH HOH . G 4 HOH A 12 331 331 HOH HOH . G 4 HOH A 13 332 332 HOH HOH . G 4 HOH A 14 333 333 HOH HOH . G 4 HOH A 15 334 334 HOH HOH . G 4 HOH A 16 335 335 HOH HOH . G 4 HOH A 17 337 337 HOH HOH . G 4 HOH A 18 340 340 HOH HOH . G 4 HOH A 19 342 342 HOH HOH . G 4 HOH A 20 347 347 HOH HOH . G 4 HOH A 21 349 349 HOH HOH . G 4 HOH A 22 350 350 HOH HOH . G 4 HOH A 23 352 352 HOH HOH . G 4 HOH A 24 353 353 HOH HOH . G 4 HOH A 25 354 354 HOH HOH . G 4 HOH A 26 360 360 HOH HOH . G 4 HOH A 27 362 362 HOH HOH . G 4 HOH A 28 364 364 HOH HOH . G 4 HOH A 29 369 369 HOH HOH . G 4 HOH A 30 372 372 HOH HOH . G 4 HOH A 31 377 377 HOH HOH . G 4 HOH A 32 378 378 HOH HOH . G 4 HOH A 33 379 379 HOH HOH . G 4 HOH A 34 380 380 HOH HOH . G 4 HOH A 35 384 384 HOH HOH . G 4 HOH A 36 386 386 HOH HOH . G 4 HOH A 37 389 389 HOH HOH . G 4 HOH A 38 390 390 HOH HOH . G 4 HOH A 39 391 391 HOH HOH . G 4 HOH A 40 392 392 HOH HOH . G 4 HOH A 41 393 393 HOH HOH . G 4 HOH A 42 400 400 HOH HOH . G 4 HOH A 43 401 401 HOH HOH . G 4 HOH A 44 409 409 HOH HOH . G 4 HOH A 45 410 410 HOH HOH . G 4 HOH A 46 411 411 HOH HOH . G 4 HOH A 47 413 413 HOH HOH . G 4 HOH A 48 415 415 HOH HOH . G 4 HOH A 49 418 418 HOH HOH . G 4 HOH A 50 420 420 HOH HOH . G 4 HOH A 51 421 421 HOH HOH . G 4 HOH A 52 426 426 HOH HOH . G 4 HOH A 53 427 427 HOH HOH . G 4 HOH A 54 428 428 HOH HOH . G 4 HOH A 55 429 429 HOH HOH . G 4 HOH A 56 430 430 HOH HOH . G 4 HOH A 57 432 432 HOH HOH . G 4 HOH A 58 433 433 HOH HOH . G 4 HOH A 59 434 434 HOH HOH . G 4 HOH A 60 439 439 HOH HOH . G 4 HOH A 61 440 440 HOH HOH . G 4 HOH A 62 441 441 HOH HOH . G 4 HOH A 63 442 442 HOH HOH . G 4 HOH A 64 443 443 HOH HOH . G 4 HOH A 65 444 444 HOH HOH . G 4 HOH A 66 445 445 HOH HOH . G 4 HOH A 67 446 446 HOH HOH . G 4 HOH A 68 447 447 HOH HOH . G 4 HOH A 69 448 448 HOH HOH . G 4 HOH A 70 452 452 HOH HOH . G 4 HOH A 71 453 453 HOH HOH . G 4 HOH A 72 454 454 HOH HOH . H 4 HOH B 1 302 302 HOH HOH . H 4 HOH B 2 303 303 HOH HOH . H 4 HOH B 3 304 304 HOH HOH . H 4 HOH B 4 305 305 HOH HOH . H 4 HOH B 5 310 310 HOH HOH . H 4 HOH B 6 311 311 HOH HOH . H 4 HOH B 7 314 314 HOH HOH . H 4 HOH B 8 316 316 HOH HOH . H 4 HOH B 9 318 318 HOH HOH . H 4 HOH B 10 319 319 HOH HOH . H 4 HOH B 11 320 320 HOH HOH . H 4 HOH B 12 322 322 HOH HOH . H 4 HOH B 13 323 323 HOH HOH . H 4 HOH B 14 324 324 HOH HOH . H 4 HOH B 15 325 325 HOH HOH . H 4 HOH B 16 326 326 HOH HOH . H 4 HOH B 17 327 327 HOH HOH . H 4 HOH B 18 329 329 HOH HOH . H 4 HOH B 19 330 330 HOH HOH . H 4 HOH B 20 336 336 HOH HOH . H 4 HOH B 21 338 338 HOH HOH . H 4 HOH B 22 339 339 HOH HOH . H 4 HOH B 23 341 341 HOH HOH . H 4 HOH B 24 343 343 HOH HOH . H 4 HOH B 25 344 344 HOH HOH . H 4 HOH B 26 345 345 HOH HOH . H 4 HOH B 27 346 346 HOH HOH . H 4 HOH B 28 348 348 HOH HOH . H 4 HOH B 29 351 351 HOH HOH . H 4 HOH B 30 355 355 HOH HOH . H 4 HOH B 31 356 356 HOH HOH . H 4 HOH B 32 358 358 HOH HOH . H 4 HOH B 33 359 359 HOH HOH . H 4 HOH B 34 361 361 HOH HOH . H 4 HOH B 35 363 363 HOH HOH . H 4 HOH B 36 365 365 HOH HOH . H 4 HOH B 37 366 366 HOH HOH . H 4 HOH B 38 367 367 HOH HOH . H 4 HOH B 39 368 368 HOH HOH . H 4 HOH B 40 370 370 HOH HOH . H 4 HOH B 41 371 371 HOH HOH . H 4 HOH B 42 373 373 HOH HOH . H 4 HOH B 43 374 374 HOH HOH . H 4 HOH B 44 375 375 HOH HOH . H 4 HOH B 45 376 376 HOH HOH . H 4 HOH B 46 381 381 HOH HOH . H 4 HOH B 47 382 382 HOH HOH . H 4 HOH B 48 383 383 HOH HOH . H 4 HOH B 49 385 385 HOH HOH . H 4 HOH B 50 387 387 HOH HOH . H 4 HOH B 51 388 388 HOH HOH . H 4 HOH B 52 394 394 HOH HOH . H 4 HOH B 53 395 395 HOH HOH . H 4 HOH B 54 396 396 HOH HOH . H 4 HOH B 55 397 397 HOH HOH . H 4 HOH B 56 398 398 HOH HOH . H 4 HOH B 57 399 399 HOH HOH . H 4 HOH B 58 402 402 HOH HOH . H 4 HOH B 59 403 403 HOH HOH . H 4 HOH B 60 404 404 HOH HOH . H 4 HOH B 61 405 405 HOH HOH . H 4 HOH B 62 406 406 HOH HOH . H 4 HOH B 63 407 407 HOH HOH . H 4 HOH B 64 408 408 HOH HOH . H 4 HOH B 65 412 412 HOH HOH . H 4 HOH B 66 414 414 HOH HOH . H 4 HOH B 67 416 416 HOH HOH . H 4 HOH B 68 417 417 HOH HOH . H 4 HOH B 69 419 419 HOH HOH . H 4 HOH B 70 422 422 HOH HOH . H 4 HOH B 71 423 423 HOH HOH . H 4 HOH B 72 424 424 HOH HOH . H 4 HOH B 73 425 425 HOH HOH . H 4 HOH B 74 431 431 HOH HOH . H 4 HOH B 75 435 435 HOH HOH . H 4 HOH B 76 436 436 HOH HOH . H 4 HOH B 77 437 437 HOH HOH . H 4 HOH B 78 438 438 HOH HOH . H 4 HOH B 79 449 449 HOH HOH . H 4 HOH B 80 451 451 HOH HOH . H 4 HOH B 81 455 455 HOH HOH . H 4 HOH B 82 456 456 HOH HOH . H 4 HOH B 83 458 458 HOH HOH . H 4 HOH B 84 459 459 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 APC . . . E 2 17.379 -6.261 41.19 0.8 31.19 ? PG APC 181 B 1 HETATM 2 O O1G APC . . . E 2 17.123 -4.861 41.704 0.8 28.16 ? O1G APC 181 B 1 HETATM 3 O O2G APC . . . E 2 17.948 -6.207 39.775 0.8 31.41 ? O2G APC 181 B 1 HETATM 4 O O3G APC . . . E 2 18.135 -7.145 42.146 0.8 24.75 ? O3G APC 181 B 1 HETATM 5 P PB APC . . . E 2 14.488 -6.385 41.325 0.8 28.41 ? PB APC 181 B 1 HETATM 6 O O1B APC . . . E 2 14.569 -5.723 42.658 0.8 25.8 ? O1B APC 181 B 1 HETATM 7 O O2B APC . . . E 2 13.475 -7.464 41.154 0.8 31.98 ? O2B APC 181 B 1 HETATM 8 O O3B APC . . . E 2 15.935 -7.014 40.981 0.8 32.79 ? O3B APC 181 B 1 HETATM 9 P PA APC . . . E 2 13.346 -3.644 40.989 0.8 33.63 ? PA APC 181 B 1 HETATM 10 O O1A APC . . . E 2 14.351 -3.076 41.902 0.8 31.35 ? O1A APC 181 B 1 HETATM 11 O O2A APC . . . E 2 12.014 -4.076 41.557 0.8 32.65 ? O2A APC 181 B 1 HETATM 12 C C3A APC . . . E 2 14.042 -5.069 40.138 0.8 28.01 ? C3A APC 181 B 1 HETATM 13 O O5' APC . . . E 2 13.096 -2.428 39.957 0.8 37.09 ? O5' APC 181 B 1 HETATM 14 C C5' APC . . . E 2 11.809 -1.933 39.563 0.8 41.27 ? C5' APC 181 B 1 HETATM 15 C C4' APC . . . E 2 11.732 -0.421 39.767 0.8 43.95 ? C4' APC 181 B 1 HETATM 16 O O4' APC . . . E 2 10.584 0.133 39.096 0.8 43.9 ? O4' APC 181 B 1 HETATM 17 C C3' APC . . . E 2 11.475 -0.137 41.235 0.8 47.34 ? C3' APC 181 B 1 HETATM 18 O O3' APC . . . E 2 12.669 -0.044 42.015 0.8 51.09 ? O3' APC 181 B 1 HETATM 19 C C2' APC . . . E 2 10.71 1.161 41.218 0.8 47.86 ? C2' APC 181 B 1 HETATM 20 O O2' APC . . . E 2 11.598 2.277 41.271 0.8 54.31 ? O2' APC 181 B 1 HETATM 21 C C1' APC . . . E 2 9.976 1.176 39.886 0.8 45.2 ? C1' APC 181 B 1 HETATM 22 N N9 APC . . . E 2 8.557 0.914 40.254 0.8 42.79 ? N9 APC 181 B 1 HETATM 23 C C8 APC . . . E 2 8.178 -0.046 41.128 0.8 41.88 ? C8 APC 181 B 1 HETATM 24 N N7 APC . . . E 2 6.845 -0.082 41.322 0.8 43.22 ? N7 APC 181 B 1 HETATM 25 C C5 APC . . . E 2 6.334 0.897 40.55 0.8 42.5 ? C5 APC 181 B 1 HETATM 26 C C6 APC . . . E 2 4.963 1.393 40.303 0.8 44.05 ? C6 APC 181 B 1 HETATM 27 N N6 APC . . . E 2 3.914 0.786 40.929 0.8 42.66 ? N6 APC 181 B 1 HETATM 28 N N1 APC . . . E 2 4.817 2.44 39.448 0.8 43.63 ? N1 APC 181 B 1 HETATM 29 C C2 APC . . . E 2 5.892 2.991 38.824 0.8 43.52 ? C2 APC 181 B 1 HETATM 30 N N3 APC . . . E 2 7.17 2.597 39.021 0.8 42.57 ? N3 APC 181 B 1 HETATM 31 C C4 APC . . . E 2 7.459 1.569 39.858 0.8 43 ? C4 APC 181 B 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #