data_2IM3 # _model_server_result.job_id OtRHMpxdZvIBedW61_jkBA _model_server_result.datetime_utc '2025-01-23 15:17:28' _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 2im3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 2IM3 # _exptl.entry_id 2IM3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _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 2IM3 _cell.length_a 128.115 _cell.length_b 128.115 _cell.length_c 112.833 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2IM3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 MET 95 A MET 95 1_555 A N CAS 96 A CAS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C CAS 96 A CAS 96 1_555 A N LEU 97 A LEU 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C GLY 211 A GLY 211 1_555 A N CAS 212 A CAS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale4 A C CAS 212 A CAS 212 1_555 A N ASP 213 A ASP 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A C TYR 280 A TYR 280 1_555 A N CAS 281 A CAS 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 A C CAS 281 A CAS 281 1_555 A N VAL 282 A VAL 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 A C GLY 289 A GLY 289 1_555 A N CAS 290 A CAS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale8 A C CAS 290 A CAS 290 1_555 A N SER 291 A SER 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OG SER 271 A SER 271 1_555 D NA NA . A NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc2 A O GLY 284 A GLY 284 1_555 D NA NA . A NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc3 A O GLY 285 A GLY 285 1_555 D NA NA . A NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? metalc ? metalc4 A OD2 ASP 328 A ASP 328 1_555 C MN MN . A MN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc5 E O2B UTP . A UTP 1001 1_555 B MN MN . A MN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _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 PA O1A UTP doub 386 n n PA O2A UTP sing 387 n n PA O3A UTP sing 388 n n PA O5' UTP sing 389 n n O2A H2A UTP sing 390 n n O3A PB UTP sing 391 n n O5' C5' UTP sing 392 n n PB O1B UTP sing 393 n n PB O2B UTP doub 394 n n PB O3B UTP sing 395 n n O1B H1B UTP sing 396 n n O3B PG UTP sing 397 n n PG O1G UTP sing 398 n n PG O2G UTP doub 399 n n PG O3G UTP sing 400 n n O1G H1G UTP sing 401 n n O3G H3G UTP sing 402 n n C5' C4' UTP sing 403 n n C5' "H5'1" UTP sing 404 n n C5' "H5'2" UTP sing 405 n n C4' O4' UTP sing 406 n n C4' C3' UTP sing 407 n n C4' H4' UTP sing 408 n n O4' C1' UTP sing 409 n n C1' C2' UTP sing 410 n n C1' N1 UTP sing 411 n n C1' H1' UTP sing 412 n n C2' O2' UTP sing 413 n n C2' C3' UTP sing 414 n n C2' H2' UTP sing 415 n n O2' HA UTP sing 416 n n C3' O3' UTP sing 417 n n C3' H3' UTP sing 418 n n O3' HB UTP sing 419 n n N1 C6 UTP sing 420 n y N1 C2 UTP sing 421 n y C6 C5 UTP doub 422 n y C6 H6 UTP sing 423 n n C2 O2 UTP doub 424 n n C2 N3 UTP sing 425 n y N3 C4 UTP sing 426 n y N3 H3 UTP sing 427 n n C4 O4 UTP doub 428 n n C4 C5 UTP sing 429 n y C5 H5 UTP sing 430 n n # _atom_sites.entry_id 2IM3 _atom_sites.fract_transf_matrix[1][1] 0.007805 _atom_sites.fract_transf_matrix[1][2] 0.004507 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009013 _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] 0.008863 _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 MN A 1 2001 2001 MN MN . C 2 MN A 1 2002 2002 MN MN . D 3 NA A 1 3001 3001 NA NA . E 4 UTP A 1 1001 1001 UTP UTP . F 5 ACY A 1 901 901 ACY ACY . G 5 ACY A 1 902 902 ACY ACY . H 5 ACY A 1 903 903 ACY ACY . I 5 ACY A 1 904 904 ACY ACY . J 6 HOH A 1 501 501 HOH HOH . J 6 HOH A 2 502 502 HOH HOH . J 6 HOH A 3 503 503 HOH HOH . J 6 HOH A 4 504 504 HOH HOH . J 6 HOH A 5 505 505 HOH HOH . J 6 HOH A 6 506 506 HOH HOH . J 6 HOH A 7 507 507 HOH HOH . J 6 HOH A 8 508 508 HOH HOH . J 6 HOH A 9 509 509 HOH HOH . J 6 HOH A 10 510 510 HOH HOH . J 6 HOH A 11 511 511 HOH HOH . J 6 HOH A 12 512 512 HOH HOH . J 6 HOH A 13 513 513 HOH HOH . J 6 HOH A 14 514 514 HOH HOH . J 6 HOH A 15 515 515 HOH HOH . J 6 HOH A 16 516 516 HOH HOH . J 6 HOH A 17 517 517 HOH HOH . J 6 HOH A 18 518 518 HOH HOH . J 6 HOH A 19 519 519 HOH HOH . J 6 HOH A 20 520 520 HOH HOH . J 6 HOH A 21 521 521 HOH HOH . J 6 HOH A 22 522 522 HOH HOH . J 6 HOH A 23 523 523 HOH HOH . J 6 HOH A 24 524 524 HOH HOH . J 6 HOH A 25 525 525 HOH HOH . J 6 HOH A 26 526 526 HOH HOH . J 6 HOH A 27 527 527 HOH HOH . J 6 HOH A 28 528 528 HOH HOH . J 6 HOH A 29 529 529 HOH HOH . J 6 HOH A 30 530 530 HOH HOH . J 6 HOH A 31 531 531 HOH HOH . J 6 HOH A 32 532 532 HOH HOH . J 6 HOH A 33 533 533 HOH HOH . J 6 HOH A 34 534 534 HOH HOH . J 6 HOH A 35 535 535 HOH HOH . J 6 HOH A 36 536 536 HOH HOH . J 6 HOH A 37 537 537 HOH HOH . J 6 HOH A 38 538 538 HOH HOH . J 6 HOH A 39 539 539 HOH HOH . J 6 HOH A 40 540 540 HOH HOH . J 6 HOH A 41 541 541 HOH HOH . J 6 HOH A 42 542 542 HOH HOH . J 6 HOH A 43 543 543 HOH HOH . J 6 HOH A 44 544 544 HOH HOH . J 6 HOH A 45 545 545 HOH HOH . J 6 HOH A 46 546 546 HOH HOH . J 6 HOH A 47 547 547 HOH HOH . J 6 HOH A 48 548 548 HOH HOH . J 6 HOH A 49 549 549 HOH HOH . J 6 HOH A 50 550 550 HOH HOH . J 6 HOH A 51 551 551 HOH HOH . J 6 HOH A 52 552 552 HOH HOH . J 6 HOH A 53 553 553 HOH HOH . J 6 HOH A 54 554 554 HOH HOH . J 6 HOH A 55 555 555 HOH HOH . J 6 HOH A 56 556 556 HOH HOH . J 6 HOH A 57 557 557 HOH HOH . J 6 HOH A 58 558 558 HOH HOH . J 6 HOH A 59 559 559 HOH HOH . J 6 HOH A 60 560 560 HOH HOH . J 6 HOH A 61 561 561 HOH HOH . J 6 HOH A 62 562 562 HOH HOH . J 6 HOH A 63 563 563 HOH HOH . J 6 HOH A 64 564 564 HOH HOH . J 6 HOH A 65 565 565 HOH HOH . J 6 HOH A 66 566 566 HOH HOH . J 6 HOH A 67 567 567 HOH HOH . J 6 HOH A 68 568 568 HOH HOH . J 6 HOH A 69 569 569 HOH HOH . J 6 HOH A 70 570 570 HOH HOH . J 6 HOH A 71 571 571 HOH HOH . J 6 HOH A 72 572 572 HOH HOH . J 6 HOH A 73 573 573 HOH HOH . J 6 HOH A 74 574 574 HOH HOH . J 6 HOH A 75 575 575 HOH HOH . J 6 HOH A 76 576 576 HOH HOH . J 6 HOH A 77 577 577 HOH HOH . J 6 HOH A 78 578 578 HOH HOH . J 6 HOH A 79 579 579 HOH HOH . J 6 HOH A 80 580 580 HOH HOH . J 6 HOH A 81 581 581 HOH HOH . J 6 HOH A 82 582 582 HOH HOH . J 6 HOH A 83 583 583 HOH HOH . J 6 HOH A 84 584 584 HOH HOH . J 6 HOH A 85 585 585 HOH HOH . J 6 HOH A 86 586 586 HOH HOH . J 6 HOH A 87 587 587 HOH HOH . J 6 HOH A 88 588 588 HOH HOH . J 6 HOH A 89 589 589 HOH HOH . J 6 HOH A 90 590 590 HOH HOH . J 6 HOH A 91 591 591 HOH HOH . J 6 HOH A 92 592 592 HOH HOH . J 6 HOH A 93 593 593 HOH HOH . J 6 HOH A 94 594 594 HOH HOH . J 6 HOH A 95 595 595 HOH HOH . J 6 HOH A 96 596 596 HOH HOH . J 6 HOH A 97 597 597 HOH HOH . J 6 HOH A 98 598 598 HOH HOH . J 6 HOH A 99 599 599 HOH HOH . J 6 HOH A 100 600 600 HOH HOH . J 6 HOH A 101 601 601 HOH HOH . J 6 HOH A 102 602 602 HOH HOH . J 6 HOH A 103 603 603 HOH HOH . J 6 HOH A 104 604 604 HOH HOH . J 6 HOH A 105 605 605 HOH HOH . J 6 HOH A 106 606 606 HOH HOH . J 6 HOH A 107 607 607 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 PA UTP . . . E 4 221.648 -69.36 -2.894 1 115.76 ? PA UTP 1001 A 1 HETATM 2 O O1A UTP . . . E 4 222.606 -70.618 -3.189 1 115.8 ? O1A UTP 1001 A 1 HETATM 3 O O2A UTP . . . E 4 221.713 -68.932 -1.477 1 116.16 ? O2A UTP 1001 A 1 HETATM 4 O O3A UTP . . . E 4 220.169 -69.82 -3.329 1 115.35 ? O3A UTP 1001 A 1 HETATM 5 O O5' UTP . . . E 4 222.065 -68.208 -3.94 1 115.42 ? O5' UTP 1001 A 1 HETATM 6 P PB UTP . . . E 4 218.89 -69.403 -2.443 1 114.39 ? PB UTP 1001 A 1 HETATM 7 O O1B UTP . . . E 4 218.079 -68.325 -3.319 1 113.41 ? O1B UTP 1001 A 1 HETATM 8 O O2B UTP . . . E 4 219.252 -68.897 -1.101 1 114.58 ? O2B UTP 1001 A 1 HETATM 9 O O3B UTP . . . E 4 217.993 -70.744 -2.405 1 116.3 ? O3B UTP 1001 A 1 HETATM 10 P PG UTP . . . E 4 216.582 -70.789 -1.634 1 118.42 ? PG UTP 1001 A 1 HETATM 11 O O1G UTP . . . E 4 215.56 -69.894 -2.496 1 118.2 ? O1G UTP 1001 A 1 HETATM 12 O O2G UTP . . . E 4 216.054 -72.306 -1.764 1 117.96 ? O2G UTP 1001 A 1 HETATM 13 O O3G UTP . . . E 4 216.662 -70.346 -0.221 1 118.66 ? O3G UTP 1001 A 1 HETATM 14 C C5' UTP . . . E 4 221.167 -67.148 -4.273 1 113.72 ? C5' UTP 1001 A 1 HETATM 15 C C4' UTP . . . E 4 221.397 -65.956 -3.367 1 111.56 ? C4' UTP 1001 A 1 HETATM 16 O O4' UTP . . . E 4 222.751 -65.98 -2.873 1 110.44 ? O4' UTP 1001 A 1 HETATM 17 C C1' UTP . . . E 4 223.155 -64.667 -2.573 1 109.76 ? C1' UTP 1001 A 1 HETATM 18 C C2' UTP . . . E 4 222.15 -63.678 -3.181 1 109.6 ? C2' UTP 1001 A 1 HETATM 19 O O2' UTP . . . E 4 221.474 -63.001 -2.14 1 109.47 ? O2' UTP 1001 A 1 HETATM 20 C C3' UTP . . . E 4 221.244 -64.589 -4.022 1 110.12 ? C3' UTP 1001 A 1 HETATM 21 O O3' UTP . . . E 4 219.88 -64.174 -3.974 1 109.77 ? O3' UTP 1001 A 1 HETATM 22 N N1 UTP . . . E 4 224.593 -64.515 -2.866 1 109.22 ? N1 UTP 1001 A 1 HETATM 23 C C6 UTP . . . E 4 225.195 -65.09 -3.97 1 108.3 ? C6 UTP 1001 A 1 HETATM 24 C C2 UTP . . . E 4 225.344 -63.779 -1.956 1 109.06 ? C2 UTP 1001 A 1 HETATM 25 O O2 UTP . . . E 4 224.854 -63.225 -0.982 1 110.01 ? O2 UTP 1001 A 1 HETATM 26 N N3 UTP . . . E 4 226.689 -63.713 -2.224 1 108.09 ? N3 UTP 1001 A 1 HETATM 27 C C4 UTP . . . E 4 227.356 -64.284 -3.285 1 107.72 ? C4 UTP 1001 A 1 HETATM 28 O O4 UTP . . . E 4 228.585 -64.181 -3.351 1 107.14 ? O4 UTP 1001 A 1 HETATM 29 C C5 UTP . . . E 4 226.515 -65.003 -4.202 1 107.79 ? C5 UTP 1001 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #