data_2IM1 # _model_server_result.job_id rUx2xzJmhKzMxDgVNIfnQA _model_server_result.datetime_utc '2024-12-04 08:36:43' _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 2im1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1001}' # _entry.id 2IM1 # _exptl.entry_id 2IM1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-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 2IM1 _cell.length_a 128.942 _cell.length_b 128.942 _cell.length_c 112.979 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2IM1 _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,K,L _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 F _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C GLY 211 A GLY 211 1_555 A N CAS 212 A CAS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale4 A C CAS 212 A CAS 212 1_555 A N ASP 213 A ASP 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C TYR 280 A TYR 280 1_555 A N CAS 281 A CAS 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale6 A C CAS 281 A CAS 281 1_555 A N VAL 282 A VAL 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 A C GLY 289 A GLY 289 1_555 A N CAS 290 A CAS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C CAS 290 A CAS 290 1_555 A N SER 291 A SER 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A NZ LYS 167 A LYS 167 1_555 D MN MN . A MN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc2 A O LEU 268 A LEU 268 1_555 E NA NA . A NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc3 A OG SER 271 A SER 271 1_555 E NA NA . A NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc4 A O GLY 284 A GLY 284 1_555 E NA NA . A NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc5 A O GLY 285 A GLY 285 1_555 E NA NA . A NA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc6 F O2B CTP . A CTP 1001 1_555 C MN MN . A MN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc7 F O1A CTP . A CTP 1001 1_555 D MN MN . A MN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc8 F O3B CTP . A CTP 1001 1_555 D MN MN . A MN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id CTP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-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 N1 C2 CTP sing 98 n n N1 C6 CTP sing 99 n n N1 C1' CTP sing 100 n n C2 N3 CTP sing 101 n n C2 O2 CTP doub 102 n n N3 C4 CTP doub 103 n n C4 C5 CTP sing 104 n n C4 N4 CTP sing 105 n n C5 C6 CTP doub 106 n n C5 H5 CTP sing 107 n n C6 H6 CTP sing 108 n n N4 HN41 CTP sing 109 n n N4 HN42 CTP sing 110 n n C1' C2' CTP sing 111 n n C1' O4' CTP sing 112 n n C1' H1' CTP sing 113 n n C2' O2' CTP sing 114 n n C2' C3' CTP sing 115 n n C2' H2' CTP sing 116 n n O2' HO2' CTP sing 117 n n C3' C4' CTP sing 118 n n C3' O3' CTP sing 119 n n C3' H3' CTP sing 120 n n C4' O4' CTP sing 121 n n C4' C5' CTP sing 122 n n C4' H4' CTP sing 123 n n O3' HO3' CTP sing 124 n n C5' O5' CTP sing 125 n n C5' "H5'1" CTP sing 126 n n C5' "H5'2" CTP sing 127 n n O5' PA CTP sing 128 n n PA O1A CTP doub 129 n n PA O2A CTP sing 130 n n PA O3A CTP sing 131 n n O2A HOA2 CTP sing 132 n n O3A PB CTP sing 133 n n PB O1B CTP doub 134 n n PB O2B CTP sing 135 n n PB O3B CTP sing 136 n n O2B HOB2 CTP sing 137 n n O3B PG CTP sing 138 n n PG O1G CTP doub 139 n n PG O2G CTP sing 140 n n PG O3G CTP sing 141 n n O2G HOG2 CTP sing 142 n n O3G HOG3 CTP sing 143 n n # _atom_sites.entry_id 2IM1 _atom_sites.fract_transf_matrix[1][1] 0.007755 _atom_sites.fract_transf_matrix[1][2] 0.004478 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008955 _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] 0.008851 _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 2 MN A 1 2003 2003 MN MN . E 3 NA A 1 3001 3001 NA NA . F 4 CTP A 1 1001 1001 CTP CTP . G 5 ACY A 1 901 901 ACY ACY . H 5 ACY A 1 902 902 ACY ACY . I 5 ACY A 1 903 903 ACY ACY . J 5 ACY A 1 904 904 ACY ACY . K 5 ACY A 1 905 905 ACY ACY . L 6 HOH A 1 501 501 HOH HOH . L 6 HOH A 2 502 502 HOH HOH . L 6 HOH A 3 503 503 HOH HOH . L 6 HOH A 4 504 504 HOH HOH . L 6 HOH A 5 505 505 HOH HOH . L 6 HOH A 6 506 506 HOH HOH . L 6 HOH A 7 507 507 HOH HOH . L 6 HOH A 8 508 508 HOH HOH . L 6 HOH A 9 509 509 HOH HOH . L 6 HOH A 10 510 510 HOH HOH . L 6 HOH A 11 511 511 HOH HOH . L 6 HOH A 12 512 512 HOH HOH . L 6 HOH A 13 513 513 HOH HOH . L 6 HOH A 14 514 514 HOH HOH . L 6 HOH A 15 515 515 HOH HOH . L 6 HOH A 16 516 516 HOH HOH . L 6 HOH A 17 517 517 HOH HOH . L 6 HOH A 18 518 518 HOH HOH . L 6 HOH A 19 519 519 HOH HOH . L 6 HOH A 20 520 520 HOH HOH . L 6 HOH A 21 521 521 HOH HOH . L 6 HOH A 22 522 522 HOH HOH . L 6 HOH A 23 523 523 HOH HOH . L 6 HOH A 24 524 524 HOH HOH . L 6 HOH A 25 525 525 HOH HOH . L 6 HOH A 26 526 526 HOH HOH . L 6 HOH A 27 527 527 HOH HOH . L 6 HOH A 28 528 528 HOH HOH . L 6 HOH A 29 529 529 HOH HOH . L 6 HOH A 30 530 530 HOH HOH . L 6 HOH A 31 531 531 HOH HOH . L 6 HOH A 32 532 532 HOH HOH . L 6 HOH A 33 533 533 HOH HOH . L 6 HOH A 34 534 534 HOH HOH . L 6 HOH A 35 535 535 HOH HOH . L 6 HOH A 36 536 536 HOH HOH . L 6 HOH A 37 537 537 HOH HOH . L 6 HOH A 38 538 538 HOH HOH . L 6 HOH A 39 539 539 HOH HOH . L 6 HOH A 40 540 540 HOH HOH . L 6 HOH A 41 541 541 HOH HOH . L 6 HOH A 42 542 542 HOH HOH . L 6 HOH A 43 543 543 HOH HOH . L 6 HOH A 44 544 544 HOH HOH . L 6 HOH A 45 545 545 HOH HOH . L 6 HOH A 46 546 546 HOH HOH . L 6 HOH A 47 547 547 HOH HOH . L 6 HOH A 48 548 548 HOH HOH . L 6 HOH A 49 549 549 HOH HOH . L 6 HOH A 50 550 550 HOH HOH . L 6 HOH A 51 551 551 HOH HOH . L 6 HOH A 52 552 552 HOH HOH . L 6 HOH A 53 553 553 HOH HOH . L 6 HOH A 54 554 554 HOH HOH . L 6 HOH A 55 555 555 HOH HOH . L 6 HOH A 56 556 556 HOH HOH . L 6 HOH A 57 557 557 HOH HOH . L 6 HOH A 58 558 558 HOH HOH . L 6 HOH A 59 559 559 HOH HOH . L 6 HOH A 60 560 560 HOH HOH . L 6 HOH A 61 561 561 HOH HOH . L 6 HOH A 62 562 562 HOH HOH . L 6 HOH A 63 563 563 HOH HOH . L 6 HOH A 64 564 564 HOH HOH . L 6 HOH A 65 565 565 HOH HOH . L 6 HOH A 66 566 566 HOH HOH . L 6 HOH A 67 567 567 HOH HOH . L 6 HOH A 68 568 568 HOH HOH . L 6 HOH A 69 569 569 HOH HOH . L 6 HOH A 70 570 570 HOH HOH . L 6 HOH A 71 571 571 HOH HOH . L 6 HOH A 72 572 572 HOH HOH . L 6 HOH A 73 573 573 HOH HOH . L 6 HOH A 74 574 574 HOH HOH . L 6 HOH A 75 575 575 HOH HOH . L 6 HOH A 76 576 576 HOH HOH . L 6 HOH A 77 577 577 HOH HOH . L 6 HOH A 78 578 578 HOH HOH . L 6 HOH A 79 579 579 HOH HOH . L 6 HOH A 80 580 580 HOH HOH . L 6 HOH A 81 581 581 HOH HOH . L 6 HOH A 82 582 582 HOH HOH . L 6 HOH A 83 583 583 HOH HOH . L 6 HOH A 84 584 584 HOH HOH . L 6 HOH A 85 585 585 HOH HOH . L 6 HOH A 86 586 586 HOH HOH . L 6 HOH A 87 587 587 HOH HOH . L 6 HOH A 88 588 588 HOH HOH . L 6 HOH A 89 589 589 HOH HOH . L 6 HOH A 90 590 590 HOH HOH . L 6 HOH A 91 591 591 HOH HOH . L 6 HOH A 92 592 592 HOH HOH . L 6 HOH A 93 593 593 HOH HOH . L 6 HOH A 94 594 594 HOH HOH . L 6 HOH A 95 595 595 HOH HOH . L 6 HOH A 96 596 596 HOH HOH . L 6 HOH A 97 597 597 HOH HOH . L 6 HOH A 98 598 598 HOH HOH . L 6 HOH A 99 599 599 HOH HOH . L 6 HOH A 100 600 600 HOH HOH . L 6 HOH A 101 601 601 HOH HOH . L 6 HOH A 102 602 602 HOH HOH . L 6 HOH A 103 603 603 HOH HOH . L 6 HOH A 104 604 604 HOH HOH . L 6 HOH A 105 605 605 HOH HOH . L 6 HOH A 106 606 606 HOH HOH . L 6 HOH A 107 607 607 HOH HOH . L 6 HOH A 108 608 608 HOH HOH . L 6 HOH A 109 609 609 HOH HOH . L 6 HOH A 110 610 610 HOH HOH . L 6 HOH A 111 611 611 HOH HOH . L 6 HOH A 112 612 612 HOH HOH . L 6 HOH A 113 613 613 HOH HOH . L 6 HOH A 114 614 614 HOH HOH . L 6 HOH A 115 615 615 HOH HOH . L 6 HOH A 116 616 616 HOH HOH . L 6 HOH A 117 617 617 HOH HOH . L 6 HOH A 118 618 618 HOH HOH . L 6 HOH A 119 619 619 HOH HOH . L 6 HOH A 120 620 620 HOH HOH . L 6 HOH A 121 621 621 HOH HOH . L 6 HOH A 122 622 622 HOH HOH . L 6 HOH A 123 623 623 HOH HOH . L 6 HOH A 124 624 624 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 N N1 CTP . . . F 4 226.1 -65.029 -2.829 1 85.06 ? N1 CTP 1001 A 1 HETATM 2 C C2 CTP . . . F 4 227.044 -64.425 -1.974 1 85.1 ? C2 CTP 1001 A 1 HETATM 3 N N3 CTP . . . F 4 228.345 -64.379 -2.353 1 84.86 ? N3 CTP 1001 A 1 HETATM 4 C C4 CTP . . . F 4 228.728 -64.902 -3.512 1 84.69 ? C4 CTP 1001 A 1 HETATM 5 C C5 CTP . . . F 4 227.809 -65.532 -4.386 1 85.28 ? C5 CTP 1001 A 1 HETATM 6 C C6 CTP . . . F 4 226.512 -65.565 -4.021 1 85.19 ? C6 CTP 1001 A 1 HETATM 7 O O2 CTP . . . F 4 226.673 -63.949 -0.878 1 85.26 ? O2 CTP 1001 A 1 HETATM 8 N N4 CTP . . . F 4 230.029 -64.808 -3.846 1 84.22 ? N4 CTP 1001 A 1 HETATM 9 C C1' CTP . . . F 4 224.678 -65.076 -2.398 1 84.04 ? C1' CTP 1001 A 1 HETATM 10 C C2' CTP . . . F 4 223.676 -64.244 -3.212 1 82.96 ? C2' CTP 1001 A 1 HETATM 11 O O2' CTP . . . F 4 222.816 -63.529 -2.341 1 81.95 ? O2' CTP 1001 A 1 HETATM 12 C C3' CTP . . . F 4 222.97 -65.321 -4.029 1 83.1 ? C3' CTP 1001 A 1 HETATM 13 C C4' CTP . . . F 4 222.954 -66.498 -3.053 1 85 ? C4' CTP 1001 A 1 HETATM 14 O O4' CTP . . . F 4 224.251 -66.416 -2.41 1 84.55 ? O4' CTP 1001 A 1 HETATM 15 O O3' CTP . . . F 4 221.668 -64.897 -4.379 1 80.33 ? O3' CTP 1001 A 1 HETATM 16 C C5' CTP . . . F 4 222.794 -67.879 -3.647 1 87.1 ? C5' CTP 1001 A 1 HETATM 17 O O5' CTP . . . F 4 223.256 -68.871 -2.735 1 89.16 ? O5' CTP 1001 A 1 HETATM 18 P PA CTP . . . F 4 222.47 -70.257 -2.509 1 89.94 ? PA CTP 1001 A 1 HETATM 19 O O1A CTP . . . F 4 222.099 -69.826 -1.003 1 91.89 ? O1A CTP 1001 A 1 HETATM 20 O O2A CTP . . . F 4 223.573 -71.19 -2.827 1 91 ? O2A CTP 1001 A 1 HETATM 21 O O3A CTP . . . F 4 221.278 -69.988 -3.559 1 90.37 ? O3A CTP 1001 A 1 HETATM 22 P PB CTP . . . F 4 219.812 -69.678 -2.977 1 88.62 ? PB CTP 1001 A 1 HETATM 23 O O1B CTP . . . F 4 218.816 -69.709 -4.244 1 90.52 ? O1B CTP 1001 A 1 HETATM 24 O O2B CTP . . . F 4 219.79 -68.401 -2.235 1 88.37 ? O2B CTP 1001 A 1 HETATM 25 O O3B CTP . . . F 4 219.459 -70.962 -2.069 1 91.49 ? O3B CTP 1001 A 1 HETATM 26 P PG CTP . . . F 4 217.935 -71.43 -1.839 1 93.35 ? PG CTP 1001 A 1 HETATM 27 O O1G CTP . . . F 4 217.407 -72.098 -3.206 1 93.11 ? O1G CTP 1001 A 1 HETATM 28 O O2G CTP . . . F 4 218.032 -72.631 -0.775 1 94.36 ? O2G CTP 1001 A 1 HETATM 29 O O3G CTP . . . F 4 217.016 -70.37 -1.362 1 93.08 ? O3G CTP 1001 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #