data_5AXU # _model_server_result.job_id AjWMKm77LfsUjoFQLfayNA _model_server_result.datetime_utc '2025-07-07 22:04:36' _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 5axu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5AXU # _exptl.entry_id 5AXU _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 90 _cell.entry_id 5AXU _cell.length_a 103.229 _cell.length_b 103.229 _cell.length_c 103.229 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AXU _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 1,2,3,4,5,6,7,8,9,10,11,12 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 6 'crystal symmetry operation' 6_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 7 'crystal symmetry operation' 7_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 8 'crystal symmetry operation' 8_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 9 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 10 'crystal symmetry operation' 10_555 -y,z,-x 0 -1 0 0 0 1 -1 0 0 0 0 0 11 'crystal symmetry operation' 11_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 12 'crystal symmetry operation' 12_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 ACE 1 A ACE 1 1_555 A N ALA 2 A ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? metalc ? metalc1 B MG MG . A MG 301 1_555 C O2B ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc2 B MG MG . A MG 301 1_555 C O3G ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc3 B MG MG . A MG 301 1_555 C O2A ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? # _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 125 n n N1 C6 CTP sing 126 n n N1 C1' CTP sing 127 n n C2 N3 CTP sing 128 n n C2 O2 CTP doub 129 n n N3 C4 CTP doub 130 n n C4 C5 CTP sing 131 n n C4 N4 CTP sing 132 n n C5 C6 CTP doub 133 n n C5 H5 CTP sing 134 n n C6 H6 CTP sing 135 n n N4 HN41 CTP sing 136 n n N4 HN42 CTP sing 137 n n C1' C2' CTP sing 138 n n C1' O4' CTP sing 139 n n C1' H1' CTP sing 140 n n C2' O2' CTP sing 141 n n C2' C3' CTP sing 142 n n C2' H2' CTP sing 143 n n O2' HO2' CTP sing 144 n n C3' C4' CTP sing 145 n n C3' O3' CTP sing 146 n n C3' H3' CTP sing 147 n n C4' O4' CTP sing 148 n n C4' C5' CTP sing 149 n n C4' H4' CTP sing 150 n n O3' HO3' CTP sing 151 n n C5' O5' CTP sing 152 n n C5' "H5'1" CTP sing 153 n n C5' "H5'2" CTP sing 154 n n O5' PA CTP sing 155 n n PA O1A CTP doub 156 n n PA O2A CTP sing 157 n n PA O3A CTP sing 158 n n O2A HOA2 CTP sing 159 n n O3A PB CTP sing 160 n n PB O1B CTP doub 161 n n PB O2B CTP sing 162 n n PB O3B CTP sing 163 n n O2B HOB2 CTP sing 164 n n O3B PG CTP sing 165 n n PG O1G CTP doub 166 n n PG O2G CTP sing 167 n n PG O3G CTP sing 168 n n O2G HOG2 CTP sing 169 n n O3G HOG3 CTP sing 170 n n # _atom_sites.entry_id 5AXU _atom_sites.fract_transf_matrix[1][1] 0.009687 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009687 _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] 0.009687 _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 1 301 301 MG MG . C 3 ATP A 1 302 302 ATP ATP . D 4 CTP A 1 303 303 CTP CTP . E 5 EDO A 1 304 304 EDO EDO . F 5 EDO A 1 305 305 EDO EDO . G 5 EDO A 1 306 306 EDO EDO . H 6 HOH A 1 401 538 HOH HOH . H 6 HOH A 2 402 456 HOH HOH . H 6 HOH A 3 403 505 HOH HOH . H 6 HOH A 4 404 435 HOH HOH . H 6 HOH A 5 405 426 HOH HOH . H 6 HOH A 6 406 537 HOH HOH . H 6 HOH A 7 407 432 HOH HOH . H 6 HOH A 8 408 475 HOH HOH . H 6 HOH A 9 409 422 HOH HOH . H 6 HOH A 10 410 459 HOH HOH . H 6 HOH A 11 411 509 HOH HOH . H 6 HOH A 12 412 421 HOH HOH . H 6 HOH A 13 413 428 HOH HOH . H 6 HOH A 14 414 427 HOH HOH . H 6 HOH A 15 415 455 HOH HOH . H 6 HOH A 16 416 407 HOH HOH . H 6 HOH A 17 417 404 HOH HOH . H 6 HOH A 18 418 478 HOH HOH . H 6 HOH A 19 419 462 HOH HOH . H 6 HOH A 20 420 474 HOH HOH . H 6 HOH A 21 421 484 HOH HOH . H 6 HOH A 22 422 414 HOH HOH . H 6 HOH A 23 423 472 HOH HOH . H 6 HOH A 24 424 406 HOH HOH . H 6 HOH A 25 425 450 HOH HOH . H 6 HOH A 26 426 408 HOH HOH . H 6 HOH A 27 427 402 HOH HOH . H 6 HOH A 28 428 433 HOH HOH . H 6 HOH A 29 429 503 HOH HOH . H 6 HOH A 30 430 451 HOH HOH . H 6 HOH A 31 431 466 HOH HOH . H 6 HOH A 32 432 463 HOH HOH . H 6 HOH A 33 433 413 HOH HOH . H 6 HOH A 34 434 445 HOH HOH . H 6 HOH A 35 435 452 HOH HOH . H 6 HOH A 36 436 431 HOH HOH . H 6 HOH A 37 437 411 HOH HOH . H 6 HOH A 38 438 417 HOH HOH . H 6 HOH A 39 439 492 HOH HOH . H 6 HOH A 40 440 523 HOH HOH . H 6 HOH A 41 441 415 HOH HOH . H 6 HOH A 42 442 470 HOH HOH . H 6 HOH A 43 443 437 HOH HOH . H 6 HOH A 44 444 419 HOH HOH . H 6 HOH A 45 445 465 HOH HOH . H 6 HOH A 46 446 521 HOH HOH . H 6 HOH A 47 447 522 HOH HOH . H 6 HOH A 48 448 447 HOH HOH . H 6 HOH A 49 449 429 HOH HOH . H 6 HOH A 50 450 486 HOH HOH . H 6 HOH A 51 451 461 HOH HOH . H 6 HOH A 52 452 446 HOH HOH . H 6 HOH A 53 453 476 HOH HOH . H 6 HOH A 54 454 520 HOH HOH . H 6 HOH A 55 455 507 HOH HOH . H 6 HOH A 56 456 439 HOH HOH . H 6 HOH A 57 457 412 HOH HOH . H 6 HOH A 58 458 496 HOH HOH . H 6 HOH A 59 459 405 HOH HOH . H 6 HOH A 60 460 527 HOH HOH . H 6 HOH A 61 461 482 HOH HOH . H 6 HOH A 62 462 442 HOH HOH . H 6 HOH A 63 463 518 HOH HOH . H 6 HOH A 64 464 416 HOH HOH . H 6 HOH A 65 465 457 HOH HOH . H 6 HOH A 66 466 430 HOH HOH . H 6 HOH A 67 467 495 HOH HOH . H 6 HOH A 68 468 501 HOH HOH . H 6 HOH A 69 469 460 HOH HOH . H 6 HOH A 70 470 436 HOH HOH . H 6 HOH A 71 471 514 HOH HOH . H 6 HOH A 72 472 512 HOH HOH . H 6 HOH A 73 473 531 HOH HOH . H 6 HOH A 74 474 513 HOH HOH . H 6 HOH A 75 475 418 HOH HOH . H 6 HOH A 76 476 425 HOH HOH . H 6 HOH A 77 477 510 HOH HOH . H 6 HOH A 78 478 403 HOH HOH . H 6 HOH A 79 479 420 HOH HOH . H 6 HOH A 80 480 477 HOH HOH . H 6 HOH A 81 481 410 HOH HOH . H 6 HOH A 82 482 499 HOH HOH . H 6 HOH A 83 483 409 HOH HOH . H 6 HOH A 84 484 458 HOH HOH . H 6 HOH A 85 485 485 HOH HOH . H 6 HOH A 86 486 490 HOH HOH . H 6 HOH A 87 487 488 HOH HOH . H 6 HOH A 88 488 401 HOH HOH . H 6 HOH A 89 489 467 HOH HOH . H 6 HOH A 90 490 517 HOH HOH . H 6 HOH A 91 491 487 HOH HOH . H 6 HOH A 92 492 438 HOH HOH . H 6 HOH A 93 493 473 HOH HOH . H 6 HOH A 94 494 468 HOH HOH . H 6 HOH A 95 495 444 HOH HOH . H 6 HOH A 96 496 506 HOH HOH . H 6 HOH A 97 497 494 HOH HOH . H 6 HOH A 98 498 526 HOH HOH . H 6 HOH A 99 499 448 HOH HOH . H 6 HOH A 100 500 504 HOH HOH . H 6 HOH A 101 501 423 HOH HOH . H 6 HOH A 102 502 441 HOH HOH . H 6 HOH A 103 503 440 HOH HOH . H 6 HOH A 104 504 528 HOH HOH . H 6 HOH A 105 505 464 HOH HOH . H 6 HOH A 106 506 489 HOH HOH . H 6 HOH A 107 507 471 HOH HOH . H 6 HOH A 108 508 524 HOH HOH . H 6 HOH A 109 509 434 HOH HOH . H 6 HOH A 110 510 540 HOH HOH . H 6 HOH A 111 511 493 HOH HOH . H 6 HOH A 112 512 443 HOH HOH . H 6 HOH A 113 513 508 HOH HOH . H 6 HOH A 114 514 491 HOH HOH . H 6 HOH A 115 515 469 HOH HOH . H 6 HOH A 116 516 453 HOH HOH . H 6 HOH A 117 517 525 HOH HOH . H 6 HOH A 118 518 502 HOH HOH . H 6 HOH A 119 519 536 HOH HOH . H 6 HOH A 120 520 449 HOH HOH . H 6 HOH A 121 521 479 HOH HOH . H 6 HOH A 122 522 534 HOH HOH . H 6 HOH A 123 523 424 HOH HOH . H 6 HOH A 124 524 498 HOH HOH . H 6 HOH A 125 525 483 HOH HOH . H 6 HOH A 126 526 516 HOH HOH . H 6 HOH A 127 527 481 HOH HOH . H 6 HOH A 128 528 454 HOH HOH . H 6 HOH A 129 529 480 HOH HOH . H 6 HOH A 130 530 532 HOH HOH . H 6 HOH A 131 531 497 HOH HOH . H 6 HOH A 132 532 511 HOH HOH . H 6 HOH A 133 533 500 HOH HOH . H 6 HOH A 134 534 515 HOH HOH . H 6 HOH A 135 535 530 HOH HOH . H 6 HOH A 136 536 535 HOH HOH . H 6 HOH A 137 537 529 HOH HOH . H 6 HOH A 138 538 539 HOH HOH . H 6 HOH A 139 539 519 HOH HOH . H 6 HOH A 140 540 533 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 . . . D 4 -7.118 9.124 12.207 0.7 28.54 ? N1 CTP 303 A 1 HETATM 2 C C2 CTP . . . D 4 -6.457 8.663 13.386 0.7 27.94 ? C2 CTP 303 A 1 HETATM 3 N N3 CTP . . . D 4 -6.721 9.224 14.588 0.7 27.57 ? N3 CTP 303 A 1 HETATM 4 C C4 CTP . . . D 4 -7.609 10.233 14.697 0.7 26.86 ? C4 CTP 303 A 1 HETATM 5 C C5 CTP . . . D 4 -8.274 10.71 13.566 0.7 27.14 ? C5 CTP 303 A 1 HETATM 6 C C6 CTP . . . D 4 -8.009 10.131 12.32 0.7 27.79 ? C6 CTP 303 A 1 HETATM 7 O O2 CTP . . . D 4 -5.619 7.745 13.375 0.7 28.89 ? O2 CTP 303 A 1 HETATM 8 N N4 CTP . . . D 4 -7.834 10.77 15.916 0.7 26.1 ? N4 CTP 303 A 1 HETATM 9 C C1' CTP . . . D 4 -6.879 8.565 10.857 0.7 29.23 ? C1' CTP 303 A 1 HETATM 10 C C2' CTP . . . D 4 -5.662 9.214 10.2 0.7 30.09 ? C2' CTP 303 A 1 HETATM 11 O O2' CTP . . . D 4 -6.017 9.785 8.937 0.7 32.31 ? O2' CTP 303 A 1 HETATM 12 C C3' CTP . . . D 4 -4.658 8.095 9.995 0.7 30.11 ? C3' CTP 303 A 1 HETATM 13 C C4' CTP . . . D 4 -5.38 6.795 10.328 0.7 29.44 ? C4' CTP 303 A 1 HETATM 14 O O4' CTP . . . D 4 -6.655 7.147 10.866 0.7 30.11 ? O4' CTP 303 A 1 HETATM 15 O O3' CTP . . . D 4 -4.151 8.06 8.656 0.7 30.48 ? O3' CTP 303 A 1 HETATM 16 C C5' CTP . . . D 4 -4.6 5.982 11.359 0.7 29.1 ? C5' CTP 303 A 1 HETATM 17 O O5' CTP . . . D 4 -3.207 6.18 11.138 0.7 27.29 ? O5' CTP 303 A 1 HETATM 18 P PA CTP . . . D 4 -2.114 6.609 12.252 0.7 25.6 ? PA CTP 303 A 1 HETATM 19 O O1A CTP . . . D 4 -1.084 7.448 11.532 0.7 24.11 ? O1A CTP 303 A 1 HETATM 20 O O2A CTP . . . D 4 -2.728 7.157 13.525 0.7 23.34 ? O2A CTP 303 A 1 HETATM 21 O O3A CTP . . . D 4 -1.507 5.158 12.621 0.7 24.44 ? O3A CTP 303 A 1 HETATM 22 P PB CTP . . . D 4 -0.614 4.235 11.639 0.7 23.73 ? PB CTP 303 A 1 HETATM 23 O O1B CTP . . . D 4 -0.668 4.768 10.225 0.7 24.65 ? O1B CTP 303 A 1 HETATM 24 O O2B CTP . . . D 4 -1.052 2.82 11.908 0.7 24.88 ? O2B CTP 303 A 1 HETATM 25 O O3B CTP . . . D 4 0.863 4.382 12.276 0.7 22.87 ? O3B CTP 303 A 1 HETATM 26 P PG CTP . . . D 4 2.081 5.253 11.66 0.7 22.25 ? PG CTP 303 A 1 HETATM 27 O O1G CTP . . . D 4 2.72 4.323 10.655 0.7 23.25 ? O1G CTP 303 A 1 HETATM 28 O O2G CTP . . . D 4 1.439 6.479 11.064 0.7 22.04 ? O2G CTP 303 A 1 HETATM 29 O O3G CTP . . . D 4 2.938 5.526 12.881 0.7 21.62 ? O3G CTP 303 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 29 #