data_5AXV # _model_server_result.job_id gnT6PNbODFEgLSrGT_UINQ _model_server_result.datetime_utc '2025-07-08 07:06:22' _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 5axv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5AXV # _exptl.entry_id 5AXV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 2 _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 5AXV _cell.length_a 103.381 _cell.length_b 103.381 _cell.length_c 103.381 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AXV _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id C _struct_conn.ptnr1_label_comp_id ACE _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ACE _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id ALA _struct_conn.ptnr2_label_seq_id 2 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id ALA _struct_conn.ptnr2_auth_seq_id 2 _struct_conn.ptnr2_symmetry 1_555 _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 1.332 _struct_conn.pdbx_value_order ? # _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 76 n n N1 C6 CTP sing 77 n n N1 C1' CTP sing 78 n n C2 N3 CTP sing 79 n n C2 O2 CTP doub 80 n n N3 C4 CTP doub 81 n n C4 C5 CTP sing 82 n n C4 N4 CTP sing 83 n n C5 C6 CTP doub 84 n n C5 H5 CTP sing 85 n n C6 H6 CTP sing 86 n n N4 HN41 CTP sing 87 n n N4 HN42 CTP sing 88 n n C1' C2' CTP sing 89 n n C1' O4' CTP sing 90 n n C1' H1' CTP sing 91 n n C2' O2' CTP sing 92 n n C2' C3' CTP sing 93 n n C2' H2' CTP sing 94 n n O2' HO2' CTP sing 95 n n C3' C4' CTP sing 96 n n C3' O3' CTP sing 97 n n C3' H3' CTP sing 98 n n C4' O4' CTP sing 99 n n C4' C5' CTP sing 100 n n C4' H4' CTP sing 101 n n O3' HO3' CTP sing 102 n n C5' O5' CTP sing 103 n n C5' "H5'1" CTP sing 104 n n C5' "H5'2" CTP sing 105 n n O5' PA CTP sing 106 n n PA O1A CTP doub 107 n n PA O2A CTP sing 108 n n PA O3A CTP sing 109 n n O2A HOA2 CTP sing 110 n n O3A PB CTP sing 111 n n PB O1B CTP doub 112 n n PB O2B CTP sing 113 n n PB O3B CTP sing 114 n n O2B HOB2 CTP sing 115 n n O3B PG CTP sing 116 n n PG O1G CTP doub 117 n n PG O2G CTP sing 118 n n PG O3G CTP sing 119 n n O2G HOG2 CTP sing 120 n n O3G HOG3 CTP sing 121 n n # _atom_sites.entry_id 5AXV _atom_sites.fract_transf_matrix[1][1] 0.009673 _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] 0.009673 _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] 0.009673 _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 CTP A 1 301 301 CTP CTP . C 3 CL A 1 302 302 CL CL . D 4 EDO A 1 303 303 EDO EDO . E 4 EDO A 1 304 304 EDO EDO . F 4 EDO A 1 305 305 EDO EDO . G 5 HOH A 1 401 423 HOH HOH . G 5 HOH A 2 402 520 HOH HOH . G 5 HOH A 3 403 472 HOH HOH . G 5 HOH A 4 404 428 HOH HOH . G 5 HOH A 5 405 466 HOH HOH . G 5 HOH A 6 406 452 HOH HOH . G 5 HOH A 7 407 471 HOH HOH . G 5 HOH A 8 408 425 HOH HOH . G 5 HOH A 9 409 489 HOH HOH . G 5 HOH A 10 410 487 HOH HOH . G 5 HOH A 11 411 416 HOH HOH . G 5 HOH A 12 412 412 HOH HOH . G 5 HOH A 13 413 504 HOH HOH . G 5 HOH A 14 414 439 HOH HOH . G 5 HOH A 15 415 476 HOH HOH . G 5 HOH A 16 416 414 HOH HOH . G 5 HOH A 17 417 498 HOH HOH . G 5 HOH A 18 418 409 HOH HOH . G 5 HOH A 19 419 430 HOH HOH . G 5 HOH A 20 420 495 HOH HOH . G 5 HOH A 21 421 483 HOH HOH . G 5 HOH A 22 422 448 HOH HOH . G 5 HOH A 23 423 505 HOH HOH . G 5 HOH A 24 424 463 HOH HOH . G 5 HOH A 25 425 403 HOH HOH . G 5 HOH A 26 426 482 HOH HOH . G 5 HOH A 27 427 481 HOH HOH . G 5 HOH A 28 428 402 HOH HOH . G 5 HOH A 29 429 406 HOH HOH . G 5 HOH A 30 430 424 HOH HOH . G 5 HOH A 31 431 479 HOH HOH . G 5 HOH A 32 432 491 HOH HOH . G 5 HOH A 33 433 408 HOH HOH . G 5 HOH A 34 434 437 HOH HOH . G 5 HOH A 35 435 475 HOH HOH . G 5 HOH A 36 436 420 HOH HOH . G 5 HOH A 37 437 473 HOH HOH . G 5 HOH A 38 438 435 HOH HOH . G 5 HOH A 39 439 480 HOH HOH . G 5 HOH A 40 440 440 HOH HOH . G 5 HOH A 41 441 419 HOH HOH . G 5 HOH A 42 442 488 HOH HOH . G 5 HOH A 43 443 454 HOH HOH . G 5 HOH A 44 444 492 HOH HOH . G 5 HOH A 45 445 484 HOH HOH . G 5 HOH A 46 446 477 HOH HOH . G 5 HOH A 47 447 516 HOH HOH . G 5 HOH A 48 448 415 HOH HOH . G 5 HOH A 49 449 507 HOH HOH . G 5 HOH A 50 450 451 HOH HOH . G 5 HOH A 51 451 474 HOH HOH . G 5 HOH A 52 452 465 HOH HOH . G 5 HOH A 53 453 485 HOH HOH . G 5 HOH A 54 454 422 HOH HOH . G 5 HOH A 55 455 427 HOH HOH . G 5 HOH A 56 456 417 HOH HOH . G 5 HOH A 57 457 418 HOH HOH . G 5 HOH A 58 458 518 HOH HOH . G 5 HOH A 59 459 478 HOH HOH . G 5 HOH A 60 460 490 HOH HOH . G 5 HOH A 61 461 431 HOH HOH . G 5 HOH A 62 462 421 HOH HOH . G 5 HOH A 63 463 436 HOH HOH . G 5 HOH A 64 464 433 HOH HOH . G 5 HOH A 65 465 512 HOH HOH . G 5 HOH A 66 466 470 HOH HOH . G 5 HOH A 67 467 404 HOH HOH . G 5 HOH A 68 468 441 HOH HOH . G 5 HOH A 69 469 446 HOH HOH . G 5 HOH A 70 470 455 HOH HOH . G 5 HOH A 71 471 407 HOH HOH . G 5 HOH A 72 472 514 HOH HOH . G 5 HOH A 73 473 443 HOH HOH . G 5 HOH A 74 474 426 HOH HOH . G 5 HOH A 75 475 461 HOH HOH . G 5 HOH A 76 476 445 HOH HOH . G 5 HOH A 77 477 413 HOH HOH . G 5 HOH A 78 478 401 HOH HOH . G 5 HOH A 79 479 453 HOH HOH . G 5 HOH A 80 480 499 HOH HOH . G 5 HOH A 81 481 456 HOH HOH . G 5 HOH A 82 482 462 HOH HOH . G 5 HOH A 83 483 508 HOH HOH . G 5 HOH A 84 484 493 HOH HOH . G 5 HOH A 85 485 449 HOH HOH . G 5 HOH A 86 486 467 HOH HOH . G 5 HOH A 87 487 458 HOH HOH . G 5 HOH A 88 488 468 HOH HOH . G 5 HOH A 89 489 519 HOH HOH . G 5 HOH A 90 490 486 HOH HOH . G 5 HOH A 91 491 429 HOH HOH . G 5 HOH A 92 492 464 HOH HOH . G 5 HOH A 93 493 521 HOH HOH . G 5 HOH A 94 494 447 HOH HOH . G 5 HOH A 95 495 515 HOH HOH . G 5 HOH A 96 496 450 HOH HOH . G 5 HOH A 97 497 497 HOH HOH . G 5 HOH A 98 498 442 HOH HOH . G 5 HOH A 99 499 460 HOH HOH . G 5 HOH A 100 500 438 HOH HOH . G 5 HOH A 101 501 434 HOH HOH . G 5 HOH A 102 502 459 HOH HOH . G 5 HOH A 103 503 457 HOH HOH . G 5 HOH A 104 504 411 HOH HOH . G 5 HOH A 105 505 503 HOH HOH . G 5 HOH A 106 506 501 HOH HOH . G 5 HOH A 107 507 469 HOH HOH . G 5 HOH A 108 508 500 HOH HOH . G 5 HOH A 109 509 522 HOH HOH . G 5 HOH A 110 510 496 HOH HOH . G 5 HOH A 111 511 506 HOH HOH . G 5 HOH A 112 512 513 HOH HOH . G 5 HOH A 113 513 444 HOH HOH . G 5 HOH A 114 514 405 HOH HOH . G 5 HOH A 115 515 511 HOH HOH . G 5 HOH A 116 516 432 HOH HOH . G 5 HOH A 117 517 494 HOH HOH . G 5 HOH A 118 518 517 HOH HOH . G 5 HOH A 119 519 410 HOH HOH . G 5 HOH A 120 520 510 HOH HOH . G 5 HOH A 121 521 509 HOH HOH . G 5 HOH A 122 522 502 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 . . . B 2 6.811 8.699 -11.975 0.7 22.01 ? N1 CTP 301 A 1 HETATM 2 C C2 CTP . . . B 2 6.118 8.408 -13.183 0.7 21.6 ? C2 CTP 301 A 1 HETATM 3 N N3 CTP . . . B 2 6.454 8.986 -14.364 0.7 21.62 ? N3 CTP 301 A 1 HETATM 4 C C4 CTP . . . B 2 7.462 9.879 -14.437 0.7 21.55 ? C4 CTP 301 A 1 HETATM 5 C C5 CTP . . . B 2 8.17 10.193 -13.273 0.7 22.49 ? C5 CTP 301 A 1 HETATM 6 C C6 CTP . . . B 2 7.823 9.588 -12.053 0.7 22.58 ? C6 CTP 301 A 1 HETATM 7 O O2 CTP . . . B 2 5.174 7.611 -13.209 0.7 21.38 ? O2 CTP 301 A 1 HETATM 8 N N4 CTP . . . B 2 7.758 10.456 -15.623 0.7 20.35 ? N4 CTP 301 A 1 HETATM 9 C C1' CTP . . . B 2 6.487 8.104 -10.644 0.7 22.72 ? C1' CTP 301 A 1 HETATM 10 C C2' CTP . . . B 2 5.234 8.733 -10.018 0.7 24.5 ? C2' CTP 301 A 1 HETATM 11 O O2' CTP . . . B 2 5.566 9.693 -9.001 0.7 24.61 ? O2' CTP 301 A 1 HETATM 12 C C3' CTP . . . B 2 4.445 7.596 -9.385 0.7 24.51 ? C3' CTP 301 A 1 HETATM 13 C C4' CTP . . . B 2 5.116 6.308 -9.831 0.7 23.39 ? C4' CTP 301 A 1 HETATM 14 O O4' CTP . . . B 2 6.242 6.695 -10.641 0.7 23.09 ? O4' CTP 301 A 1 HETATM 15 O O3' CTP . . . B 2 4.504 7.644 -7.957 0.7 25.92 ? O3' CTP 301 A 1 HETATM 16 C C5' CTP . . . B 2 4.094 5.441 -10.579 0.7 22.54 ? C5' CTP 301 A 1 HETATM 17 O O5' CTP . . . B 2 3.774 6.134 -11.793 0.7 22.45 ? O5' CTP 301 A 1 HETATM 18 P PA CTP . . . B 2 2.307 6.572 -12.353 0.7 21.26 ? PA CTP 301 A 1 HETATM 19 O O1A CTP . . . B 2 2.545 7.182 -13.712 0.7 18.42 ? O1A CTP 301 A 1 HETATM 20 O O2A CTP . . . B 2 1.552 7.366 -11.32 0.7 21.57 ? O2A CTP 301 A 1 HETATM 21 O O3A CTP . . . B 2 1.657 5.089 -12.556 0.7 21.85 ? O3A CTP 301 A 1 HETATM 22 P PB CTP . . . B 2 0.729 4.191 -11.562 0.7 20.85 ? PB CTP 301 A 1 HETATM 23 O O1B CTP . . . B 2 1.179 2.771 -11.768 0.7 21.9 ? O1B CTP 301 A 1 HETATM 24 O O2B CTP . . . B 2 0.725 4.717 -10.148 0.7 22.85 ? O2B CTP 301 A 1 HETATM 25 O O3B CTP . . . B 2 -0.766 4.262 -12.212 0.7 21.31 ? O3B CTP 301 A 1 HETATM 26 P PG CTP . . . B 2 -2.05 5.101 -11.662 0.7 20.74 ? PG CTP 301 A 1 HETATM 27 O O1G CTP . . . B 2 -2.935 5.261 -12.872 0.7 19.75 ? O1G CTP 301 A 1 HETATM 28 O O2G CTP . . . B 2 -2.625 4.21 -10.576 0.7 22.14 ? O2G CTP 301 A 1 HETATM 29 O O3G CTP . . . B 2 -1.491 6.402 -11.179 0.7 21.25 ? O3G CTP 301 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 29 #