data_1P5Z # _model_server_result.job_id TvfJE5W1pQrHUdBn03dH2Q _model_server_result.datetime_utc '2024-10-16 10:38:00' _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 1p5z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":304}' # _entry.id 1P5Z # _exptl.entry_id 1P5Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 243.217 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description CYTARABINE _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 1P5Z _cell.length_a 80.72 _cell.length_b 80.72 _cell.length_c 94.28 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1P5Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 80.72 80.72 47.14 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 A OG SER 38 B SER 35 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc2 A OE1 GLU 130 B GLU 127 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 D O2B ADP . B ADP 301 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc4 B MG MG . B MG 401 1_555 E O HOH . B HOH 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc5 B MG MG . B MG 401 1_555 E O HOH . B HOH 576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc6 B MG MG . B MG 401 1_555 E O HOH . B HOH 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _chem_comp.formula 'C9 H13 N3 O5' _chem_comp.formula_weight 243.217 _chem_comp.id AR3 _chem_comp.mon_nstd_flag . _chem_comp.name CYTARABINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-BETA-D-ARABINOFURANOSYLCYTOSINE;ARA-C # 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 O5' C5' AR3 sing 57 n n O5' H5' AR3 sing 58 n n C5' C4' AR3 sing 59 n n C5' "H5'1" AR3 sing 60 n n C5' "H5'2" AR3 sing 61 n n C4' O4' AR3 sing 62 n n C4' C3' AR3 sing 63 n n C4' H4' AR3 sing 64 n n O4' C1' AR3 sing 65 n n C1' N1 AR3 sing 66 n n C1' C2' AR3 sing 67 n n C1' H1' AR3 sing 68 n n N1 C6 AR3 sing 69 n y N1 C2 AR3 sing 70 n y C6 C5 AR3 doub 71 n y C6 H6 AR3 sing 72 n n C5 C4 AR3 sing 73 n y C5 H5 AR3 sing 74 n n C4 N3 AR3 doub 75 n y C4 N4 AR3 sing 76 n n N3 C2 AR3 sing 77 n y C2 O2 AR3 doub 78 n n N4 HN41 AR3 sing 79 n n N4 HN42 AR3 sing 80 n n C2' O1 AR3 sing 81 n n C2' C3' AR3 sing 82 n n C2' H2' AR3 sing 83 n n O1 HO1 AR3 sing 84 n n C3' O3' AR3 sing 85 n n C3' H3' AR3 sing 86 n n O3' H1 AR3 sing 87 n n # _atom_sites.entry_id 1P5Z _atom_sites.fract_transf_matrix[1][1] 0.012389 _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] 0.012389 _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] 0.010607 _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 B 1 401 401 MG MG . C 3 AR3 B 1 304 304 AR3 ARA . D 4 ADP B 1 301 301 ADP ADP . E 5 HOH B 1 402 1 HOH HOH . E 5 HOH B 2 403 2 HOH HOH . E 5 HOH B 3 404 3 HOH HOH . E 5 HOH B 4 405 4 HOH HOH . E 5 HOH B 5 406 5 HOH HOH . E 5 HOH B 6 407 6 HOH HOH . E 5 HOH B 7 408 7 HOH HOH . E 5 HOH B 8 409 8 HOH HOH . E 5 HOH B 9 410 9 HOH HOH . E 5 HOH B 10 411 10 HOH HOH . E 5 HOH B 11 412 11 HOH HOH . E 5 HOH B 12 413 12 HOH HOH . E 5 HOH B 13 414 13 HOH HOH . E 5 HOH B 14 415 14 HOH HOH . E 5 HOH B 15 416 15 HOH HOH . E 5 HOH B 16 417 16 HOH HOH . E 5 HOH B 17 418 17 HOH HOH . E 5 HOH B 18 419 18 HOH HOH . E 5 HOH B 19 420 19 HOH HOH . E 5 HOH B 20 421 20 HOH HOH . E 5 HOH B 21 422 21 HOH HOH . E 5 HOH B 22 423 22 HOH HOH . E 5 HOH B 23 424 23 HOH HOH . E 5 HOH B 24 425 24 HOH HOH . E 5 HOH B 25 426 25 HOH HOH . E 5 HOH B 26 427 26 HOH HOH . E 5 HOH B 27 428 27 HOH HOH . E 5 HOH B 28 429 28 HOH HOH . E 5 HOH B 29 430 29 HOH HOH . E 5 HOH B 30 431 30 HOH HOH . E 5 HOH B 31 432 31 HOH HOH . E 5 HOH B 32 433 32 HOH HOH . E 5 HOH B 33 434 33 HOH HOH . E 5 HOH B 34 435 34 HOH HOH . E 5 HOH B 35 436 35 HOH HOH . E 5 HOH B 36 437 36 HOH HOH . E 5 HOH B 37 438 37 HOH HOH . E 5 HOH B 38 439 38 HOH HOH . E 5 HOH B 39 440 39 HOH HOH . E 5 HOH B 40 441 40 HOH HOH . E 5 HOH B 41 442 41 HOH HOH . E 5 HOH B 42 443 42 HOH HOH . E 5 HOH B 43 444 43 HOH HOH . E 5 HOH B 44 445 44 HOH HOH . E 5 HOH B 45 446 45 HOH HOH . E 5 HOH B 46 447 46 HOH HOH . E 5 HOH B 47 448 47 HOH HOH . E 5 HOH B 48 449 48 HOH HOH . E 5 HOH B 49 450 49 HOH HOH . E 5 HOH B 50 451 50 HOH HOH . E 5 HOH B 51 452 51 HOH HOH . E 5 HOH B 52 453 52 HOH HOH . E 5 HOH B 53 454 53 HOH HOH . E 5 HOH B 54 455 54 HOH HOH . E 5 HOH B 55 456 55 HOH HOH . E 5 HOH B 56 457 56 HOH HOH . E 5 HOH B 57 458 57 HOH HOH . E 5 HOH B 58 459 58 HOH HOH . E 5 HOH B 59 460 59 HOH HOH . E 5 HOH B 60 461 60 HOH HOH . E 5 HOH B 61 462 61 HOH HOH . E 5 HOH B 62 463 62 HOH HOH . E 5 HOH B 63 464 63 HOH HOH . E 5 HOH B 64 465 64 HOH HOH . E 5 HOH B 65 466 65 HOH HOH . E 5 HOH B 66 467 66 HOH HOH . E 5 HOH B 67 468 67 HOH HOH . E 5 HOH B 68 469 68 HOH HOH . E 5 HOH B 69 470 69 HOH HOH . E 5 HOH B 70 471 70 HOH HOH . E 5 HOH B 71 472 71 HOH HOH . E 5 HOH B 72 473 72 HOH HOH . E 5 HOH B 73 474 73 HOH HOH . E 5 HOH B 74 475 74 HOH HOH . E 5 HOH B 75 476 75 HOH HOH . E 5 HOH B 76 477 76 HOH HOH . E 5 HOH B 77 478 77 HOH HOH . E 5 HOH B 78 479 78 HOH HOH . E 5 HOH B 79 480 79 HOH HOH . E 5 HOH B 80 481 81 HOH HOH . E 5 HOH B 81 482 82 HOH HOH . E 5 HOH B 82 483 83 HOH HOH . E 5 HOH B 83 484 84 HOH HOH . E 5 HOH B 84 485 86 HOH HOH . E 5 HOH B 85 486 87 HOH HOH . E 5 HOH B 86 487 88 HOH HOH . E 5 HOH B 87 488 89 HOH HOH . E 5 HOH B 88 489 90 HOH HOH . E 5 HOH B 89 490 91 HOH HOH . E 5 HOH B 90 491 92 HOH HOH . E 5 HOH B 91 492 93 HOH HOH . E 5 HOH B 92 493 94 HOH HOH . E 5 HOH B 93 494 95 HOH HOH . E 5 HOH B 94 495 96 HOH HOH . E 5 HOH B 95 496 97 HOH HOH . E 5 HOH B 96 497 98 HOH HOH . E 5 HOH B 97 498 99 HOH HOH . E 5 HOH B 98 499 100 HOH HOH . E 5 HOH B 99 500 101 HOH HOH . E 5 HOH B 100 501 102 HOH HOH . E 5 HOH B 101 502 103 HOH HOH . E 5 HOH B 102 503 104 HOH HOH . E 5 HOH B 103 504 106 HOH HOH . E 5 HOH B 104 505 107 HOH HOH . E 5 HOH B 105 506 108 HOH HOH . E 5 HOH B 106 507 109 HOH HOH . E 5 HOH B 107 508 110 HOH HOH . E 5 HOH B 108 509 111 HOH HOH . E 5 HOH B 109 510 112 HOH HOH . E 5 HOH B 110 511 113 HOH HOH . E 5 HOH B 111 512 114 HOH HOH . E 5 HOH B 112 513 115 HOH HOH . E 5 HOH B 113 514 116 HOH HOH . E 5 HOH B 114 515 118 HOH HOH . E 5 HOH B 115 516 119 HOH HOH . E 5 HOH B 116 517 120 HOH HOH . E 5 HOH B 117 518 122 HOH HOH . E 5 HOH B 118 519 127 HOH HOH . E 5 HOH B 119 520 130 HOH HOH . E 5 HOH B 120 521 131 HOH HOH . E 5 HOH B 121 522 134 HOH HOH . E 5 HOH B 122 523 135 HOH HOH . E 5 HOH B 123 524 136 HOH HOH . E 5 HOH B 124 525 137 HOH HOH . E 5 HOH B 125 526 139 HOH HOH . E 5 HOH B 126 527 141 HOH HOH . E 5 HOH B 127 528 142 HOH HOH . E 5 HOH B 128 529 144 HOH HOH . E 5 HOH B 129 530 145 HOH HOH . E 5 HOH B 130 531 150 HOH HOH . E 5 HOH B 131 532 151 HOH HOH . E 5 HOH B 132 533 152 HOH HOH . E 5 HOH B 133 534 155 HOH HOH . E 5 HOH B 134 535 156 HOH HOH . E 5 HOH B 135 536 157 HOH HOH . E 5 HOH B 136 537 158 HOH HOH . E 5 HOH B 137 538 159 HOH HOH . E 5 HOH B 138 539 160 HOH HOH . E 5 HOH B 139 540 161 HOH HOH . E 5 HOH B 140 541 162 HOH HOH . E 5 HOH B 141 542 163 HOH HOH . E 5 HOH B 142 543 164 HOH HOH . E 5 HOH B 143 544 166 HOH HOH . E 5 HOH B 144 545 169 HOH HOH . E 5 HOH B 145 546 171 HOH HOH . E 5 HOH B 146 547 172 HOH HOH . E 5 HOH B 147 548 173 HOH HOH . E 5 HOH B 148 549 174 HOH HOH . E 5 HOH B 149 550 175 HOH HOH . E 5 HOH B 150 551 176 HOH HOH . E 5 HOH B 151 552 177 HOH HOH . E 5 HOH B 152 553 178 HOH HOH . E 5 HOH B 153 554 181 HOH HOH . E 5 HOH B 154 555 183 HOH HOH . E 5 HOH B 155 556 184 HOH HOH . E 5 HOH B 156 557 188 HOH HOH . E 5 HOH B 157 558 191 HOH HOH . E 5 HOH B 158 559 193 HOH HOH . E 5 HOH B 159 560 195 HOH HOH . E 5 HOH B 160 561 196 HOH HOH . E 5 HOH B 161 562 197 HOH HOH . E 5 HOH B 162 563 198 HOH HOH . E 5 HOH B 163 564 200 HOH HOH . E 5 HOH B 164 565 202 HOH HOH . E 5 HOH B 165 566 203 HOH HOH . E 5 HOH B 166 567 204 HOH HOH . E 5 HOH B 167 568 205 HOH HOH . E 5 HOH B 168 569 206 HOH HOH . E 5 HOH B 169 570 207 HOH HOH . E 5 HOH B 170 571 208 HOH HOH . E 5 HOH B 171 572 209 HOH HOH . E 5 HOH B 172 573 210 HOH HOH . E 5 HOH B 173 574 211 HOH HOH . E 5 HOH B 174 575 402 HOH HOH . E 5 HOH B 175 576 403 HOH HOH . E 5 HOH B 176 577 404 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 O O5' AR3 . . . C 3 69.603 37.846 20.126 1 23.71 ? O5' AR3 304 B 1 HETATM 2 C C5' AR3 . . . C 3 70.084 37.18 21.29 1 21.06 ? C5' AR3 304 B 1 HETATM 3 C C4' AR3 . . . C 3 70.191 35.672 21.069 1 19.55 ? C4' AR3 304 B 1 HETATM 4 O O4' AR3 . . . C 3 68.908 35.015 20.82 1 21.14 ? O4' AR3 304 B 1 HETATM 5 C C1' AR3 . . . C 3 68.945 34.157 19.69 1 20.86 ? C1' AR3 304 B 1 HETATM 6 N N1 AR3 . . . C 3 67.581 34.094 19.091 1 19.44 ? N1 AR3 304 B 1 HETATM 7 C C6 AR3 . . . C 3 66.781 35.11 19.044 1 18.89 ? C6 AR3 304 B 1 HETATM 8 C C5 AR3 . . . C 3 65.581 35.014 18.562 1 18.04 ? C5 AR3 304 B 1 HETATM 9 C C4 AR3 . . . C 3 65.145 33.836 18.102 1 18.43 ? C4 AR3 304 B 1 HETATM 10 N N3 AR3 . . . C 3 65.955 32.8 18.065 1 18.92 ? N3 AR3 304 B 1 HETATM 11 C C2 AR3 . . . C 3 67.182 32.939 18.562 1 19.01 ? C2 AR3 304 B 1 HETATM 12 O O2 AR3 . . . C 3 67.993 31.922 18.522 1 19.48 ? O2 AR3 304 B 1 HETATM 13 N N4 AR3 . . . C 3 63.889 33.644 17.594 1 18.8 ? N4 AR3 304 B 1 HETATM 14 C C2' AR3 . . . C 3 70.097 34.681 18.834 1 19.44 ? C2' AR3 304 B 1 HETATM 15 O O1 AR3 . . . C 3 69.589 35.628 17.902 1 18.86 ? O1 AR3 304 B 1 HETATM 16 C C3' AR3 . . . C 3 71.052 35.302 19.868 1 18.63 ? C3' AR3 304 B 1 HETATM 17 O O3' AR3 . . . C 3 72.081 34.348 20.236 1 20.6 ? O3' AR3 304 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 17 #