data_1P62
#
_model_server_result.job_id            H-V46Hcz0LWhokXmohgcbw 
_model_server_result.datetime_utc      '2024-11-14 07:01:05' 
_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          1p62 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":302}' 
#
_entry.id    1P62 
#
_exptl.entry_id    1P62 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              263.198 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GEMCITABINE 
_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            1P62 
_cell.length_a            81.2 
_cell.length_b            81.2 
_cell.length_c            94.6 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1P62 
_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 81.2 81.2 47.3 
#
_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
metalc ? metalc1 A OG SER 38 B SER 35 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc2 A OE1 GLU 130 B GLU 127 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc3 C O2B ADP . B ADP 301 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
metalc ? metalc4 B MG MG . B MG 401 1_555 E O HOH . B HOH 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc5 B MG MG . B MG 401 1_555 E O HOH . B HOH 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? 
metalc ? metalc6 B MG MG . B MG 401 1_555 E O HOH . B HOH 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? 
#
_chem_comp.formula           'C9 H11 F2 N3 O4' 
_chem_comp.formula_weight    263.198 
_chem_comp.id                GEO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GEMCITABINE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "2',2'-DIFLUORODEOXYCYTIDINE" 
#
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' GEO sing 127 n n 
O5' H5' GEO sing 128 n n 
C5' C4' GEO sing 129 n n 
C5' "H5'1" GEO sing 130 n n 
C5' "H5'2" GEO sing 131 n n 
C4' O4' GEO sing 132 n n 
C4' C3' GEO sing 133 n n 
C4' H4' GEO sing 134 n n 
O4' C1' GEO sing 135 n n 
C1' N1 GEO sing 136 n n 
C1' C2' GEO sing 137 n n 
C1' H1' GEO sing 138 n n 
N1 C6 GEO sing 139 n y 
N1 C2 GEO sing 140 n y 
C6 C5 GEO doub 141 n y 
C6 H6 GEO sing 142 n n 
C5 C4 GEO sing 143 n y 
C5 H5 GEO sing 144 n n 
C4 N3 GEO doub 145 n y 
C4 N4 GEO sing 146 n n 
N3 C2 GEO sing 147 n y 
C2 O2 GEO doub 148 n n 
N4 HN41 GEO sing 149 n n 
N4 HN42 GEO sing 150 n n 
C2' F1 GEO sing 151 n n 
C2' F2 GEO sing 152 n n 
C2' C3' GEO sing 153 n n 
C3' O3' GEO sing 154 n n 
C3' H3' GEO sing 155 n n 
O3' H1 GEO sing 156 n n 
#
_atom_sites.entry_id                     1P62 
_atom_sites.fract_transf_matrix[1][1]    0.012315 
_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]    0.012315 
_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]    0.010571 
_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 ADP B 1 301 301 ADP ADP . 
D 4 GEO B 1 302 302 GEO GEM . 
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 28 HOH HOH . 
E 5 HOH B 28 429 29 HOH HOH . 
E 5 HOH B 29 430 30 HOH HOH . 
E 5 HOH B 30 431 31 HOH HOH . 
E 5 HOH B 31 432 32 HOH HOH . 
E 5 HOH B 32 433 33 HOH HOH . 
E 5 HOH B 33 434 34 HOH HOH . 
E 5 HOH B 34 435 35 HOH HOH . 
E 5 HOH B 35 436 36 HOH HOH . 
E 5 HOH B 36 437 37 HOH HOH . 
E 5 HOH B 37 438 38 HOH HOH . 
E 5 HOH B 38 439 39 HOH HOH . 
E 5 HOH B 39 440 40 HOH HOH . 
E 5 HOH B 40 441 41 HOH HOH . 
E 5 HOH B 41 442 42 HOH HOH . 
E 5 HOH B 42 443 43 HOH HOH . 
E 5 HOH B 43 444 44 HOH HOH . 
E 5 HOH B 44 445 45 HOH HOH . 
E 5 HOH B 45 446 46 HOH HOH . 
E 5 HOH B 46 447 48 HOH HOH . 
E 5 HOH B 47 448 49 HOH HOH . 
E 5 HOH B 48 449 50 HOH HOH . 
E 5 HOH B 49 450 51 HOH HOH . 
E 5 HOH B 50 451 52 HOH HOH . 
E 5 HOH B 51 452 53 HOH HOH . 
E 5 HOH B 52 453 54 HOH HOH . 
E 5 HOH B 53 454 55 HOH HOH . 
E 5 HOH B 54 455 56 HOH HOH . 
E 5 HOH B 55 456 57 HOH HOH . 
E 5 HOH B 56 457 58 HOH HOH . 
E 5 HOH B 57 458 59 HOH HOH . 
E 5 HOH B 58 459 60 HOH HOH . 
E 5 HOH B 59 460 61 HOH HOH . 
E 5 HOH B 60 461 62 HOH HOH . 
E 5 HOH B 61 462 63 HOH HOH . 
E 5 HOH B 62 463 64 HOH HOH . 
E 5 HOH B 63 464 65 HOH HOH . 
E 5 HOH B 64 465 66 HOH HOH . 
E 5 HOH B 65 466 67 HOH HOH . 
E 5 HOH B 66 467 69 HOH HOH . 
E 5 HOH B 67 468 70 HOH HOH . 
E 5 HOH B 68 469 71 HOH HOH . 
E 5 HOH B 69 470 72 HOH HOH . 
E 5 HOH B 70 471 73 HOH HOH . 
E 5 HOH B 71 472 74 HOH HOH . 
E 5 HOH B 72 473 75 HOH HOH . 
E 5 HOH B 73 474 76 HOH HOH . 
E 5 HOH B 74 475 77 HOH HOH . 
E 5 HOH B 75 476 78 HOH HOH . 
E 5 HOH B 76 477 79 HOH HOH . 
E 5 HOH B 77 478 81 HOH HOH . 
E 5 HOH B 78 479 82 HOH HOH . 
E 5 HOH B 79 480 83 HOH HOH . 
E 5 HOH B 80 481 84 HOH HOH . 
E 5 HOH B 81 482 86 HOH HOH . 
E 5 HOH B 82 483 87 HOH HOH . 
E 5 HOH B 83 484 88 HOH HOH . 
E 5 HOH B 84 485 89 HOH HOH . 
E 5 HOH B 85 486 90 HOH HOH . 
E 5 HOH B 86 487 92 HOH HOH . 
E 5 HOH B 87 488 93 HOH HOH . 
E 5 HOH B 88 489 96 HOH HOH . 
E 5 HOH B 89 490 97 HOH HOH . 
E 5 HOH B 90 491 98 HOH HOH . 
E 5 HOH B 91 492 99 HOH HOH . 
E 5 HOH B 92 493 100 HOH HOH . 
E 5 HOH B 93 494 101 HOH HOH . 
E 5 HOH B 94 495 102 HOH HOH . 
E 5 HOH B 95 496 103 HOH HOH . 
E 5 HOH B 96 497 104 HOH HOH . 
E 5 HOH B 97 498 107 HOH HOH . 
E 5 HOH B 98 499 108 HOH HOH . 
E 5 HOH B 99 500 109 HOH HOH . 
E 5 HOH B 100 501 110 HOH HOH . 
E 5 HOH B 101 502 111 HOH HOH . 
E 5 HOH B 102 503 112 HOH HOH . 
E 5 HOH B 103 504 113 HOH HOH . 
E 5 HOH B 104 505 115 HOH HOH . 
E 5 HOH B 105 506 116 HOH HOH . 
E 5 HOH B 106 507 118 HOH HOH . 
E 5 HOH B 107 508 119 HOH HOH . 
E 5 HOH B 108 509 120 HOH HOH . 
E 5 HOH B 109 510 122 HOH HOH . 
E 5 HOH B 110 511 127 HOH HOH . 
E 5 HOH B 111 512 130 HOH HOH . 
E 5 HOH B 112 513 131 HOH HOH . 
E 5 HOH B 113 514 135 HOH HOH . 
E 5 HOH B 114 515 136 HOH HOH . 
E 5 HOH B 115 516 137 HOH HOH . 
E 5 HOH B 116 517 139 HOH HOH . 
E 5 HOH B 117 518 141 HOH HOH . 
E 5 HOH B 118 519 144 HOH HOH . 
E 5 HOH B 119 520 145 HOH HOH . 
E 5 HOH B 120 521 152 HOH HOH . 
E 5 HOH B 121 522 158 HOH HOH . 
E 5 HOH B 122 523 159 HOH HOH . 
E 5 HOH B 123 524 160 HOH HOH . 
E 5 HOH B 124 525 161 HOH HOH . 
E 5 HOH B 125 526 163 HOH HOH . 
E 5 HOH B 126 527 164 HOH HOH . 
E 5 HOH B 127 528 166 HOH HOH . 
E 5 HOH B 128 529 169 HOH HOH . 
E 5 HOH B 129 530 171 HOH HOH . 
E 5 HOH B 130 531 173 HOH HOH . 
E 5 HOH B 131 532 175 HOH HOH . 
E 5 HOH B 132 533 177 HOH HOH . 
E 5 HOH B 133 534 195 HOH HOH . 
E 5 HOH B 134 535 198 HOH HOH . 
E 5 HOH B 135 536 200 HOH HOH . 
E 5 HOH B 136 537 204 HOH HOH . 
E 5 HOH B 137 538 205 HOH HOH . 
E 5 HOH B 138 539 206 HOH HOH . 
E 5 HOH B 139 540 208 HOH HOH . 
E 5 HOH B 140 541 209 HOH HOH . 
E 5 HOH B 141 542 210 HOH HOH . 
E 5 HOH B 142 543 402 HOH HOH . 
E 5 HOH B 143 544 403 HOH HOH . 
E 5 HOH B 144 545 404 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' GEO . . . D 4 69.971 38.095 20.611 1 31.86 ? O5' GEO 302 B 1 
HETATM 2 C C5' GEO . . . D 4 70.268 37.346 21.792 1 25.46 ? C5' GEO 302 B 1 
HETATM 3 C C4' GEO . . . D 4 70.467 35.86 21.371 1 28.45 ? C4' GEO 302 B 1 
HETATM 4 O O4' GEO . . . D 4 69.149 35.328 21.046 1 27.84 ? O4' GEO 302 B 1 
HETATM 5 C C1' GEO . . . D 4 69.21 34.473 19.901 1 25.35 ? C1' GEO 302 B 1 
HETATM 6 N N1 GEO . . . D 4 67.922 34.422 19.161 1 24.18 ? N1 GEO 302 B 1 
HETATM 7 C C6 GEO . . . D 4 67.146 35.472 18.997 1 25.52 ? C6 GEO 302 B 1 
HETATM 8 C C5 GEO . . . D 4 65.911 35.351 18.582 1 26.41 ? C5 GEO 302 B 1 
HETATM 9 C C4 GEO . . . D 4 65.456 34.201 18.16 1 21.48 ? C4 GEO 302 B 1 
HETATM 10 N N3 GEO . . . D 4 66.25 33.126 18.194 1 21.36 ? N3 GEO 302 B 1 
HETATM 11 C C2 GEO . . . D 4 67.498 33.222 18.696 1 24.48 ? C2 GEO 302 B 1 
HETATM 12 O O2 GEO . . . D 4 68.273 32.128 18.727 1 20.76 ? O2 GEO 302 B 1 
HETATM 13 N N4 GEO . . . D 4 64.225 34.032 17.639 1 21.72 ? N4 GEO 302 B 1 
HETATM 14 C C2' GEO . . . D 4 70.386 35.084 19.098 1 26.77 ? C2' GEO 302 B 1 
HETATM 15 F F1 GEO . . . D 4 69.943 36.062 18.337 1 25.86 ? F1 GEO 302 B 1 
HETATM 16 F F2 GEO . . . D 4 70.869 34.206 18.263 1 26.2 ? F2 GEO 302 B 1 
HETATM 17 C C3' GEO . . . D 4 71.368 35.602 20.169 1 27.34 ? C3' GEO 302 B 1 
HETATM 18 O O3' GEO . . . D 4 72.407 34.586 20.411 1 27.23 ? O3' GEO 302 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           18 
#