data_4FHD
#
_model_server_result.job_id            sOABqNn0vTDo73lSvVcVrw 
_model_server_result.datetime_utc      '2024-11-20 11:35:16' 
_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          4fhd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":408}' 
#
_entry.id    4FHD 
#
_exptl.entry_id    4FHD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              484.457 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-[[(5R)-1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-methyl-2,4-bis(oxidanylidene)-1,3-diazinan-5-yl]methyl]pyrimidine-2,4-dione 
_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            4FHD 
_cell.length_a            53.32 
_cell.length_b            58.92 
_cell.length_c            131.62 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4FHD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,I,J,K 
_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                      5 
_struct_asym.id                             I 
_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 SG CYS 117 A CYS 90 1_555 B FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc2 A SG CYS 121 A CYS 94 1_555 B FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc3 A SG CYS 124 A CYS 97 1_555 B FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc4 B FE3 SF4 . A SF4 401 1_555 C O EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc5 B FE3 SF4 . A SF4 401 1_555 C N EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
#
_chem_comp.formula           'C20 H28 N4 O10' 
_chem_comp.formula_weight    484.457 
_chem_comp.id                0TT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-[[(5R)-1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-methyl-2,4-bis(oxidanylidene)-1,3-diazinan-5-yl]methyl]pyrimidine-2,4-dione 
_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
C1 CI 0TT sing 1 n n 
O6 CL 0TT doub 2 n n 
CI CL 0TT sing 3 n n 
CI CH 0TT sing 4 n n 
CI CJ 0TT sing 5 n n 
CL N4 0TT sing 6 n n 
CH CF 0TT sing 7 n n 
CJ N3 0TT sing 8 n n 
N4 CK 0TT sing 9 n n 
CF CE 0TT doub 10 n n 
CF CG 0TT sing 11 n n 
O4 CG 0TT doub 12 n n 
CE N1 0TT sing 13 n n 
CG N2 0TT sing 14 n n 
N3 CK 0TT sing 15 n n 
N3 C2 0TT sing 16 n n 
CK O5 0TT doub 17 n n 
CM CD 0TT sing 18 n n 
CM CA 0TT sing 19 n n 
N1 CD 0TT sing 20 n n 
N1 CB 0TT sing 21 n n 
N2 CB 0TT sing 22 n n 
C2 O7 0TT sing 23 n n 
C2 C3 0TT sing 24 n n 
CD OB 0TT sing 25 n n 
CA O1 0TT sing 26 n n 
CA C9 0TT sing 27 n n 
CB O3 0TT doub 28 n n 
O7 C5 0TT sing 29 n n 
C3 C4 0TT sing 30 n n 
OB C9 0TT sing 31 n n 
C9 C8 0TT sing 32 n n 
C8 OA 0TT sing 33 n n 
C5 C4 0TT sing 34 n n 
C5 C6 0TT sing 35 n n 
C4 O9 0TT sing 36 n n 
O8 C6 0TT sing 37 n n 
O8 H1 0TT sing 38 n n 
C6 H2 0TT sing 39 n n 
C6 H3 0TT sing 40 n n 
C5 H4 0TT sing 41 n n 
C4 H5 0TT sing 42 n n 
O9 H6 0TT sing 43 n n 
C3 H7 0TT sing 44 n n 
C3 H8 0TT sing 45 n n 
C2 H9 0TT sing 46 n n 
CJ H10 0TT sing 47 n n 
CJ H11 0TT sing 48 n n 
N4 H12 0TT sing 49 n n 
C1 H13 0TT sing 50 n n 
C1 H14 0TT sing 51 n n 
C1 H15 0TT sing 52 n n 
CH H16 0TT sing 53 n n 
CH H17 0TT sing 54 n n 
CE H18 0TT sing 55 n n 
N2 H19 0TT sing 56 n n 
CD H20 0TT sing 57 n n 
CM H21 0TT sing 58 n n 
CM H22 0TT sing 59 n n 
CA H23 0TT sing 60 n n 
O1 H24 0TT sing 61 n n 
C9 H25 0TT sing 62 n n 
C8 H26 0TT sing 63 n n 
C8 H27 0TT sing 64 n n 
OA H28 0TT sing 65 n n 
#
_atom_sites.entry_id                     4FHD 
_atom_sites.fract_transf_matrix[1][1]    0.018755 
_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]    0.016972 
_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]    0.007598 
_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 SF4 A 1 401 1 SF4 FS4 . 
C 3 EEM A 1 402 1 EEM SA2 . 
D 4 SO4 A 1 403 1 SO4 SO4 . 
E 4 SO4 A 1 404 2 SO4 SO4 . 
F 4 SO4 A 1 405 3 SO4 SO4 . 
G 4 SO4 A 1 406 4 SO4 SO4 . 
H 4 SO4 A 1 407 5 SO4 SO4 . 
I 5 0TT A 1 408 1 0TT SP . 
J 6 POP A 1 409 1 POP POP . 
K 7 HOH A 1 501 1 HOH HOH . 
K 7 HOH A 2 502 2 HOH HOH . 
K 7 HOH A 3 503 3 HOH HOH . 
K 7 HOH A 4 504 4 HOH HOH . 
K 7 HOH A 5 505 5 HOH HOH . 
K 7 HOH A 6 506 6 HOH HOH . 
K 7 HOH A 7 507 7 HOH HOH . 
K 7 HOH A 8 508 8 HOH HOH . 
K 7 HOH A 9 509 9 HOH HOH . 
K 7 HOH A 10 510 10 HOH HOH . 
K 7 HOH A 11 511 11 HOH HOH . 
K 7 HOH A 12 512 14 HOH HOH . 
K 7 HOH A 13 513 15 HOH HOH . 
K 7 HOH A 14 514 16 HOH HOH . 
K 7 HOH A 15 515 17 HOH HOH . 
K 7 HOH A 16 516 18 HOH HOH . 
K 7 HOH A 17 517 19 HOH HOH . 
K 7 HOH A 18 518 22 HOH HOH . 
K 7 HOH A 19 519 23 HOH HOH . 
K 7 HOH A 20 520 24 HOH HOH . 
K 7 HOH A 21 521 27 HOH HOH . 
K 7 HOH A 22 522 28 HOH HOH . 
K 7 HOH A 23 523 29 HOH HOH . 
K 7 HOH A 24 524 30 HOH HOH . 
K 7 HOH A 25 525 31 HOH HOH . 
K 7 HOH A 26 526 32 HOH HOH . 
K 7 HOH A 27 527 34 HOH HOH . 
K 7 HOH A 28 528 35 HOH HOH . 
K 7 HOH A 29 529 36 HOH HOH . 
K 7 HOH A 30 530 37 HOH HOH . 
K 7 HOH A 31 531 38 HOH HOH . 
K 7 HOH A 32 532 39 HOH HOH . 
K 7 HOH A 33 533 40 HOH HOH . 
K 7 HOH A 34 534 41 HOH HOH . 
K 7 HOH A 35 535 42 HOH HOH . 
K 7 HOH A 36 536 43 HOH HOH . 
K 7 HOH A 37 537 44 HOH HOH . 
K 7 HOH A 38 538 45 HOH HOH . 
K 7 HOH A 39 539 46 HOH HOH . 
K 7 HOH A 40 540 47 HOH HOH . 
K 7 HOH A 41 541 48 HOH HOH . 
K 7 HOH A 42 542 49 HOH HOH . 
K 7 HOH A 43 543 50 HOH HOH . 
K 7 HOH A 44 544 51 HOH HOH . 
K 7 HOH A 45 545 52 HOH HOH . 
K 7 HOH A 46 546 53 HOH HOH . 
K 7 HOH A 47 547 54 HOH HOH . 
K 7 HOH A 48 548 55 HOH HOH . 
K 7 HOH A 49 549 56 HOH HOH . 
K 7 HOH A 50 550 57 HOH HOH . 
K 7 HOH A 51 551 58 HOH HOH . 
K 7 HOH A 52 552 59 HOH HOH . 
K 7 HOH A 53 553 60 HOH HOH . 
K 7 HOH A 54 554 61 HOH HOH . 
K 7 HOH A 55 555 62 HOH HOH . 
K 7 HOH A 56 556 63 HOH HOH . 
K 7 HOH A 57 557 64 HOH HOH . 
K 7 HOH A 58 558 65 HOH HOH . 
K 7 HOH A 59 559 66 HOH HOH . 
K 7 HOH A 60 560 68 HOH HOH . 
K 7 HOH A 61 561 69 HOH HOH . 
K 7 HOH A 62 562 70 HOH HOH . 
K 7 HOH A 63 563 73 HOH HOH . 
K 7 HOH A 64 564 75 HOH HOH . 
K 7 HOH A 65 565 77 HOH HOH . 
K 7 HOH A 66 566 78 HOH HOH . 
K 7 HOH A 67 567 80 HOH HOH . 
K 7 HOH A 68 568 81 HOH HOH . 
K 7 HOH A 69 569 82 HOH HOH . 
K 7 HOH A 70 570 83 HOH HOH . 
K 7 HOH A 71 571 84 HOH HOH . 
K 7 HOH A 72 572 85 HOH HOH . 
K 7 HOH A 73 573 86 HOH HOH . 
K 7 HOH A 74 574 87 HOH HOH . 
K 7 HOH A 75 575 88 HOH HOH . 
K 7 HOH A 76 576 89 HOH HOH . 
K 7 HOH A 77 577 94 HOH HOH . 
K 7 HOH A 78 578 95 HOH HOH . 
K 7 HOH A 79 579 96 HOH HOH . 
K 7 HOH A 80 580 98 HOH HOH . 
K 7 HOH A 81 581 99 HOH HOH . 
K 7 HOH A 82 582 108 HOH HOH . 
K 7 HOH A 83 583 109 HOH HOH . 
K 7 HOH A 84 584 110 HOH HOH . 
K 7 HOH A 85 585 111 HOH HOH . 
K 7 HOH A 86 586 114 HOH HOH . 
K 7 HOH A 87 587 118 HOH HOH . 
K 7 HOH A 88 588 121 HOH HOH . 
K 7 HOH A 89 589 122 HOH HOH . 
K 7 HOH A 90 590 126 HOH HOH . 
K 7 HOH A 91 591 130 HOH HOH . 
K 7 HOH A 92 592 131 HOH HOH . 
K 7 HOH A 93 593 132 HOH HOH . 
K 7 HOH A 94 594 133 HOH HOH . 
K 7 HOH A 95 595 135 HOH HOH . 
K 7 HOH A 96 596 136 HOH HOH . 
K 7 HOH A 97 597 137 HOH HOH . 
K 7 HOH A 98 598 138 HOH HOH . 
K 7 HOH A 99 599 139 HOH HOH . 
K 7 HOH A 100 600 140 HOH HOH . 
K 7 HOH A 101 601 141 HOH HOH . 
K 7 HOH A 102 602 142 HOH HOH . 
K 7 HOH A 103 603 143 HOH HOH . 
K 7 HOH A 104 604 144 HOH HOH . 
K 7 HOH A 105 605 145 HOH HOH . 
K 7 HOH A 106 606 146 HOH HOH . 
K 7 HOH A 107 607 147 HOH HOH . 
K 7 HOH A 108 608 148 HOH HOH . 
K 7 HOH A 109 609 149 HOH HOH . 
K 7 HOH A 110 610 150 HOH HOH . 
K 7 HOH A 111 611 151 HOH HOH . 
K 7 HOH A 112 612 152 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 O8 0TT . . . I 5 -19.46 -3.946 26.491 1 39.77 ? O8 0TT 408 A 1 
HETATM 2 C C6 0TT . . . I 5 -19.761 -2.574 26.742 1 39.65 ? C6 0TT 408 A 1 
HETATM 3 C C5 0TT . . . I 5 -21.094 -2.197 26.143 1 40.48 ? C5 0TT 408 A 1 
HETATM 4 O O7 0TT . . . I 5 -20.907 -2.035 24.723 1 39.94 ? O7 0TT 408 A 1 
HETATM 5 C C4 0TT . . . I 5 -22.215 -3.236 26.311 1 40.25 ? C4 0TT 408 A 1 
HETATM 6 O O9 0TT . . . I 5 -23.457 -2.525 26.429 1 41.74 ? O9 0TT 408 A 1 
HETATM 7 C C3 0TT . . . I 5 -22.072 -4.039 25.049 1 39.96 ? C3 0TT 408 A 1 
HETATM 8 C C2 0TT . . . I 5 -21.741 -2.949 24.005 1 40.04 ? C2 0TT 408 A 1 
HETATM 9 N N3 0TT . . . I 5 -21.018 -3.332 22.781 1 39.31 ? N3 0TT 408 A 1 
HETATM 10 C CJ 0TT . . . I 5 -21.521 -2.928 21.455 1 38.85 ? CJ 0TT 408 A 1 
HETATM 11 C CK 0TT . . . I 5 -19.861 -4.079 22.89 1 38.89 ? CK 0TT 408 A 1 
HETATM 12 O O5 0TT . . . I 5 -19.364 -4.474 23.944 1 38.4 ? O5 0TT 408 A 1 
HETATM 13 N N4 0TT . . . I 5 -19.198 -4.36 21.696 1 38.15 ? N4 0TT 408 A 1 
HETATM 14 C CL 0TT . . . I 5 -19.289 -3.631 20.535 1 38.74 ? CL 0TT 408 A 1 
HETATM 15 O O6 0TT . . . I 5 -18.626 -3.957 19.569 1 39.27 ? O6 0TT 408 A 1 
HETATM 16 C CI 0TT . . . I 5 -20.412 -2.595 20.44 1 38.95 ? CI 0TT 408 A 1 
HETATM 17 C C1 0TT . . . I 5 -20.981 -2.695 19.008 1 38.08 ? C1 0TT 408 A 1 
HETATM 18 C CH 0TT . . . I 5 -19.889 -1.124 20.595 1 38.81 ? CH 0TT 408 A 1 
HETATM 19 C CF 0TT . . . I 5 -19.708 -0.531 21.958 1 39.74 ? CF 0TT 408 A 1 
HETATM 20 C CE 0TT . . . I 5 -20.6 0.338 22.495 1 40.85 ? CE 0TT 408 A 1 
HETATM 21 C CG 0TT . . . I 5 -18.54 -0.9 22.746 1 39.76 ? CG 0TT 408 A 1 
HETATM 22 O O4 0TT . . . I 5 -17.675 -1.682 22.389 1 38.26 ? O4 0TT 408 A 1 
HETATM 23 N N2 0TT . . . I 5 -18.454 -0.305 23.986 1 40.37 ? N2 0TT 408 A 1 
HETATM 24 C CB 0TT . . . I 5 -19.343 0.582 24.539 1 41.48 ? CB 0TT 408 A 1 
HETATM 25 O O3 0TT . . . I 5 -19.152 1.042 25.666 1 41.6 ? O3 0TT 408 A 1 
HETATM 26 N N1 0TT . . . I 5 -20.439 0.914 23.765 1 42.09 ? N1 0TT 408 A 1 
HETATM 27 C CD 0TT . . . I 5 -21.396 1.859 24.387 1 43.88 ? CD 0TT 408 A 1 
HETATM 28 O OB 0TT . . . I 5 -22.29 0.993 25.069 1 44.32 ? OB 0TT 408 A 1 
HETATM 29 C CM 0TT . . . I 5 -22.283 2.703 23.52 1 44.74 ? CM 0TT 408 A 1 
HETATM 30 C CA 0TT . . . I 5 -23.448 2.953 24.507 1 44.93 ? CA 0TT 408 A 1 
HETATM 31 O O1 0TT . . . I 5 -23.333 4.245 25.079 1 45.77 ? O1 0TT 408 A 1 
HETATM 32 C C9 0TT . . . I 5 -23.379 1.793 25.532 1 45.02 ? C9 0TT 408 A 1 
HETATM 33 C C8 0TT . . . I 5 -24.573 0.9 25.689 1 45.4 ? C8 0TT 408 A 1 
HETATM 34 O OA 0TT . . . I 5 -24.365 0.089 26.868 1 46.05 ? OA 0TT 408 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          19 
_model_server_stats.element_count           34 
#