data_3ABT
#
_model_server_result.job_id            XrI5-R1FT1CQ586G_RyY8w 
_model_server_result.datetime_utc      '2024-12-03 14:48:48' 
_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          3abt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1}' 
#
_entry.id    3ABT 
#
_exptl.entry_id    3ABT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              1009.677 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-(pentafluorophenyl)-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate' 
_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         120 
_cell.entry_id            3ABT 
_cell.length_a            183.84 
_cell.length_b            183.84 
_cell.length_c            109.15 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3ABT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_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 
_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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C36 H38 F5 N9 O16 P2' 
_chem_comp.formula_weight    1009.677 
_chem_comp.id                2PF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-(pentafluorophenyl)-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate' 
_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
O4' C1' 2PF sing 1 n n 
NAI C1' 2PF sing 2 n n 
C2' C1' 2PF sing 3 n n 
C1' H1' 2PF sing 4 n n 
C2' C3' 2PF sing 5 n n 
C2' O2' 2PF sing 6 n n 
C2' H2' 2PF sing 7 n n 
O2' HO2' 2PF sing 8 n n 
C4' C3' 2PF sing 9 n n 
C3' O3' 2PF sing 10 n n 
C3' H3' 2PF sing 11 n n 
O3' HO3' 2PF sing 12 n n 
C5' C4' 2PF sing 13 n n 
O4' C4' 2PF sing 14 n n 
C4' H4' 2PF sing 15 n n 
C5' O5' 2PF sing 16 n n 
C5' H5' 2PF sing 17 n n 
C5' "H5'A" 2PF sing 18 n n 
PAA O5' 2PF sing 19 n n 
CAC CAA 2PF doub 20 n y 
CAA FAA 2PF sing 21 n n 
CAA CAB 2PF sing 22 n y 
OAW PAA 2PF sing 23 n n 
OAC PAA 2PF doub 24 n n 
PAA OAB 2PF sing 25 n n 
CAD CAB 2PF doub 26 n y 
CAB CBZ 2PF sing 27 n n 
CAD FAB 2PF sing 28 n n 
OAB HOAB 2PF sing 29 n n 
FAC CAC 2PF sing 30 n n 
CAE CAC 2PF sing 31 n y 
CAF CAD 2PF sing 32 n y 
FAD CAF 2PF sing 33 n n 
FAE CAE 2PF sing 34 n n 
CAE CAF 2PF doub 35 n y 
CAR NAI 2PF sing 36 n n 
NAI CAJ 2PF sing 37 n n 
CAP CAJ 2PF sing 38 n y 
CAJ NAK 2PF doub 39 n y 
NAK CAL 2PF sing 40 n y 
NAM CAL 2PF doub 41 n y 
CAL HAL 2PF sing 42 n n 
CAN NAM 2PF sing 43 n y 
NAO CAN 2PF sing 44 n n 
CAP CAN 2PF doub 45 n y 
NAO HNAO 2PF sing 46 n n 
NAO HNAA 2PF sing 47 n n 
NAQ CAP 2PF sing 48 n n 
NAQ CAR 2PF doub 49 n n 
CAR HAR 2PF sing 50 n n 
OAW PAX 2PF sing 51 n n 
OAY PAX 2PF doub 52 n n 
PAX OBA 2PF sing 53 n n 
PAX OAZ 2PF sing 54 n n 
OAZ HOAZ 2PF sing 55 n n 
CBB OBA 2PF sing 56 n n 
CBB CBC 2PF sing 57 n n 
CBB HBB 2PF sing 58 n n 
CBB HBBA 2PF sing 59 n n 
CBE CBC 2PF sing 60 n n 
CBC OBD 2PF sing 61 n n 
CBC HBC 2PF sing 62 n n 
OBD HOBD 2PF sing 63 n n 
OBF CBE 2PF sing 64 n n 
CBE CBG 2PF sing 65 n n 
CBE HBE 2PF sing 66 n n 
OBF HOBF 2PF sing 67 n n 
CBI CBG 2PF sing 68 n n 
CBG OBH 2PF sing 69 n n 
CBG HBG 2PF sing 70 n n 
OBH HOBH 2PF sing 71 n n 
CBI NBJ 2PF sing 72 n n 
CBI HBI 2PF sing 73 n n 
CBI HBIA 2PF sing 74 n n 
NBJ CBK 2PF sing 75 n n 
NBJ CBT 2PF sing 76 n n 
NBL CBK 2PF doub 77 n n 
CBR CBK 2PF sing 78 n n 
NBL CBM 2PF sing 79 n n 
OBN CBM 2PF doub 80 n n 
CBM NBO 2PF sing 81 n n 
NBO CBP 2PF sing 82 n n 
NBO HNBO 2PF sing 83 n n 
CBR CBP 2PF sing 84 n n 
CBP OBQ 2PF doub 85 n n 
CBZ CBR 2PF sing 86 n n 
CBR NBS 2PF sing 87 n n 
CCB NBS 2PF sing 88 n n 
CBU NBS 2PF sing 89 n n 
CBV CBT 2PF doub 90 n y 
CBT CBU 2PF sing 91 n y 
CBU CBW 2PF doub 92 n y 
CBV CCE 2PF sing 93 n y 
CBV HBV 2PF sing 94 n n 
CBX CBW 2PF sing 95 n y 
CBW HBW 2PF sing 96 n n 
CCE CBX 2PF doub 97 n y 
CBX CBY 2PF sing 98 n n 
CBY HBY 2PF sing 99 n n 
CBY HBYA 2PF sing 100 n n 
CBY HBYB 2PF sing 101 n n 
CBZ CCA 2PF sing 102 n n 
CBZ HBZ 2PF sing 103 n n 
CCA CCB 2PF sing 104 n n 
CCA HCA 2PF sing 105 n n 
CCA HCAA 2PF sing 106 n n 
CCB OCC 2PF sing 107 n n 
CCB HCB 2PF sing 108 n n 
OCC HOCC 2PF sing 109 n n 
CCD CCE 2PF sing 110 n n 
CCD HCD 2PF sing 111 n n 
CCD HCDA 2PF sing 112 n n 
CCD HCDB 2PF sing 113 n n 
#
_atom_sites.entry_id                     3ABT 
_atom_sites.fract_transf_matrix[1][1]    0.00544 
_atom_sites.fract_transf_matrix[1][2]    0.003141 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006281 
_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]    0.009162 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          B 
_pdbx_nonpoly_scheme.entity_id        2 
_pdbx_nonpoly_scheme.mon_id           2PF 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      1 
_pdbx_nonpoly_scheme.auth_seq_num     1 
_pdbx_nonpoly_scheme.pdb_mon_id       2PF 
_pdbx_nonpoly_scheme.auth_mon_id      2PF 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 C C1' 2PF . . . B 2 -21.682 38.234 22.693 1 43.12 ? C1' 2PF 1 A 1 
HETATM 2 C C2' 2PF . . . B 2 -21.84 39.739 22.486 1 43.13 ? C2' 2PF 1 A 1 
HETATM 3 O O2' 2PF . . . B 2 -21.03 40.438 23.435 1 43.43 ? O2' 2PF 1 A 1 
HETATM 4 C C3' 2PF . . . B 2 -23.308 39.826 22.899 1 43.02 ? C3' 2PF 1 A 1 
HETATM 5 O O3' 2PF . . . B 2 -23.431 39.651 24.313 1 42.8 ? O3' 2PF 1 A 1 
HETATM 6 C C4' 2PF . . . B 2 -23.889 38.608 22.175 1 42.66 ? C4' 2PF 1 A 1 
HETATM 7 O O4' 2PF . . . B 2 -22.786 37.714 21.935 1 42.43 ? O4' 2PF 1 A 1 
HETATM 8 C C5' 2PF . . . B 2 -24.448 39.071 20.829 1 42.21 ? C5' 2PF 1 A 1 
HETATM 9 O O5' 2PF . . . B 2 -25.552 39.954 21.037 1 41.74 ? O5' 2PF 1 A 1 
HETATM 10 C CAA 2PF . . . B 2 -31.556 49.952 12.997 1 60.85 ? CAA 2PF 1 A 1 
HETATM 11 F FAA 2PF . . . B 2 -30.524 49.089 13.089 1 62.41 ? FAA 2PF 1 A 1 
HETATM 12 P PAA 2PF . . . B 2 -25.809 41.188 20.036 1 41.16 ? PAA 2PF 1 A 1 
HETATM 13 C CAB 2PF . . . B 2 -31.602 51.049 13.853 1 59.34 ? CAB 2PF 1 A 1 
HETATM 14 F FAB 2PF . . . B 2 -32.75 53.053 14.507 1 60.85 ? FAB 2PF 1 A 1 
HETATM 15 O OAB 2PF . . . B 2 -26.686 42.172 20.708 1 41.47 ? OAB 2PF 1 A 1 
HETATM 16 C CAC 2PF . . . B 2 -32.544 49.748 12.04 1 61.58 ? CAC 2PF 1 A 1 
HETATM 17 F FAC 2PF . . . B 2 -32.471 48.693 11.201 1 61.28 ? FAC 2PF 1 A 1 
HETATM 18 O OAC 2PF . . . B 2 -24.511 41.653 19.499 1 41.12 ? OAC 2PF 1 A 1 
HETATM 19 C CAD 2PF . . . B 2 -32.661 51.949 13.737 1 60.32 ? CAD 2PF 1 A 1 
HETATM 20 F FAD 2PF . . . B 2 -34.675 52.623 12.676 1 61.8 ? FAD 2PF 1 A 1 
HETATM 21 C CAE 2PF . . . B 2 -33.6 50.647 11.932 1 61.97 ? CAE 2PF 1 A 1 
HETATM 22 F FAE 2PF . . . B 2 -34.565 50.453 11.009 1 62.98 ? FAE 2PF 1 A 1 
HETATM 23 C CAF 2PF . . . B 2 -33.654 51.746 12.782 1 61.45 ? CAF 2PF 1 A 1 
HETATM 24 N NAI 2PF . . . B 2 -20.392 37.723 22.176 1 43.72 ? NAI 2PF 1 A 1 
HETATM 25 C CAJ 2PF . . . B 2 -19.73 36.676 22.659 1 44.16 ? CAJ 2PF 1 A 1 
HETATM 26 N NAK 2PF . . . B 2 -19.996 35.813 23.729 1 43.99 ? NAK 2PF 1 A 1 
HETATM 27 C CAL 2PF . . . B 2 -19.098 34.693 24.091 1 43.9 ? CAL 2PF 1 A 1 
HETATM 28 N NAM 2PF . . . B 2 -17.934 34.581 23.183 1 44.08 ? NAM 2PF 1 A 1 
HETATM 29 C CAN 2PF . . . B 2 -17.708 35.475 22.128 1 44.38 ? CAN 2PF 1 A 1 
HETATM 30 N NAO 2PF . . . B 2 -16.641 35.317 21.351 1 45.01 ? NAO 2PF 1 A 1 
HETATM 31 C CAP 2PF . . . B 2 -18.591 36.519 21.88 1 44.38 ? CAP 2PF 1 A 1 
HETATM 32 N NAQ 2PF . . . B 2 -18.607 37.483 20.964 1 44.39 ? NAQ 2PF 1 A 1 
HETATM 33 C CAR 2PF . . . B 2 -19.705 38.213 21.146 1 44.16 ? CAR 2PF 1 A 1 
HETATM 34 O OAW 2PF . . . B 2 -26.623 40.516 18.82 1 42 ? OAW 2PF 1 A 1 
HETATM 35 P PAX 2PF . . . B 2 -28.202 40.227 18.952 1 42.74 ? PAX 2PF 1 A 1 
HETATM 36 O OAY 2PF . . . B 2 -28.668 39.529 17.734 1 42.48 ? OAY 2PF 1 A 1 
HETATM 37 O OAZ 2PF . . . B 2 -28.472 39.606 20.269 1 43.28 ? OAZ 2PF 1 A 1 
HETATM 38 O OBA 2PF . . . B 2 -28.844 41.703 18.972 1 43.42 ? OBA 2PF 1 A 1 
HETATM 39 C CBB 2PF . . . B 2 -28.882 42.482 17.773 1 44.51 ? CBB 2PF 1 A 1 
HETATM 40 C CBC 2PF . . . B 2 -29.364 43.906 18.054 1 45.64 ? CBC 2PF 1 A 1 
HETATM 41 O OBD 2PF . . . B 2 -28.591 44.471 19.116 1 45.99 ? OBD 2PF 1 A 1 
HETATM 42 C CBE 2PF . . . B 2 -29.238 44.771 16.799 1 46.78 ? CBE 2PF 1 A 1 
HETATM 43 O OBF 2PF . . . B 2 -30.137 44.285 15.799 1 46.72 ? OBF 2PF 1 A 1 
HETATM 44 C CBG 2PF . . . B 2 -29.551 46.241 17.09 1 47.77 ? CBG 2PF 1 A 1 
HETATM 45 O OBH 2PF . . . B 2 -28.696 46.719 18.132 1 47.63 ? OBH 2PF 1 A 1 
HETATM 46 C CBI 2PF . . . B 2 -29.344 47.084 15.831 1 49.59 ? CBI 2PF 1 A 1 
HETATM 47 N NBJ 2PF . . . B 2 -29.425 48.532 16.127 1 51.15 ? NBJ 2PF 1 A 1 
HETATM 48 C CBK 2PF . . . B 2 -30.657 49.172 16.278 1 52.28 ? CBK 2PF 1 A 1 
HETATM 49 N NBL 2PF . . . B 2 -31.851 48.447 16.202 1 51.74 ? NBL 2PF 1 A 1 
HETATM 50 C CBM 2PF . . . B 2 -33.081 49.078 16.426 1 52.25 ? CBM 2PF 1 A 1 
HETATM 51 O OBN 2PF . . . B 2 -34.118 48.42 16.353 1 52.51 ? OBN 2PF 1 A 1 
HETATM 52 N NBO 2PF . . . B 2 -33.138 50.44 16.746 1 52.7 ? NBO 2PF 1 A 1 
HETATM 53 C CBP 2PF . . . B 2 -31.982 51.23 16.813 1 53.33 ? CBP 2PF 1 A 1 
HETATM 54 O OBQ 2PF . . . B 2 -32.077 52.409 17.148 1 53.26 ? OBQ 2PF 1 A 1 
HETATM 55 C CBR 2PF . . . B 2 -30.665 50.702 16.237 1 53.86 ? CBR 2PF 1 A 1 
HETATM 56 N NBS 2PF . . . B 2 -29.496 51.258 16.94 1 53.96 ? NBS 2PF 1 A 1 
HETATM 57 C CBT 2PF . . . B 2 -28.268 49.27 16.4 1 51.47 ? CBT 2PF 1 A 1 
HETATM 58 C CBU 2PF . . . B 2 -28.346 50.627 16.699 1 52.28 ? CBU 2PF 1 A 1 
HETATM 59 C CBV 2PF . . . B 2 -27.032 48.636 16.339 1 51.57 ? CBV 2PF 1 A 1 
HETATM 60 C CBW 2PF . . . B 2 -27.167 51.336 16.908 1 51.8 ? CBW 2PF 1 A 1 
HETATM 61 C CBX 2PF . . . B 2 -25.929 50.708 16.845 1 51.37 ? CBX 2PF 1 A 1 
HETATM 62 C CBY 2PF . . . B 2 -24.651 51.517 17.074 1 51 ? CBY 2PF 1 A 1 
HETATM 63 C CBZ 2PF . . . B 2 -30.422 51.23 14.82 1 56.29 ? CBZ 2PF 1 A 1 
HETATM 64 C CCA 2PF . . . B 2 -30.146 52.703 15.12 1 55.83 ? CCA 2PF 1 A 1 
HETATM 65 C CCB 2PF . . . B 2 -29.315 52.618 16.402 1 55.12 ? CCB 2PF 1 A 1 
HETATM 66 O OCC 2PF . . . B 2 -29.786 53.582 17.347 1 56.16 ? OCC 2PF 1 A 1 
HETATM 67 C CCD 2PF . . . B 2 -24.636 48.693 16.565 1 51.48 ? CCD 2PF 1 A 1 
HETATM 68 C CCE 2PF . . . B 2 -25.862 49.348 16.567 1 51.48 ? CCE 2PF 1 A 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           68 
#