data_4EK9
#
_model_server_result.job_id            YPEwHQOhyVbUdoFgQwUupA 
_model_server_result.datetime_utc      '2024-10-12 19:28:39' 
_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          4ek9 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    4EK9 
#
_exptl.entry_id    4EK9 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              294.31 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-deoxy-5'-(dimethylamino)adenosine" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
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_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            4EK9 
_cell.length_a            152.81 
_cell.length_b            152.81 
_cell.length_c            51.37 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 4EK9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
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_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
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_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           'C12 H18 N6 O3' 
_chem_comp.formula_weight    294.31 
_chem_comp.id                EP4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-deoxy-5'-(dimethylamino)adenosine" 
_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
CE N2 EP4 sing 83 n n 
CG N2 EP4 sing 84 n n 
N2 C5' EP4 sing 85 n n 
C5' C4' EP4 sing 86 n n 
C4' O4' EP4 sing 87 n n 
C4' C3' EP4 sing 88 n n 
O4' C1' EP4 sing 89 n n 
C3' O3' EP4 sing 90 n n 
C3' C2' EP4 sing 91 n n 
C1' N9 EP4 sing 92 n n 
C1' C2' EP4 sing 93 n n 
N3 C2 EP4 doub 94 n y 
N3 C4 EP4 sing 95 n y 
C2 N1 EP4 sing 96 n y 
N9 C4 EP4 sing 97 n y 
N9 C8 EP4 sing 98 n y 
C4 C5 EP4 doub 99 n y 
N1 C6 EP4 doub 100 n y 
C2' O2' EP4 sing 101 n n 
C8 N7 EP4 doub 102 n y 
C5 C6 EP4 sing 103 n y 
C5 N7 EP4 sing 104 n y 
C6 N6 EP4 sing 105 n n 
CG H1 EP4 sing 106 n n 
CG H2 EP4 sing 107 n n 
CG H3 EP4 sing 108 n n 
CE H5 EP4 sing 109 n n 
CE H6 EP4 sing 110 n n 
CE H7 EP4 sing 111 n n 
C5' H8 EP4 sing 112 n n 
C5' H9 EP4 sing 113 n n 
C4' H10 EP4 sing 114 n n 
C1' H11 EP4 sing 115 n n 
C2 H12 EP4 sing 116 n n 
N6 H13 EP4 sing 117 n n 
N6 H14 EP4 sing 118 n n 
C8 H15 EP4 sing 119 n n 
C2' H16 EP4 sing 120 n n 
O2' H17 EP4 sing 121 n n 
C3' H18 EP4 sing 122 n n 
O3' H19 EP4 sing 123 n n 
#
_atom_sites.entry_id                     4EK9 
_atom_sites.fract_transf_matrix[1][1]    0.006544 
_atom_sites.fract_transf_matrix[1][2]    0.003778 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007556 
_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]    0.019467 
_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 EP4 A 1 501 500 EP4 EPZ . 
C 3 SO4 A 1 502 1 SO4 SO4 . 
D 3 SO4 A 1 503 2 SO4 SO4 . 
E 4 GOL A 1 504 3 GOL GOL . 
F 5 HOH A 1 601 1 HOH HOH . 
F 5 HOH A 2 602 2 HOH HOH . 
F 5 HOH A 3 603 3 HOH HOH . 
F 5 HOH A 4 604 4 HOH HOH . 
F 5 HOH A 5 605 5 HOH HOH . 
F 5 HOH A 6 606 6 HOH HOH . 
F 5 HOH A 7 607 7 HOH HOH . 
F 5 HOH A 8 608 8 HOH HOH . 
F 5 HOH A 9 609 9 HOH HOH . 
F 5 HOH A 10 610 10 HOH HOH . 
F 5 HOH A 11 611 11 HOH HOH . 
F 5 HOH A 12 612 12 HOH HOH . 
F 5 HOH A 13 613 13 HOH HOH . 
F 5 HOH A 14 614 14 HOH HOH . 
F 5 HOH A 15 615 15 HOH HOH . 
F 5 HOH A 16 616 16 HOH HOH . 
F 5 HOH A 17 617 17 HOH HOH . 
F 5 HOH A 18 618 18 HOH HOH . 
F 5 HOH A 19 619 19 HOH HOH . 
F 5 HOH A 20 620 20 HOH HOH . 
F 5 HOH A 21 621 21 HOH HOH . 
F 5 HOH A 22 622 22 HOH HOH . 
F 5 HOH A 23 623 23 HOH HOH . 
F 5 HOH A 24 624 24 HOH HOH . 
F 5 HOH A 25 625 25 HOH HOH . 
F 5 HOH A 26 626 26 HOH HOH . 
F 5 HOH A 27 627 27 HOH HOH . 
F 5 HOH A 28 628 28 HOH HOH . 
F 5 HOH A 29 629 29 HOH HOH . 
F 5 HOH A 30 630 30 HOH HOH . 
F 5 HOH A 31 631 31 HOH HOH . 
F 5 HOH A 32 632 32 HOH HOH . 
F 5 HOH A 33 633 33 HOH HOH . 
F 5 HOH A 34 634 34 HOH HOH . 
F 5 HOH A 35 635 35 HOH HOH . 
F 5 HOH A 36 636 36 HOH HOH . 
F 5 HOH A 37 637 37 HOH HOH . 
F 5 HOH A 38 638 38 HOH HOH . 
F 5 HOH A 39 639 39 HOH HOH . 
F 5 HOH A 40 640 40 HOH HOH . 
F 5 HOH A 41 641 41 HOH HOH . 
F 5 HOH A 42 642 42 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 C CG EP4 . . . B 2 45.824 53.269 9.259 1 41.18 ? CG EP4 501 A 1 
HETATM 2 N N2 EP4 . . . B 2 44.652 52.631 9.884 1 40.57 ? N2 EP4 501 A 1 
HETATM 3 C CE EP4 . . . B 2 43.519 52.821 8.975 1 41.98 ? CE EP4 501 A 1 
HETATM 4 C C5' EP4 . . . B 2 44.952 51.204 10.134 1 40.82 ? C5' EP4 501 A 1 
HETATM 5 C C4' EP4 . . . B 2 43.985 50.548 11.145 1 43.51 ? C4' EP4 501 A 1 
HETATM 6 O O4' EP4 . . . B 2 44.46 49.189 11.298 1 47.44 ? O4' EP4 501 A 1 
HETATM 7 C C1' EP4 . . . B 2 44.044 48.773 12.618 1 43.25 ? C1' EP4 501 A 1 
HETATM 8 N N9 EP4 . . . B 2 44.765 47.55 13.077 1 45.53 ? N9 EP4 501 A 1 
HETATM 9 C C4 EP4 . . . B 2 44.213 46.32 13.079 1 46.37 ? C4 EP4 501 A 1 
HETATM 10 N N3 EP4 . . . B 2 42.987 45.889 12.705 1 43.01 ? N3 EP4 501 A 1 
HETATM 11 C C2 EP4 . . . B 2 42.67 44.513 12.812 1 47.92 ? C2 EP4 501 A 1 
HETATM 12 N N1 EP4 . . . B 2 43.635 43.623 13.316 1 47.25 ? N1 EP4 501 A 1 
HETATM 13 C C6 EP4 . . . B 2 44.842 44.129 13.674 1 49.02 ? C6 EP4 501 A 1 
HETATM 14 N N6 EP4 . . . B 2 45.806 43.31 14.132 1 49.35 ? N6 EP4 501 A 1 
HETATM 15 C C5 EP4 . . . B 2 45.143 45.453 13.555 1 48.16 ? C5 EP4 501 A 1 
HETATM 16 N N7 EP4 . . . B 2 46.266 46.175 13.831 1 47.49 ? N7 EP4 501 A 1 
HETATM 17 C C8 EP4 . . . B 2 46.03 47.462 13.534 1 45.28 ? C8 EP4 501 A 1 
HETATM 18 C C2' EP4 . . . B 2 44.439 49.932 13.458 1 42.31 ? C2' EP4 501 A 1 
HETATM 19 O O2' EP4 . . . B 2 43.608 49.845 14.644 1 41.44 ? O2' EP4 501 A 1 
HETATM 20 C C3' EP4 . . . B 2 44.103 51.142 12.56 1 41.51 ? C3' EP4 501 A 1 
HETATM 21 O O3' EP4 . . . B 2 42.804 51.603 12.929 1 40.55 ? O3' EP4 501 A 1 
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_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           21 
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