data_6R4T
#
_model_server_result.job_id            bZLlDBM0n5FLt36F92PuMw 
_model_server_result.datetime_utc      '2024-11-29 04:18:55' 
_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          6r4t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":503}' 
#
_entry.id    6R4T 
#
_exptl.entry_id    6R4T 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine 
_entity.pdbx_number_of_molecules    2 
_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            6R4T 
_cell.length_a            111.09 
_cell.length_b            118.97 
_cell.length_c            150.72 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6R4T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    'C 2c 2' 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,K 1 1 
B,H,I,J,L 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 E N N 
? 4 J N 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 OD1 ASP 112 A ASP 109 1_555 D MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc2 A OD1 ASP 114 A ASP 111 1_555 D MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc3 A SG CYS 124 A CYS 121 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
metalc ? metalc4 A SG CYS 125 A CYS 122 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc5 A SG CYS 131 A CYS 128 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc6 A SG CYS 134 A CYS 131 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? 
metalc ? metalc7 D MN MN . A MN 502 1_555 E O2B HEJ . A HEJ 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? 
metalc ? metalc8 D MN MN . A MN 502 1_555 E O2G HEJ . A HEJ 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? 
metalc ? metalc9 D MN MN . A MN 502 1_555 E O2A HEJ . A HEJ 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc10 D MN MN . A MN 502 1_555 K O HOH . A HOH 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? 
metalc ? metalc11 B OD1 ASP 112 D ASP 109 1_555 I MN MN . D MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc12 B OD1 ASP 114 D ASP 111 1_555 I MN MN . D MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc13 B SG CYS 124 D CYS 121 1_555 H ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc14 B SG CYS 125 D CYS 122 1_555 H ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
metalc ? metalc15 B SG CYS 131 D CYS 128 1_555 H ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc16 B SG CYS 134 D CYS 131 1_555 H ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? 
metalc ? metalc17 I MN MN . D MN 502 1_555 J O2A HEJ . D HEJ 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc18 I MN MN . D MN 502 1_555 J O2G HEJ . D HEJ 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? 
metalc ? metalc19 I MN MN . D MN 502 1_555 J O2B HEJ . D HEJ 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc20 I MN MN . D MN 502 1_555 L O HOH . D HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                HEJ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Vidarabine-TRIPHOSPHATE 
#
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
O3G PG HEJ doub 138 n n 
O1G PG HEJ sing 139 n n 
PG O2G HEJ sing 140 n n 
PG O3B HEJ sing 141 n n 
O1B PB HEJ doub 142 n n 
O3B PB HEJ sing 143 n n 
O31 C2' HEJ sing 144 n n 
PB O3A HEJ sing 145 n n 
PB O2B HEJ sing 146 n n 
C3' O3' HEJ sing 147 n n 
C3' C2' HEJ sing 148 n n 
C3' C4' HEJ sing 149 n n 
C5' C4' HEJ sing 150 n n 
C5' O5' HEJ sing 151 n n 
O3A PA HEJ sing 152 n n 
C2' C1' HEJ sing 153 n n 
C4' O4' HEJ sing 154 n n 
O5' PA HEJ sing 155 n n 
O2A PA HEJ doub 156 n n 
PA O1A HEJ sing 157 n n 
C1' O4' HEJ sing 158 n n 
C1' N9 HEJ sing 159 n n 
C8 N9 HEJ sing 160 n y 
C8 N7 HEJ doub 161 n y 
N9 C4 HEJ sing 162 n y 
N7 C5 HEJ sing 163 n y 
C4 C5 HEJ doub 164 n y 
C4 N3 HEJ sing 165 n y 
C5 C6 HEJ sing 166 n y 
N3 C2 HEJ doub 167 n y 
C6 N6 HEJ sing 168 n n 
C6 N1 HEJ doub 169 n y 
C2 N1 HEJ sing 170 n y 
N6 H1 HEJ sing 171 n n 
N6 H2 HEJ sing 172 n n 
C2 H3 HEJ sing 173 n n 
C8 H4 HEJ sing 174 n n 
C1' H5 HEJ sing 175 n n 
C4' H6 HEJ sing 176 n n 
C5' H7 HEJ sing 177 n n 
C5' H8 HEJ sing 178 n n 
O1A H9 HEJ sing 179 n n 
O2B H10 HEJ sing 180 n n 
O2G H11 HEJ sing 181 n n 
O1G H12 HEJ sing 182 n n 
C3' H13 HEJ sing 183 n n 
O3' H14 HEJ sing 184 n n 
C2' H15 HEJ sing 185 n n 
O31 H16 HEJ sing 186 n n 
#
_atom_sites.entry_id                     6R4T 
_atom_sites.fract_transf_matrix[1][1]    0.009002 
_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]    0.008405 
_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]    0.006635 
_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
C 2 ZN A 1 501 430 ZN ZN . 
D 3 MN A 1 502 1 MN MN . 
E 4 HEJ A 1 503 1 HEJ HEJ . 
F 5 EDO A 1 504 1 EDO EDO . 
G 5 EDO A 1 505 2 EDO EDO . 
H 2 ZN D 1 501 430 ZN ZN . 
I 3 MN D 1 502 1 MN MN . 
J 4 HEJ D 1 503 1 HEJ HEJ . 
K 6 HOH A 1 601 26 HOH HOH . 
K 6 HOH A 2 602 77 HOH HOH . 
K 6 HOH A 3 603 35 HOH HOH . 
K 6 HOH A 4 604 48 HOH HOH . 
K 6 HOH A 5 605 22 HOH HOH . 
K 6 HOH A 6 606 15 HOH HOH . 
K 6 HOH A 7 607 32 HOH HOH . 
K 6 HOH A 8 608 30 HOH HOH . 
K 6 HOH A 9 609 37 HOH HOH . 
K 6 HOH A 10 610 47 HOH HOH . 
K 6 HOH A 11 611 33 HOH HOH . 
K 6 HOH A 12 612 80 HOH HOH . 
K 6 HOH A 13 613 27 HOH HOH . 
K 6 HOH A 14 614 81 HOH HOH . 
K 6 HOH A 15 615 36 HOH HOH . 
K 6 HOH A 16 616 43 HOH HOH . 
K 6 HOH A 17 617 14 HOH HOH . 
K 6 HOH A 18 618 64 HOH HOH . 
K 6 HOH A 19 619 9 HOH HOH . 
K 6 HOH A 20 620 46 HOH HOH . 
K 6 HOH A 21 621 34 HOH HOH . 
K 6 HOH A 22 622 39 HOH HOH . 
K 6 HOH A 23 623 50 HOH HOH . 
K 6 HOH A 24 624 44 HOH HOH . 
K 6 HOH A 25 625 49 HOH HOH . 
L 6 HOH D 1 601 10 HOH HOH . 
L 6 HOH D 2 602 59 HOH HOH . 
L 6 HOH D 3 603 54 HOH HOH . 
L 6 HOH D 4 604 21 HOH HOH . 
L 6 HOH D 5 605 55 HOH HOH . 
L 6 HOH D 6 606 78 HOH HOH . 
L 6 HOH D 7 607 11 HOH HOH . 
L 6 HOH D 8 608 51 HOH HOH . 
L 6 HOH D 9 609 66 HOH HOH . 
L 6 HOH D 10 610 1 HOH HOH . 
L 6 HOH D 11 611 52 HOH HOH . 
L 6 HOH D 12 612 73 HOH HOH . 
L 6 HOH D 13 613 7 HOH HOH . 
L 6 HOH D 14 614 68 HOH HOH . 
L 6 HOH D 15 615 5 HOH HOH . 
L 6 HOH D 16 616 58 HOH HOH . 
L 6 HOH D 17 617 3 HOH HOH . 
L 6 HOH D 18 618 2 HOH HOH . 
L 6 HOH D 19 619 6 HOH HOH . 
L 6 HOH D 20 620 82 HOH HOH . 
L 6 HOH D 21 621 12 HOH HOH . 
L 6 HOH D 22 622 70 HOH HOH . 
L 6 HOH D 23 623 20 HOH HOH . 
L 6 HOH D 24 624 19 HOH HOH . 
L 6 HOH D 25 625 13 HOH HOH . 
L 6 HOH D 26 626 74 HOH HOH . 
L 6 HOH D 27 627 4 HOH HOH . 
L 6 HOH D 28 628 17 HOH HOH . 
L 6 HOH D 29 629 16 HOH HOH . 
L 6 HOH D 30 630 72 HOH HOH . 
L 6 HOH D 31 631 56 HOH HOH . 
L 6 HOH D 32 632 57 HOH HOH . 
L 6 HOH D 33 633 67 HOH HOH . 
L 6 HOH D 34 634 45 HOH HOH . 
L 6 HOH D 35 635 53 HOH HOH . 
L 6 HOH D 36 636 61 HOH HOH . 
L 6 HOH D 37 637 29 HOH HOH . 
L 6 HOH D 38 638 38 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 N N6 HEJ . . . E 4 23.794 6.65 39.078 1 147.11 ? N6 HEJ 503 A 1 
HETATM 2 C C6 HEJ . . . E 4 24.225 5.755 38.188 1 145.46 ? C6 HEJ 503 A 1 
HETATM 3 N N1 HEJ . . . E 4 24.606 4.537 38.638 1 145.83 ? N1 HEJ 503 A 1 
HETATM 4 C C2 HEJ . . . E 4 25.04 3.628 37.752 1 145.88 ? C2 HEJ 503 A 1 
HETATM 5 N N3 HEJ . . . E 4 25.167 3.741 36.427 1 145.55 ? N3 HEJ 503 A 1 
HETATM 6 C C4 HEJ . . . E 4 24.79 4.954 36.011 1 143.33 ? C4 HEJ 503 A 1 
HETATM 7 C C5 HEJ . . . E 4 24.315 5.996 36.799 1 144.48 ? C5 HEJ 503 A 1 
HETATM 8 N N7 HEJ . . . E 4 24.009 7.098 36.016 1 144.07 ? N7 HEJ 503 A 1 
HETATM 9 C C8 HEJ . . . E 4 24.296 6.704 34.796 1 143.4 ? C8 HEJ 503 A 1 
HETATM 10 N N9 HEJ . . . E 4 24.77 5.422 34.72 1 140.57 ? N9 HEJ 503 A 1 
HETATM 11 C C1' HEJ . . . E 4 25.174 4.723 33.498 1 134.23 ? C1' HEJ 503 A 1 
HETATM 12 O O4' HEJ . . . E 4 26.051 5.567 32.764 1 133.52 ? O4' HEJ 503 A 1 
HETATM 13 C C4' HEJ . . . E 4 25.541 5.722 31.422 1 132.39 ? C4' HEJ 503 A 1 
HETATM 14 C C5' HEJ . . . E 4 25.982 7.028 30.827 1 131.86 ? C5' HEJ 503 A 1 
HETATM 15 O O5' HEJ . . . E 4 25.554 8.146 31.632 1 128.72 ? O5' HEJ 503 A 1 
HETATM 16 P PA HEJ . . . E 4 24.935 9.374 30.868 1 123.01 ? PA HEJ 503 A 1 
HETATM 17 O O2A HEJ . . . E 4 25.828 9.666 29.652 1 124.63 ? O2A HEJ 503 A 1 
HETATM 18 O O1A HEJ . . . E 4 24.757 10.591 31.685 1 122.87 ? O1A HEJ 503 A 1 
HETATM 19 O O3A HEJ . . . E 4 23.527 8.891 30.302 1 122.86 ? O3A HEJ 503 A 1 
HETATM 20 P PB HEJ . . . E 4 23.081 8.344 28.873 1 119.37 ? PB HEJ 503 A 1 
HETATM 21 O O1B HEJ . . . E 4 22.31 7.099 29.015 1 114.81 ? O1B HEJ 503 A 1 
HETATM 22 O O2B HEJ . . . E 4 24.312 8.19 27.967 1 116.74 ? O2B HEJ 503 A 1 
HETATM 23 O O3B HEJ . . . E 4 22.175 9.499 28.264 1 117.45 ? O3B HEJ 503 A 1 
HETATM 24 P PG HEJ . . . E 4 22.635 10.969 27.872 1 114.77 ? PG HEJ 503 A 1 
HETATM 25 O O3G HEJ . . . E 4 22.137 11.24 26.483 1 112.39 ? O3G HEJ 503 A 1 
HETATM 26 O O2G HEJ . . . E 4 24.142 10.934 27.77 1 118.52 ? O2G HEJ 503 A 1 
HETATM 27 O O1G HEJ . . . E 4 22.152 11.905 28.874 1 112.58 ? O1G HEJ 503 A 1 
HETATM 28 C C3' HEJ . . . E 4 24.044 5.576 31.596 1 130.05 ? C3' HEJ 503 A 1 
HETATM 29 O O3' HEJ . . . E 4 23.426 5.252 30.357 1 127.75 ? O3' HEJ 503 A 1 
HETATM 30 C C2' HEJ . . . E 4 23.969 4.431 32.597 1 129.76 ? C2' HEJ 503 A 1 
HETATM 31 O O31 HEJ . . . E 4 22.772 4.451 33.372 1 128.71 ? O31 HEJ 503 A 1 
HETATM 32 H H1 HEJ . . . E 4 23.748 6.427 40.067 1 176.5 ? H1 HEJ 503 A 1 
HETATM 33 H H2 HEJ . . . E 4 23.501 7.578 38.791 1 176.5 ? H2 HEJ 503 A 1 
HETATM 34 H H3 HEJ . . . E 4 25.327 2.67 38.182 1 175.03 ? H3 HEJ 503 A 1 
HETATM 35 H H4 HEJ . . . E 4 24.173 7.33 33.913 1 172.05 ? H4 HEJ 503 A 1 
HETATM 36 H H5 HEJ . . . E 4 25.754 3.838 33.753 1 161.05 ? H5 HEJ 503 A 1 
HETATM 37 H H6 HEJ . . . E 4 25.99 4.897 30.872 1 158.84 ? H6 HEJ 503 A 1 
HETATM 38 H H7 HEJ . . . E 4 27.067 7.048 30.742 1 158.2 ? H7 HEJ 503 A 1 
HETATM 39 H H8 HEJ . . . E 4 25.571 7.136 29.825 1 158.2 ? H8 HEJ 503 A 1 
HETATM 40 H H13 HEJ . . . E 4 23.581 6.482 31.983 1 156.03 ? H13 HEJ 503 A 1 
HETATM 41 H H14 HEJ . . . E 4 23.238 4.278 30.383 1 153.27 ? H14 HEJ 503 A 1 
HETATM 42 H H15 HEJ . . . E 4 24.063 3.469 32.096 1 155.68 ? H15 HEJ 503 A 1 
HETATM 43 H H16 HEJ . . . E 4 22.603 3.51 33.638 1 154.42 ? H16 HEJ 503 A 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           409 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           43 
#