data_6R4T
#
_model_server_result.job_id            JyFck-wrKrhbSsiL-dDJpA 
_model_server_result.datetime_utc      '2024-10-19 23:47:19' 
_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":"J","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 . . . J 4 -1.373 36.85 -1.023 1 153.91 ? N6 HEJ 503 D 1 
HETATM 2 C C6 HEJ . . . J 4 -0.712 36.322 0.008 1 154.14 ? C6 HEJ 503 D 1 
HETATM 3 N N1 HEJ . . . J 4 0.391 35.58 -0.244 1 155.01 ? N1 HEJ 503 D 1 
HETATM 4 C C2 HEJ . . . J 4 1.059 35.05 0.788 1 154.33 ? C2 HEJ 503 D 1 
HETATM 5 N N3 HEJ . . . J 4 0.799 35.138 2.093 1 154.02 ? N3 HEJ 503 D 1 
HETATM 6 C C4 HEJ . . . J 4 -0.297 35.876 2.312 1 151.63 ? C4 HEJ 503 D 1 
HETATM 7 C C5 HEJ . . . J 4 -1.093 36.488 1.355 1 152.51 ? C5 HEJ 503 D 1 
HETATM 8 N N7 HEJ . . . J 4 -2.146 37.162 1.955 1 150.67 ? N7 HEJ 503 D 1 
HETATM 9 C C8 HEJ . . . J 4 -1.972 36.935 3.234 1 150.92 ? C8 HEJ 503 D 1 
HETATM 10 N N9 HEJ . . . J 4 -0.885 36.153 3.521 1 148.89 ? N9 HEJ 503 D 1 
HETATM 11 C C1' HEJ . . . J 4 -0.397 35.753 4.839 1 143.53 ? C1' HEJ 503 D 1 
HETATM 12 O O4' HEJ . . . J 4 -1.307 34.826 5.402 1 144.36 ? O4' HEJ 503 D 1 
HETATM 13 C C4' HEJ . . . J 4 -1.631 35.24 6.743 1 144.9 ? C4' HEJ 503 D 1 
HETATM 14 C C5' HEJ . . . J 4 -2.994 34.735 7.112 1 152.07 ? C5' HEJ 503 D 1 
HETATM 15 O O5' HEJ . . . J 4 -3.952 35.195 6.13 1 159.05 ? O5' HEJ 503 D 1 
HETATM 16 P PA HEJ . . . J 4 -5.334 35.764 6.615 1 159.84 ? PA HEJ 503 D 1 
HETATM 17 O O2A HEJ . . . J 4 -5.876 34.798 7.673 1 161.99 ? O2A HEJ 503 D 1 
HETATM 18 O O1A HEJ . . . J 4 -6.321 36.061 5.554 1 158.96 ? O1A HEJ 503 D 1 
HETATM 19 O O3A HEJ . . . J 4 -4.915 37.095 7.379 1 153.42 ? O3A HEJ 503 D 1 
HETATM 20 P PB HEJ . . . J 4 -4.6 37.4 8.909 1 153.27 ? PB HEJ 503 D 1 
HETATM 21 O O1B HEJ . . . J 4 -3.291 38.07 9.022 1 159.4 ? O1B HEJ 503 D 1 
HETATM 22 O O2B HEJ . . . J 4 -4.636 36.103 9.736 1 138.25 ? O2B HEJ 503 D 1 
HETATM 23 O O3B HEJ . . . J 4 -5.755 38.342 9.46 1 152.59 ? O3B HEJ 503 D 1 
HETATM 24 P PG HEJ . . . J 4 -7.277 37.932 9.681 1 157.41 ? PG HEJ 503 D 1 
HETATM 25 O O3G HEJ . . . J 4 -7.659 38.398 11.052 1 157.81 ? O3G HEJ 503 D 1 
HETATM 26 O O2G HEJ . . . J 4 -7.321 36.422 9.716 1 162.55 ? O2G HEJ 503 D 1 
HETATM 27 O O1G HEJ . . . J 4 -8.098 38.481 8.62 1 158.88 ? O1G HEJ 503 D 1 
HETATM 28 C C3' HEJ . . . J 4 -1.468 36.748 6.713 1 138.67 ? C3' HEJ 503 D 1 
HETATM 29 O O3' HEJ . . . J 4 -1.245 37.25 8.028 1 134.95 ? O3' HEJ 503 D 1 
HETATM 30 C C2' HEJ . . . J 4 -0.228 36.909 5.835 1 138.27 ? C2' HEJ 503 D 1 
HETATM 31 O O31 HEJ . . . J 4 -0.29 38.15 5.135 1 135.85 ? O31 HEJ 503 D 1 
HETATM 32 H H1 HEJ . . . J 4 -1.061 36.704 -1.978 1 184.66 ? H1 HEJ 503 D 1 
HETATM 33 H H2 HEJ . . . J 4 -2.205 37.413 -0.882 1 184.66 ? H2 HEJ 503 D 1 
HETATM 34 H H3 HEJ . . . J 4 1.937 34.468 0.512 1 185.17 ? H3 HEJ 503 D 1 
HETATM 35 H H4 HEJ . . . J 4 -2.624 37.327 4.014 1 181.07 ? H4 HEJ 503 D 1 
HETATM 36 H H5 HEJ . . . J 4 0.538 35.213 4.695 1 172.2 ? H5 HEJ 503 D 1 
HETATM 37 H H6 HEJ . . . J 4 -0.876 34.768 7.371 1 173.85 ? H6 HEJ 503 D 1 
HETATM 38 H H7 HEJ . . . J 4 -3.001 33.647 7.145 1 182.46 ? H7 HEJ 503 D 1 
HETATM 39 H H8 HEJ . . . J 4 -3.281 35.097 8.098 1 182.46 ? H8 HEJ 503 D 1 
HETATM 40 H H13 HEJ . . . J 4 -2.34 37.243 6.287 1 166.38 ? H13 HEJ 503 D 1 
HETATM 41 H H14 HEJ . . . J 4 -0.897 36.489 8.563 1 161.91 ? H14 HEJ 503 D 1 
HETATM 42 H H15 HEJ . . . J 4 0.702 36.809 6.393 1 165.89 ? H15 HEJ 503 D 1 
HETATM 43 H H16 HEJ . . . J 4 0.487 38.681 5.449 1 162.99 ? H16 HEJ 503 D 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#