data_6PKX
#
_model_server_result.job_id            opEYxRCYetWTKK6U2MsRNA 
_model_server_result.datetime_utc      '2025-02-05 09:56:32' 
_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          6pkx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1602}' 
#
_entry.id    6PKX 
#
_exptl.entry_id    6PKX 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_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            6PKX 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PKX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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    ? 
_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
? 3 F N N 
? 3 H 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
disulf ? disulf1 A SG CYS 304 A CYS 303 1_555 A SG CYS 327 A CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf2 A SG CYS 1013 A CYS 1012 1_555 A SG CYS 1025 A CYS 1024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
disulf ? disulf3 B SG CYS 304 B CYS 303 1_555 B SG CYS 327 B CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
disulf ? disulf4 B SG CYS 1013 B CYS 1012 1_555 B SG CYS 1025 B CYS 1024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf5 C SG CYS 304 C CYS 303 1_555 C SG CYS 327 C CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf6 C SG CYS 1013 C CYS 1012 1_555 C SG CYS 1025 C CYS 1024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
disulf ? disulf7 D SG CYS 304 D CYS 303 1_555 D SG CYS 327 D CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
disulf ? disulf8 D SG CYS 1013 D CYS 1012 1_555 D SG CYS 1025 D CYS 1024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc1 B OE1 GLN 861 B GLN 860 1_555 E CA CA . B CA 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc2 B OD1 ASN 884 B ASN 883 1_555 E CA CA . B CA 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? 
metalc ? metalc3 D OE1 GLN 861 D GLN 860 1_555 G CA CA . D CA 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc4 D OD1 ASN 884 D ASN 883 1_555 G CA CA . D CA 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? 
#
_chem_comp.formula           'C15 H23 N5 O14 P2' 
_chem_comp.formula_weight    559.316 
_chem_comp.id                AR6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Adenosine-5-Diphosphoribose 
#
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
N1 C2 AR6 doub 13 n y 
N1 C6 AR6 sing 14 n y 
C2 N3 AR6 sing 15 n y 
N3 C4 AR6 doub 16 n y 
C4 C5 AR6 sing 17 n y 
C4 N9 AR6 sing 18 n y 
C5 C6 AR6 doub 19 n y 
C5 N7 AR6 sing 20 n y 
C6 N6 AR6 sing 21 n n 
N7 C8 AR6 doub 22 n y 
C8 N9 AR6 sing 23 n y 
N9 C1' AR6 sing 24 n n 
PA O1A AR6 sing 25 n n 
PA O2A AR6 doub 26 n n 
PA O3A AR6 sing 27 n n 
PA O5' AR6 sing 28 n n 
PB O1B AR6 sing 29 n n 
PB O2B AR6 doub 30 n n 
PB O3A AR6 sing 31 n n 
PB O5D AR6 sing 32 n n 
C1' C2' AR6 sing 33 n n 
C1' O4' AR6 sing 34 n n 
C1D O1D AR6 sing 35 n n 
C1D C2D AR6 sing 36 n n 
C1D O4D AR6 sing 37 n n 
C2' O2' AR6 sing 38 n n 
C2' C3' AR6 sing 39 n n 
C2D O2D AR6 sing 40 n n 
C2D C3D AR6 sing 41 n n 
C3' O3' AR6 sing 42 n n 
C3' C4' AR6 sing 43 n n 
C3D O3D AR6 sing 44 n n 
C3D C4D AR6 sing 45 n n 
C4' O4' AR6 sing 46 n n 
C4' C5' AR6 sing 47 n n 
C4D O4D AR6 sing 48 n n 
C4D C5D AR6 sing 49 n n 
C5' O5' AR6 sing 50 n n 
C5D O5D AR6 sing 51 n n 
C2 H2 AR6 sing 52 n n 
N6 HN6 AR6 sing 53 n n 
N6 HN6A AR6 sing 54 n n 
C8 H8 AR6 sing 55 n n 
C1' H1' AR6 sing 56 n n 
C1D H1D AR6 sing 57 n n 
C2' H2' AR6 sing 58 n n 
O2' HO2' AR6 sing 59 n n 
C2D H2D AR6 sing 60 n n 
O2D HO2D AR6 sing 61 n n 
C3' H3' AR6 sing 62 n n 
O3' HO3' AR6 sing 63 n n 
C3D H3D AR6 sing 64 n n 
O3D HO3D AR6 sing 65 n n 
C4' H4' AR6 sing 66 n n 
C4D H4D AR6 sing 67 n n 
C5' H5' AR6 sing 68 n n 
C5' "H5'A" AR6 sing 69 n n 
C5D H5D AR6 sing 70 n n 
C5D H5DA AR6 sing 71 n n 
O1A H1A AR6 sing 72 n n 
O1B H1B AR6 sing 73 n n 
O1D HD1 AR6 sing 74 n n 
#
_atom_sites.entry_id                     6PKX 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
E 2 CA B 1 1601 1475 CA CA . 
F 3 AR6 B 1 1602 1476 AR6 ADR . 
G 2 CA D 1 1601 1475 CA CA . 
H 3 AR6 D 1 1602 1476 AR6 ADR . 
#
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 N1 AR6 . . . F 3 -128.548 197.993 139.78 1 30 ? N1 AR6 1602 B 1 
HETATM 2 C C2 AR6 . . . F 3 -129.151 199.161 139.825 1 30 ? C2 AR6 1602 B 1 
HETATM 3 N N3 AR6 . . . F 3 -129.931 199.576 138.855 1 30 ? N3 AR6 1602 B 1 
HETATM 4 C C4 AR6 . . . F 3 -130.133 198.821 137.783 1 30 ? C4 AR6 1602 B 1 
HETATM 5 C C5 AR6 . . . F 3 -129.522 197.598 137.701 1 30 ? C5 AR6 1602 B 1 
HETATM 6 C C6 AR6 . . . F 3 -128.705 197.201 138.754 1 30 ? C6 AR6 1602 B 1 
HETATM 7 N N6 AR6 . . . F 3 -128.03 195.927 138.735 1 30 ? N6 AR6 1602 B 1 
HETATM 8 N N7 AR6 . . . F 3 -129.886 197.05 136.54 1 30 ? N7 AR6 1602 B 1 
HETATM 9 C C8 AR6 . . . F 3 -130.7 197.89 135.937 1 30 ? C8 AR6 1602 B 1 
HETATM 10 N N9 AR6 . . . F 3 -130.842 198.975 136.678 1 30 ? N9 AR6 1602 B 1 
HETATM 11 P PA AR6 . . . F 3 -136.256 198.309 134.641 1 30 ? PA AR6 1602 B 1 
HETATM 12 P PB AR6 . . . F 3 -134.293 196.303 134.742 1 30 ? PB AR6 1602 B 1 
HETATM 13 C C1' AR6 . . . F 3 -131.624 200.146 136.413 1 30 ? C1' AR6 1602 B 1 
HETATM 14 O O1A AR6 . . . F 3 -136.007 197.948 133.206 1 30 ? O1A AR6 1602 B 1 
HETATM 15 O O1B AR6 . . . F 3 -133.286 197.165 134.038 1 30 ? O1B AR6 1602 B 1 
HETATM 16 C C1D AR6 . . . F 3 -132.278 192.21 137.696 1 30 ? C1D AR6 1602 B 1 
HETATM 17 O O1D AR6 . . . F 3 -131.688 192.068 138.988 1 30 ? O1D AR6 1602 B 1 
HETATM 18 C C2' AR6 . . . F 3 -131.135 200.826 135.414 1 30 ? C2' AR6 1602 B 1 
HETATM 19 O O2' AR6 . . . F 3 -130.235 201.891 135.934 1 30 ? O2' AR6 1602 B 1 
HETATM 20 O O2A AR6 . . . F 3 -137.729 198.155 134.928 1 30 ? O2A AR6 1602 B 1 
HETATM 21 O O2B AR6 . . . F 3 -135.032 195.463 133.736 1 30 ? O2B AR6 1602 B 1 
HETATM 22 C C2D AR6 . . . F 3 -131.236 191.966 136.574 1 30 ? C2D AR6 1602 B 1 
HETATM 23 O O2D AR6 . . . F 3 -130.195 191.253 137.059 1 30 ? O2D AR6 1602 B 1 
HETATM 24 C C3' AR6 . . . F 3 -132.325 201.436 134.719 1 30 ? C3' AR6 1602 B 1 
HETATM 25 O O3' AR6 . . . F 3 -132.373 202.763 134.957 1 30 ? O3' AR6 1602 B 1 
HETATM 26 O O3A AR6 . . . F 3 -135.353 197.272 135.524 1 30 ? O3A AR6 1602 B 1 
HETATM 27 C C3D AR6 . . . F 3 -130.713 193.319 136.182 1 30 ? C3D AR6 1602 B 1 
HETATM 28 O O3D AR6 . . . F 3 -129.397 193.539 136.891 1 30 ? O3D AR6 1602 B 1 
HETATM 29 C C4' AR6 . . . F 3 -133.562 200.746 135.363 1 30 ? C4' AR6 1602 B 1 
HETATM 30 O O4' AR6 . . . F 3 -133.108 199.725 135.96 1 30 ? O4' AR6 1602 B 1 
HETATM 31 C C4D AR6 . . . F 3 -131.646 194.155 136.53 1 30 ? C4D AR6 1602 B 1 
HETATM 32 O O4D AR6 . . . F 3 -132.658 193.408 137.547 1 30 ? O4D AR6 1602 B 1 
HETATM 33 C C5' AR6 . . . F 3 -134.561 200.268 134.277 1 30 ? C5' AR6 1602 B 1 
HETATM 34 O O5' AR6 . . . F 3 -135.732 199.843 134.912 1 30 ? O5' AR6 1602 B 1 
HETATM 35 C C5D AR6 . . . F 3 -132.449 194.589 135.332 1 30 ? C5D AR6 1602 B 1 
HETATM 36 O O5D AR6 . . . F 3 -133.505 195.348 135.808 1 30 ? O5D AR6 1602 B 1 
HETATM 37 H H2 AR6 . . . F 3 -129.016 199.699 140.568 1 30 ? H2 AR6 1602 B 1 
HETATM 38 H HN6 AR6 . . . F 3 -127.982 195.475 138.007 1 30 ? HN6 AR6 1602 B 1 
HETATM 39 H HN6A AR6 . . . F 3 -127.678 195.631 139.458 1 30 ? HN6A AR6 1602 B 1 
HETATM 40 H H8 AR6 . . . F 3 -131.097 197.763 135.104 1 30 ? H8 AR6 1602 B 1 
HETATM 41 H H1' AR6 . . . F 3 -131.684 200.712 137.196 1 30 ? H1' AR6 1602 B 1 
HETATM 42 H H1D AR6 . . . F 3 -133.028 191.609 137.604 1 30 ? H1D AR6 1602 B 1 
HETATM 43 H H2' AR6 . . . F 3 -130.646 200.298 134.777 1 30 ? H2' AR6 1602 B 1 
HETATM 44 H HO2' AR6 . . . F 3 -129.718 202.095 135.297 1 30 ? HO2' AR6 1602 B 1 
HETATM 45 H H2D AR6 . . . F 3 -131.649 191.543 135.81 1 30 ? H2D AR6 1602 B 1 
HETATM 46 H HO2D AR6 . . . F 3 -129.673 191.788 137.462 1 30 ? HO2D AR6 1602 B 1 
HETATM 47 H H3' AR6 . . . F 3 -132.279 201.263 133.772 1 30 ? H3' AR6 1602 B 1 
HETATM 48 H HO3' AR6 . . . F 3 -133.186 203 134.952 1 30 ? HO3' AR6 1602 B 1 
HETATM 49 H H3D AR6 . . . F 3 -130.572 193.348 135.23 1 30 ? H3D AR6 1602 B 1 
HETATM 50 H HO3D AR6 . . . F 3 -129.48 194.078 137.54 1 30 ? HO3D AR6 1602 B 1 
HETATM 51 H H4' AR6 . . . F 3 -133.985 201.347 135.989 1 30 ? H4' AR6 1602 B 1 
HETATM 52 H H4D AR6 . . . F 3 -131.277 194.928 136.961 1 30 ? H4D AR6 1602 B 1 
HETATM 53 H H5' AR6 . . . F 3 -134.755 200.999 133.677 1 30 ? H5' AR6 1602 B 1 
HETATM 54 H "H5'A" AR6 . . . F 3 -134.162 199.532 133.793 1 30 ? "H5'A" AR6 1602 B 1 
HETATM 55 H H5D AR6 . . . F 3 -132.799 193.812 134.883 1 30 ? H5D AR6 1602 B 1 
HETATM 56 H H5DA AR6 . . . F 3 -131.919 195.125 134.733 1 30 ? H5DA AR6 1602 B 1 
HETATM 57 H HD1 AR6 . . . F 3 -131.942 192.715 139.479 1 30 ? HD1 AR6 1602 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           57 
#