data_8K6I
#
_model_server_result.job_id            xYZ51r9anBngzK-Fqoxa2A 
_model_server_result.datetime_utc      '2025-02-24 20:42:41' 
_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          8k6i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    8K6I 
#
_exptl.entry_id    8K6I 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          5 
_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    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         90 
_cell.entry_id            8K6I 
_cell.length_a            57.377 
_cell.length_b            165.308 
_cell.length_c            224.652 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8K6I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 21' 
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_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,G,H,I,J,K,L,M 
_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                      5 
_struct_asym.id                             H 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     8K6I 
_atom_sites.fract_transf_matrix[1][1]    0.017429 
_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]    0.006049 
_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]    0.004451 
_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
G 4 PO4 C 1 401 3 PO4 PO4 . 
H 5 AR6 D 1 401 401 AR6 AR6 . 
I 6 HOH A 1 401 30 HOH HOH . 
I 6 HOH A 2 402 21 HOH HOH . 
I 6 HOH A 3 403 11 HOH HOH . 
I 6 HOH A 4 404 16 HOH HOH . 
I 6 HOH A 5 405 32 HOH HOH . 
I 6 HOH A 6 406 31 HOH HOH . 
I 6 HOH A 7 407 7 HOH HOH . 
I 6 HOH A 8 408 35 HOH HOH . 
I 6 HOH A 9 409 33 HOH HOH . 
J 6 HOH B 1 401 25 HOH HOH . 
J 6 HOH B 2 402 9 HOH HOH . 
J 6 HOH B 3 403 22 HOH HOH . 
J 6 HOH B 4 404 19 HOH HOH . 
J 6 HOH B 5 405 8 HOH HOH . 
J 6 HOH B 6 406 23 HOH HOH . 
J 6 HOH B 7 407 10 HOH HOH . 
J 6 HOH B 8 408 1 HOH HOH . 
J 6 HOH B 9 409 17 HOH HOH . 
J 6 HOH B 10 410 18 HOH HOH . 
K 6 HOH C 1 501 26 HOH HOH . 
K 6 HOH C 2 502 28 HOH HOH . 
K 6 HOH C 3 503 4 HOH HOH . 
K 6 HOH C 4 504 3 HOH HOH . 
K 6 HOH C 5 505 12 HOH HOH . 
L 6 HOH D 1 501 13 HOH HOH . 
L 6 HOH D 2 502 20 HOH HOH . 
L 6 HOH D 3 503 14 HOH HOH . 
L 6 HOH D 4 504 36 HOH HOH . 
L 6 HOH D 5 505 34 HOH HOH . 
L 6 HOH D 6 506 29 HOH HOH . 
L 6 HOH D 7 507 27 HOH HOH . 
L 6 HOH D 8 508 5 HOH HOH . 
L 6 HOH D 9 509 24 HOH HOH . 
M 6 HOH F 1 101 2 HOH HOH . 
M 6 HOH F 2 102 15 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 P PB AR6 . . . H 5 -6.329 146.426 30.52 1 38.84 ? PB AR6 401 D 1 
HETATM 2 O O1B AR6 . . . H 5 -7.674 146.287 31.155 1 31.25 ? O1B AR6 401 D 1 
HETATM 3 C C1D AR6 . . . H 5 -4.505 147.91 34.289 1 43.99 ? C1D AR6 401 D 1 
HETATM 4 O O1D AR6 . . . H 5 -4.649 148.768 35.418 1 59.17 ? O1D AR6 401 D 1 
HETATM 5 O O2B AR6 . . . H 5 -6.124 146.977 29.148 1 33.49 ? O2B AR6 401 D 1 
HETATM 6 C C2D AR6 . . . H 5 -3.207 147.155 34.303 1 31.76 ? C2D AR6 401 D 1 
HETATM 7 O O2D AR6 . . . H 5 -2.211 147.929 34.94 1 45.35 ? O2D AR6 401 D 1 
HETATM 8 O O3A AR6 . . . H 5 -5.522 145.057 30.701 1 47.72 ? O3A AR6 401 D 1 
HETATM 9 C C3D AR6 . . . H 5 -2.828 147.004 32.872 1 30.54 ? C3D AR6 401 D 1 
HETATM 10 O O3D AR6 . . . H 5 -1.417 147.057 32.722 1 54.55 ? O3D AR6 401 D 1 
HETATM 11 C C4D AR6 . . . H 5 -3.47 148.196 32.215 1 37.54 ? C4D AR6 401 D 1 
HETATM 12 O O4D AR6 . . . H 5 -4.459 148.685 33.104 1 35.98 ? O4D AR6 401 D 1 
HETATM 13 C C5D AR6 . . . H 5 -4.2 147.825 30.956 1 58.53 ? C5D AR6 401 D 1 
HETATM 14 O O5D AR6 . . . H 5 -5.484 147.417 31.4 1 59.97 ? O5D AR6 401 D 1 
HETATM 15 H H1D AR6 . . . H 5 -5.335 147.193 34.245 1 52.62 ? H1D AR6 401 D 1 
HETATM 16 H H2D AR6 . . . H 5 -3.327 146.169 34.757 1 37.94 ? H2D AR6 401 D 1 
HETATM 17 H HO2D AR6 . . . H 5 -1.5 147.338 35.219 1 54.26 ? HO2D AR6 401 D 1 
HETATM 18 H H3D AR6 . . . H 5 -3.238 146.056 32.496 1 36.48 ? H3D AR6 401 D 1 
HETATM 19 H HO3D AR6 . . . H 5 -1.186 146.85 31.807 1 65.3 ? HO3D AR6 401 D 1 
HETATM 20 H H4D AR6 . . . H 5 -2.718 148.968 32.007 1 44.89 ? H4D AR6 401 D 1 
HETATM 21 H H5D AR6 . . . H 5 -4.298 148.69 30.315 1 70.07 ? H5D AR6 401 D 1 
HETATM 22 H H5DA AR6 . . . H 5 -3.666 147.049 30.404 1 70.07 ? H5DA AR6 401 D 1 
HETATM 23 H HD1 AR6 . . . H 5 -4.684 149.688 35.126 1 70.84 ? HD1 AR6 401 D 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           23 
#