data_6D5K
#
_model_server_result.job_id            ZfGV9OyhVoP6mjNSMJFjPw 
_model_server_result.datetime_utc      '2024-11-01 01:12:01' 
_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          6d5k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    6D5K 
#
_exptl.entry_id    6D5K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              251.242 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-DEOXYADENOSINE" 
_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         120 
_cell.entry_id            6D5K 
_cell.length_a            112.252 
_cell.length_b            112.252 
_cell.length_c            117.993 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6D5K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA trimeric 3 author_and_software_defined_assembly 1 
PISA hexameric 6 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -78.662 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 D N N 
? 2 I 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 D C5' 5AD . A 5AD 301 1_555 E CO B12 . A B12 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc2 F CO B12 . A B12 303 1_555 I C5' 5AD . B 5AD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
metalc ? metalc3 C OD1 ASN 160 C ASN 214 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc4 L O1A ATP . C ATP 301 1_555 M MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc5 L O3G ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc6 L O2B ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? 
metalc ? metalc7 L O2A ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? 
metalc ? metalc8 M MG MG . C MG 302 1_555 T O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc9 M MG MG . C MG 302 1_555 T O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? 
metalc ? metalc10 M MG MG . C MG 302 1_555 T O HOH . C HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc11 M MG MG . C MG 302 1_555 T O HOH . C HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc12 Q MG MG . C MG 306 1_555 T O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? 
metalc ? metalc13 Q MG MG . C MG 306 1_555 T O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
#
_chem_comp.formula           'C10 H13 N5 O3' 
_chem_comp.formula_weight    251.242 
_chem_comp.id                5AD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-DEOXYADENOSINE" 
_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
N1 C2 5AD doub 1 n y 
N1 C6 5AD sing 2 n y 
C2 N3 5AD sing 3 n y 
C2 H2 5AD sing 4 n n 
N3 C4 5AD doub 5 n y 
C4 N9 5AD sing 6 n y 
C4 C5 5AD sing 7 n y 
N9 C8 5AD sing 8 n y 
N9 C1' 5AD sing 9 n n 
C8 N7 5AD doub 10 n y 
C8 H8 5AD sing 11 n n 
N7 C5 5AD sing 12 n y 
C5 C6 5AD doub 13 n y 
C6 N6 5AD sing 14 n n 
N6 HN61 5AD sing 15 n n 
N6 HN62 5AD sing 16 n n 
C1' C2' 5AD sing 17 n n 
C1' O4' 5AD sing 18 n n 
C1' H1' 5AD sing 19 n n 
C2' C3' 5AD sing 20 n n 
C2' O2' 5AD sing 21 n n 
C2' H2' 5AD sing 22 n n 
C3' C4' 5AD sing 23 n n 
C3' O3' 5AD sing 24 n n 
C3' H3' 5AD sing 25 n n 
C4' C5' 5AD sing 26 n n 
C4' O4' 5AD sing 27 n n 
C4' H4' 5AD sing 28 n n 
C5' "H5'1" 5AD sing 29 n n 
C5' "H5'2" 5AD sing 30 n n 
C5' "H5'3" 5AD sing 31 n n 
O2' HO2' 5AD sing 32 n n 
O3' HO3' 5AD sing 33 n n 
#
_atom_sites.entry_id                     6D5K 
_atom_sites.fract_transf_matrix[1][1]    0.008909 
_atom_sites.fract_transf_matrix[1][2]    0.005143 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010287 
_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]    0.008475 
_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
D 2 5AD A 1 301 1 5AD 5AD . 
E 3 B12 A 1 302 2 B12 B12 . 
F 3 B12 A 1 303 4 B12 B12 . 
G 4 SO4 A 1 304 3 SO4 SO4 . 
H 4 SO4 A 1 305 6 SO4 SO4 . 
I 2 5AD B 1 301 3 5AD 5AD . 
J 4 SO4 B 1 302 1 SO4 SO4 . 
K 4 SO4 B 1 303 5 SO4 SO4 . 
L 5 ATP C 1 301 1 ATP ATP . 
M 6 MG C 1 302 1 MG MG . 
N 7 EPE C 1 303 1 EPE EPE . 
O 4 SO4 C 1 304 2 SO4 SO4 . 
P 4 SO4 C 1 305 4 SO4 SO4 . 
Q 6 MG C 1 306 2 MG MG . 
R 8 HOH A 1 401 7 HOH HOH . 
R 8 HOH A 2 402 64 HOH HOH . 
R 8 HOH A 3 403 58 HOH HOH . 
R 8 HOH A 4 404 70 HOH HOH . 
S 8 HOH B 1 401 71 HOH HOH . 
S 8 HOH B 2 402 54 HOH HOH . 
S 8 HOH B 3 403 19 HOH HOH . 
S 8 HOH B 4 404 63 HOH HOH . 
S 8 HOH B 5 405 44 HOH HOH . 
S 8 HOH B 6 406 40 HOH HOH . 
T 8 HOH C 1 401 1 HOH HOH . 
T 8 HOH C 2 402 5 HOH HOH . 
T 8 HOH C 3 403 2 HOH HOH . 
T 8 HOH C 4 404 3 HOH HOH . 
T 8 HOH C 5 405 6 HOH HOH . 
T 8 HOH C 6 406 16 HOH HOH . 
T 8 HOH C 7 407 4 HOH HOH . 
T 8 HOH C 8 408 13 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 N1 5AD . . . D 2 -26.274 52.146 -16.458 0.93 71.1 ? N1 5AD 301 A 1 
HETATM 2 C C2 5AD . . . D 2 -25.552 51.459 -17.346 0.93 63.61 ? C2 5AD 301 A 1 
HETATM 3 N N3 5AD . . . D 2 -24.281 51.642 -17.711 0.93 65.64 ? N3 5AD 301 A 1 
HETATM 4 C C4 5AD . . . D 2 -23.752 52.702 -17.097 0.93 68.67 ? C4 5AD 301 A 1 
HETATM 5 N N9 5AD . . . D 2 -22.492 53.225 -17.265 0.93 68.78 ? N9 5AD 301 A 1 
HETATM 6 C C8 5AD . . . D 2 -22.449 54.348 -16.49 0.93 73.03 ? C8 5AD 301 A 1 
HETATM 7 N N7 5AD . . . D 2 -23.554 54.581 -15.816 0.93 68.53 ? N7 5AD 301 A 1 
HETATM 8 C C5 5AD . . . D 2 -24.379 53.531 -16.187 0.93 72 ? C5 5AD 301 A 1 
HETATM 9 C C6 5AD . . . D 2 -25.702 53.195 -15.824 0.93 75.05 ? C6 5AD 301 A 1 
HETATM 10 N N6 5AD . . . D 2 -26.376 53.786 -14.835 0.93 72.78 ? N6 5AD 301 A 1 
HETATM 11 C C1' 5AD . . . D 2 -21.41 52.659 -18.072 0.93 82.71 ? C1' 5AD 301 A 1 
HETATM 12 C C2' 5AD . . . D 2 -20.318 53.655 -18.486 0.93 84.21 ? C2' 5AD 301 A 1 
HETATM 13 C C3' 5AD . . . D 2 -19.225 53.348 -17.472 0.93 80.17 ? C3' 5AD 301 A 1 
HETATM 14 C C4' 5AD . . . D 2 -19.357 51.839 -17.387 0.93 77.57 ? C4' 5AD 301 A 1 
HETATM 15 C C5' 5AD . . . D 2 -18.704 51.188 -16.191 0.93 79.33 ? C5' 5AD 301 A 1 
HETATM 16 O O4' 5AD . . . D 2 -20.779 51.614 -17.348 0.93 81.94 ? O4' 5AD 301 A 1 
HETATM 17 O O2' 5AD . . . D 2 -19.865 53.265 -19.775 0.93 80.15 ? O2' 5AD 301 A 1 
HETATM 18 O O3' 5AD . . . D 2 -17.946 53.673 -17.995 0.93 81 ? O3' 5AD 301 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           18 
#