data_6D5X
#
_model_server_result.job_id            sq_U2twyVaiCARWM2x1G2A 
_model_server_result.datetime_utc      '2024-11-01 01:31:43' 
_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          6d5x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":301}' 
#
_entry.id    6D5X 
#
_exptl.entry_id    6D5X 
_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            6D5X 
_cell.length_a            112.685 
_cell.length_b            112.685 
_cell.length_c            117.939 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6D5X 
_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 -78.626 
#
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 A OD1 ASN 160 A ASN 214 1_555 G MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc2 D C5' 5AD . A 5AD 301 1_555 E CO B12 . A B12 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc3 G MG MG . A MG 304 1_555 H O3G 3PO . A 3PO 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? 
metalc ? metalc4 G MG MG . A MG 304 1_555 H O2B 3PO . A 3PO 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? 
metalc ? metalc5 G MG MG . A MG 304 1_555 H O1A 3PO . A 3PO 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc6 G MG MG . A MG 304 1_555 R O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
metalc ? metalc7 G MG MG . A MG 304 1_555 R O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc8 I C5' 5AD . B 5AD 301 1_555 J CO B12 . B B12 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc9 S O HOH . B HOH 418 1_555 M MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc10 C OD1 ASN 160 C ASN 214 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc11 L O1A ATP . C ATP 301 1_555 M MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc12 L O3G ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc13 L O2B ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
metalc ? metalc14 L O2A ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.888 ? 
metalc ? metalc15 M MG MG . C MG 302 1_555 T O HOH . C HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
metalc ? metalc16 M MG MG . C MG 302 1_555 T O HOH . C HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc17 M MG MG . C MG 302 1_555 T O HOH . C HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc18 M MG MG . C MG 302 1_555 T O HOH . C HOH 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc19 Q MG MG . C MG 306 1_555 T O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc20 Q MG MG . C MG 306 1_555 T O HOH . C HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
#
_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 18 n y 
N1 C6 5AD sing 19 n y 
C2 N3 5AD sing 20 n y 
C2 H2 5AD sing 21 n n 
N3 C4 5AD doub 22 n y 
C4 N9 5AD sing 23 n y 
C4 C5 5AD sing 24 n y 
N9 C8 5AD sing 25 n y 
N9 C1' 5AD sing 26 n n 
C8 N7 5AD doub 27 n y 
C8 H8 5AD sing 28 n n 
N7 C5 5AD sing 29 n y 
C5 C6 5AD doub 30 n y 
C6 N6 5AD sing 31 n n 
N6 HN61 5AD sing 32 n n 
N6 HN62 5AD sing 33 n n 
C1' C2' 5AD sing 34 n n 
C1' O4' 5AD sing 35 n n 
C1' H1' 5AD sing 36 n n 
C2' C3' 5AD sing 37 n n 
C2' O2' 5AD sing 38 n n 
C2' H2' 5AD sing 39 n n 
C3' C4' 5AD sing 40 n n 
C3' O3' 5AD sing 41 n n 
C3' H3' 5AD sing 42 n n 
C4' C5' 5AD sing 43 n n 
C4' O4' 5AD sing 44 n n 
C4' H4' 5AD sing 45 n n 
C5' "H5'1" 5AD sing 46 n n 
C5' "H5'2" 5AD sing 47 n n 
C5' "H5'3" 5AD sing 48 n n 
O2' HO2' 5AD sing 49 n n 
O3' HO3' 5AD sing 50 n n 
#
_atom_sites.entry_id                     6D5X 
_atom_sites.fract_transf_matrix[1][1]    0.008874 
_atom_sites.fract_transf_matrix[1][2]    0.005124 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010247 
_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]    0.008479 
_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 4 SO4 A 1 303 3 SO4 SO4 . 
G 5 MG A 1 304 3 MG MG . 
H 6 3PO A 1 305 1 3PO 3PO . 
I 2 5AD B 1 301 3 5AD 5AD . 
J 3 B12 B 1 302 4 B12 B12 . 
K 4 SO4 B 1 303 1 SO4 SO4 . 
L 7 ATP C 1 301 1 ATP ATP . 
M 5 MG C 1 302 1 MG MG . 
N 4 SO4 C 1 303 2 SO4 SO4 . 
O 4 SO4 C 1 304 4 SO4 SO4 . 
P 4 SO4 C 1 305 5 SO4 SO4 . 
Q 5 MG C 1 306 2 MG MG . 
R 8 HOH A 1 401 169 HOH HOH . 
R 8 HOH A 2 402 55 HOH HOH . 
R 8 HOH A 3 403 125 HOH HOH . 
R 8 HOH A 4 404 164 HOH HOH . 
R 8 HOH A 5 405 7 HOH HOH . 
R 8 HOH A 6 406 19 HOH HOH . 
R 8 HOH A 7 407 131 HOH HOH . 
R 8 HOH A 8 408 154 HOH HOH . 
R 8 HOH A 9 409 120 HOH HOH . 
R 8 HOH A 10 410 18 HOH HOH . 
R 8 HOH A 11 411 181 HOH HOH . 
R 8 HOH A 12 412 68 HOH HOH . 
S 8 HOH B 1 401 118 HOH HOH . 
S 8 HOH B 2 402 143 HOH HOH . 
S 8 HOH B 3 403 126 HOH HOH . 
S 8 HOH B 4 404 11 HOH HOH . 
S 8 HOH B 5 405 27 HOH HOH . 
S 8 HOH B 6 406 13 HOH HOH . 
S 8 HOH B 7 407 193 HOH HOH . 
S 8 HOH B 8 408 165 HOH HOH . 
S 8 HOH B 9 409 183 HOH HOH . 
S 8 HOH B 10 410 8 HOH HOH . 
S 8 HOH B 11 411 24 HOH HOH . 
S 8 HOH B 12 412 162 HOH HOH . 
S 8 HOH B 13 413 124 HOH HOH . 
S 8 HOH B 14 414 112 HOH HOH . 
S 8 HOH B 15 415 28 HOH HOH . 
S 8 HOH B 16 416 179 HOH HOH . 
S 8 HOH B 17 417 9 HOH HOH . 
S 8 HOH B 18 418 74 HOH HOH . 
S 8 HOH B 19 419 76 HOH HOH . 
S 8 HOH B 20 420 42 HOH HOH . 
S 8 HOH B 21 421 122 HOH HOH . 
S 8 HOH B 22 422 69 HOH HOH . 
S 8 HOH B 23 423 21 HOH HOH . 
S 8 HOH B 24 424 25 HOH HOH . 
S 8 HOH B 25 425 78 HOH HOH . 
S 8 HOH B 26 426 29 HOH HOH . 
S 8 HOH B 27 427 129 HOH HOH . 
T 8 HOH C 1 401 10 HOH HOH . 
T 8 HOH C 2 402 152 HOH HOH . 
T 8 HOH C 3 403 6 HOH HOH . 
T 8 HOH C 4 404 150 HOH HOH . 
T 8 HOH C 5 405 46 HOH HOH . 
T 8 HOH C 6 406 16 HOH HOH . 
T 8 HOH C 7 407 23 HOH HOH . 
T 8 HOH C 8 408 136 HOH HOH . 
T 8 HOH C 9 409 121 HOH HOH . 
T 8 HOH C 10 410 2 HOH HOH . 
T 8 HOH C 11 411 5 HOH HOH . 
T 8 HOH C 12 412 4 HOH HOH . 
T 8 HOH C 13 413 114 HOH HOH . 
T 8 HOH C 14 414 171 HOH HOH . 
T 8 HOH C 15 415 17 HOH HOH . 
T 8 HOH C 16 416 3 HOH HOH . 
T 8 HOH C 17 417 191 HOH HOH . 
T 8 HOH C 18 418 113 HOH HOH . 
T 8 HOH C 19 419 15 HOH HOH . 
T 8 HOH C 20 420 22 HOH HOH . 
T 8 HOH C 21 421 153 HOH HOH . 
T 8 HOH C 22 422 1 HOH HOH . 
T 8 HOH C 23 423 31 HOH HOH . 
T 8 HOH C 24 424 182 HOH HOH . 
T 8 HOH C 25 425 30 HOH HOH . 
T 8 HOH C 26 426 14 HOH HOH . 
T 8 HOH C 27 427 115 HOH HOH . 
T 8 HOH C 28 428 133 HOH HOH . 
T 8 HOH C 29 429 158 HOH HOH . 
T 8 HOH C 30 430 151 HOH HOH . 
T 8 HOH C 31 431 39 HOH HOH . 
T 8 HOH C 32 432 168 HOH HOH . 
T 8 HOH C 33 433 194 HOH HOH . 
T 8 HOH C 34 434 173 HOH HOH . 
T 8 HOH C 35 435 142 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 . . . I 2 -45.998 52.25 -12.049 0.81 58.1 ? N1 5AD 301 B 1 
HETATM 2 C C2 5AD . . . I 2 -45.59 53.289 -11.315 0.81 68.84 ? C2 5AD 301 B 1 
HETATM 3 N N3 5AD . . . I 2 -46.323 54.179 -10.64 0.81 84.18 ? N3 5AD 301 B 1 
HETATM 4 C C4 5AD . . . I 2 -47.631 53.922 -10.771 0.81 94.58 ? C4 5AD 301 B 1 
HETATM 5 N N9 5AD . . . I 2 -48.678 54.611 -10.21 0.81 90.46 ? N9 5AD 301 B 1 
HETATM 6 C C8 5AD . . . I 2 -49.814 53.969 -10.631 0.81 92.96 ? C8 5AD 301 B 1 
HETATM 7 N N7 5AD . . . I 2 -49.586 52.934 -11.402 0.81 89.52 ? N7 5AD 301 B 1 
HETATM 8 C C5 5AD . . . I 2 -48.203 52.89 -11.498 0.81 86.86 ? C5 5AD 301 B 1 
HETATM 9 C C6 5AD . . . I 2 -47.324 52.015 -12.164 0.81 72.08 ? C6 5AD 301 B 1 
HETATM 10 N N6 5AD . . . I 2 -47.728 50.967 -12.886 0.81 63.99 ? N6 5AD 301 B 1 
HETATM 11 C C1' 5AD . . . I 2 -48.595 55.77 -9.327 0.81 95.1 ? C1' 5AD 301 B 1 
HETATM 12 C C2' 5AD . . . I 2 -49.931 56.499 -9.112 0.81 102.35 ? C2' 5AD 301 B 1 
HETATM 13 C C3' 5AD . . . I 2 -50.338 56.041 -7.71 0.81 102.47 ? C3' 5AD 301 B 1 
HETATM 14 C C4' 5AD . . . I 2 -48.99 55.848 -7.027 0.81 98.49 ? C4' 5AD 301 B 1 
HETATM 15 C C5' 5AD . . . I 2 -48.98 54.895 -5.853 0.81 98.05 ? C5' 5AD 301 B 1 
HETATM 16 O O4' 5AD . . . I 2 -48.129 55.336 -8.061 0.81 100.03 ? O4' 5AD 301 B 1 
HETATM 17 O O2' 5AD . . . I 2 -49.748 57.909 -9.18 0.81 103.23 ? O2' 5AD 301 B 1 
HETATM 18 O O3' 5AD . . . I 2 -51.069 57.05 -7.021 0.81 99.93 ? O3' 5AD 301 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           377 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           18 
#