data_6FD2
#
_model_server_result.job_id            TsGjPZDCLcEeNOGONACfCw 
_model_server_result.datetime_utc      '2024-12-26 22:01:37' 
_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          6fd2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":504}' 
#
_entry.id    6FD2 
#
_exptl.entry_id    6FD2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              251.242 
_entity.id                          5 
_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            6FD2 
_cell.length_a            121.82 
_cell.length_b            121.82 
_cell.length_c            233.78 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6FD2 
_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
? 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,K 1 1 
B,G,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
? 5 F N N 
? 5 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 SG CYS 206 B CYS 206 1_555 D FE2 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? 
metalc ? metalc2 A SG CYS 210 B CYS 210 1_555 D FE3 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? 
metalc ? metalc3 A SG CYS 214 B CYS 214 1_555 D FE1 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? 
metalc ? metalc4 D FE4 SF4 . B SF4 502 1_555 E O MET . B MET 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc5 D FE4 SF4 . B SF4 502 1_555 E N MET . B MET 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc6 B SG CYS 206 A CYS 206 1_555 H FE2 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
metalc ? metalc7 B SG CYS 210 A CYS 210 1_555 H FE3 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? 
metalc ? metalc8 B SG CYS 214 A CYS 214 1_555 H FE1 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? 
metalc ? metalc9 H FE4 SF4 . A SF4 502 1_555 I N MET . A MET 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc10 H FE4 SF4 . A SF4 502 1_555 I O MET . A MET 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
#
_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                     6FD2 
_atom_sites.fract_transf_matrix[1][1]    0.008209 
_atom_sites.fract_transf_matrix[1][2]    0.004739 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009479 
_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]    0.004278 
_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 D5E B 1 501 800 D5E XXX . 
D 3 SF4 B 1 502 1401 SF4 FS4 . 
E 4 MET B 1 503 1408 MET MET . 
F 5 5AD B 1 504 1418 5AD 5AD . 
G 2 D5E A 1 501 800 D5E XXX . 
H 3 SF4 A 1 502 1401 SF4 FS4 . 
I 4 MET A 1 503 1408 MET MET . 
J 5 5AD A 1 504 1418 5AD 5AD . 
K 6 HOH B 1 601 4 HOH HOH . 
K 6 HOH B 2 602 27 HOH HOH . 
K 6 HOH B 3 603 8 HOH HOH . 
K 6 HOH B 4 604 10 HOH HOH . 
K 6 HOH B 5 605 9 HOH HOH . 
K 6 HOH B 6 606 6 HOH HOH . 
K 6 HOH B 7 607 13 HOH HOH . 
K 6 HOH B 8 608 23 HOH HOH . 
K 6 HOH B 9 609 16 HOH HOH . 
K 6 HOH B 10 610 31 HOH HOH . 
K 6 HOH B 11 611 33 HOH HOH . 
K 6 HOH B 12 612 32 HOH HOH . 
K 6 HOH B 13 613 26 HOH HOH . 
K 6 HOH B 14 614 15 HOH HOH . 
K 6 HOH B 15 615 12 HOH HOH . 
K 6 HOH B 16 616 25 HOH HOH . 
K 6 HOH B 17 617 7 HOH HOH . 
K 6 HOH B 18 618 17 HOH HOH . 
K 6 HOH B 19 619 24 HOH HOH . 
K 6 HOH B 20 620 22 HOH HOH . 
K 6 HOH B 21 621 30 HOH HOH . 
K 6 HOH B 22 622 18 HOH HOH . 
K 6 HOH B 23 623 14 HOH HOH . 
K 6 HOH B 24 624 11 HOH HOH . 
L 6 HOH A 1 601 39 HOH HOH . 
L 6 HOH A 2 602 40 HOH HOH . 
L 6 HOH A 3 603 1 HOH HOH . 
L 6 HOH A 4 604 2 HOH HOH . 
L 6 HOH A 5 605 3 HOH HOH . 
L 6 HOH A 6 606 37 HOH HOH . 
L 6 HOH A 7 607 5 HOH HOH . 
L 6 HOH A 8 608 42 HOH HOH . 
L 6 HOH A 9 609 19 HOH HOH . 
L 6 HOH A 10 610 41 HOH HOH . 
L 6 HOH A 11 611 36 HOH HOH . 
L 6 HOH A 12 612 43 HOH HOH . 
L 6 HOH A 13 613 34 HOH HOH . 
L 6 HOH A 14 614 35 HOH HOH . 
L 6 HOH A 15 615 38 HOH HOH . 
L 6 HOH A 16 616 21 HOH HOH . 
L 6 HOH A 17 617 20 HOH HOH . 
L 6 HOH A 18 618 29 HOH HOH . 
L 6 HOH A 19 619 28 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 . . . J 5 77.681 -41.86 -9.586 1 96.85 ? N1 5AD 504 A 1 
HETATM 2 C C2 5AD . . . J 5 77.666 -43.178 -9.185 1 95.98 ? C2 5AD 504 A 1 
HETATM 3 N N3 5AD . . . J 5 77.201 -44.156 -10.039 1 98.96 ? N3 5AD 504 A 1 
HETATM 4 C C4 5AD . . . J 5 76.758 -43.827 -11.277 1 99.24 ? C4 5AD 504 A 1 
HETATM 5 N N9 5AD . . . J 5 76.248 -44.566 -12.319 1 86.55 ? N9 5AD 504 A 1 
HETATM 6 C C8 5AD . . . J 5 75.966 -43.704 -13.342 1 94.06 ? C8 5AD 504 A 1 
HETATM 7 N N7 5AD . . . J 5 76.284 -42.453 -12.95 1 98.58 ? N7 5AD 504 A 1 
HETATM 8 C C5 5AD . . . J 5 76.77 -42.503 -11.69 1 97.55 ? C5 5AD 504 A 1 
HETATM 9 C C6 5AD . . . J 5 77.235 -41.517 -10.841 1 89.42 ? C6 5AD 504 A 1 
HETATM 10 N N6 5AD . . . J 5 77.248 -40.252 -11.241 1 86.04 ? N6 5AD 504 A 1 
HETATM 11 C C1' 5AD . . . J 5 76.051 -46.019 -12.368 1 74.58 ? C1' 5AD 504 A 1 
HETATM 12 C C2' 5AD . . . J 5 74.646 -46.333 -12.831 1 74.76 ? C2' 5AD 504 A 1 
HETATM 13 C C3' 5AD . . . J 5 74.804 -46.997 -14.182 1 78.99 ? C3' 5AD 504 A 1 
HETATM 14 C C4' 5AD . . . J 5 76.273 -47.361 -14.265 1 80.86 ? C4' 5AD 504 A 1 
HETATM 15 C C5' 5AD . . . J 5 76.844 -47.165 -15.664 1 81.57 ? C5' 5AD 504 A 1 
HETATM 16 O O4' 5AD . . . J 5 76.948 -46.549 -13.326 1 79.02 ? O4' 5AD 504 A 1 
HETATM 17 O O2' 5AD . . . J 5 74.069 -47.226 -11.905 1 78.87 ? O2' 5AD 504 A 1 
HETATM 18 O O3' 5AD . . . J 5 74.037 -48.169 -14.248 1 92.21 ? O3' 5AD 504 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           327 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           18 
#