data_3KPD
#
_model_server_result.job_id            UTJehAoZlZ1NoQR-CE5TpQ 
_model_server_result.datetime_utc      '2025-07-21 12:23:28' 
_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          3kpd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1}' 
#
_entry.id    3KPD 
#
_exptl.entry_id    3KPD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              297.334 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-DEOXY-5'-METHYLTHIOADENOSINE" 
_entity.pdbx_number_of_molecules    5 
_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            3KPD 
_cell.length_a            58.671 
_cell.length_b            165.794 
_cell.length_c            122.997 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KPD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F 1 1,2 
B,C,G,H,I 2 1 
D,J,K 3 1,3 
#
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' 3_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 58.671 0 -61.4985 
3 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 F N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
#
_chem_comp.formula           'C11 H15 N5 O3 S' 
_chem_comp.formula_weight    297.334 
_chem_comp.id                MTA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-DEOXY-5'-METHYLTHIOADENOSINE" 
_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
CS S5' MTA sing 222 n n 
CS HCS1 MTA sing 223 n n 
CS HCS2 MTA sing 224 n n 
CS HCS3 MTA sing 225 n n 
S5' C5' MTA sing 226 n n 
C5' C4' MTA sing 227 n n 
C5' "H5'1" MTA sing 228 n n 
C5' "H5'2" MTA sing 229 n n 
C4' O4' MTA sing 230 n n 
C4' C3' MTA sing 231 n n 
C4' H4' MTA sing 232 n n 
O4' C1' MTA sing 233 n n 
C2' O2' MTA sing 234 n n 
C2' C3' MTA sing 235 n n 
C2' C1' MTA sing 236 n n 
C2' H2' MTA sing 237 n n 
O2' HO2' MTA sing 238 n n 
C3' O3' MTA sing 239 n n 
C3' H3' MTA sing 240 n n 
O3' H3T MTA sing 241 n n 
C1' N9 MTA sing 242 n n 
C1' H1' MTA sing 243 n n 
N9 C8 MTA sing 244 n y 
N9 C4 MTA sing 245 n y 
C8 N7 MTA doub 246 n y 
C8 H8 MTA sing 247 n n 
N7 C5 MTA sing 248 n y 
C5 C6 MTA sing 249 n y 
C5 C4 MTA doub 250 n y 
C6 N6 MTA sing 251 n n 
C6 N1 MTA doub 252 n y 
N6 H61 MTA sing 253 n n 
N6 H62 MTA sing 254 n n 
N1 C2 MTA sing 255 n y 
C2 N3 MTA doub 256 n y 
C2 H2 MTA sing 257 n n 
N3 C4 MTA sing 258 n y 
#
_atom_sites.entry_id                     3KPD 
_atom_sites.fract_transf_matrix[1][1]    0.017044 
_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]    0.006032 
_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]    0.00813 
_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 MTA A 1 1 1 MTA MTA . 
F 2 MTA A 1 2 2 MTA MTA . 
G 3 SAM B 1 1000 1000 SAM SAM . 
H 3 SAM C 1 1000 1000 SAM SAM . 
I 2 MTA C 1 1 1 MTA MTA . 
J 2 MTA D 1 1 1 MTA MTA . 
K 2 MTA D 1 2 2 MTA MTA . 
#
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 C CS MTA . . . I 2 -9.408 41.689 -16.228 1 72.62 ? CS MTA 1 C 1 
HETATM 2 S S5' MTA . . . I 2 -8.662 41.272 -17.772 1 76.39 ? S5' MTA 1 C 1 
HETATM 3 C C5' MTA . . . I 2 -9.75 41.437 -19.169 1 73.04 ? C5' MTA 1 C 1 
HETATM 4 C C4' MTA . . . I 2 -9.557 42.645 -20.124 1 71.05 ? C4' MTA 1 C 1 
HETATM 5 O O4' MTA . . . I 2 -10.83 43.284 -20.337 1 69.41 ? O4' MTA 1 C 1 
HETATM 6 C C2' MTA . . . I 2 -9.578 44.647 -18.832 1 68.9 ? C2' MTA 1 C 1 
HETATM 7 O O2' MTA . . . I 2 -9.142 46.008 -18.827 1 69.16 ? O2' MTA 1 C 1 
HETATM 8 C C3' MTA . . . I 2 -8.649 43.775 -19.646 1 69.93 ? C3' MTA 1 C 1 
HETATM 9 O O3' MTA . . . I 2 -8.21 44.548 -20.774 1 69.9 ? O3' MTA 1 C 1 
HETATM 10 C C1' MTA . . . I 2 -10.939 44.466 -19.512 1 67.67 ? C1' MTA 1 C 1 
HETATM 11 N N9 MTA . . . I 2 -12.03 44.308 -18.512 1 63.9 ? N9 MTA 1 C 1 
HETATM 12 C C8 MTA . . . I 2 -11.95 43.617 -17.361 1 63.59 ? C8 MTA 1 C 1 
HETATM 13 N N7 MTA . . . I 2 -13.118 43.668 -16.67 1 63.04 ? N7 MTA 1 C 1 
HETATM 14 C C5 MTA . . . I 2 -13.984 44.405 -17.392 1 61.39 ? C5 MTA 1 C 1 
HETATM 15 C C6 MTA . . . I 2 -15.392 44.86 -17.253 1 59.94 ? C6 MTA 1 C 1 
HETATM 16 N N6 MTA . . . I 2 -16.165 44.533 -16.188 1 58.99 ? N6 MTA 1 C 1 
HETATM 17 N N1 MTA . . . I 2 -15.9 45.621 -18.239 1 59.99 ? N1 MTA 1 C 1 
HETATM 18 C C2 MTA . . . I 2 -15.178 45.962 -19.313 1 60.42 ? C2 MTA 1 C 1 
HETATM 19 N N3 MTA . . . I 2 -13.905 45.583 -19.495 1 62.05 ? N3 MTA 1 C 1 
HETATM 20 C C4 MTA . . . I 2 -13.256 44.819 -18.597 1 61.95 ? C4 MTA 1 C 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           243 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           20 
#