data_3KPD
#
_model_server_result.job_id            JNB4jpTArjs90p1DaoAniw 
_model_server_result.datetime_utc      '2025-02-28 07:16:22' 
_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":"H","auth_seq_id":1000}' 
#
_entry.id    3KPD 
#
_exptl.entry_id    3KPD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              398.437 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYLMETHIONINE 
_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         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
? 3 G N N 
? 3 H N N 
#
_chem_comp.formula           'C15 H22 N6 O5 S' 
_chem_comp.formula_weight    398.437 
_chem_comp.id                SAM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              S-ADENOSYLMETHIONINE 
_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
N CA SAM sing 299 n n 
N HN1 SAM sing 300 n n 
N HN2 SAM sing 301 n n 
CA C SAM sing 302 n n 
CA CB SAM sing 303 n n 
CA HA SAM sing 304 n n 
C O SAM doub 305 n n 
C OXT SAM sing 306 n n 
CB CG SAM sing 307 n n 
CB HB1 SAM sing 308 n n 
CB HB2 SAM sing 309 n n 
CG SD SAM sing 310 n n 
CG HG1 SAM sing 311 n n 
CG HG2 SAM sing 312 n n 
SD CE SAM sing 313 n n 
SD C5' SAM sing 314 n n 
CE HE1 SAM sing 315 n n 
CE HE2 SAM sing 316 n n 
CE HE3 SAM sing 317 n n 
C5' C4' SAM sing 318 n n 
C5' "H5'1" SAM sing 319 n n 
C5' "H5'2" SAM sing 320 n n 
C4' O4' SAM sing 321 n n 
C4' C3' SAM sing 322 n n 
C4' H4' SAM sing 323 n n 
O4' C1' SAM sing 324 n n 
C3' O3' SAM sing 325 n n 
C3' C2' SAM sing 326 n n 
C3' H3' SAM sing 327 n n 
O3' HO3' SAM sing 328 n n 
C2' O2' SAM sing 329 n n 
C2' C1' SAM sing 330 n n 
C2' H2' SAM sing 331 n n 
O2' HO2' SAM sing 332 n n 
C1' N9 SAM sing 333 n n 
C1' H1' SAM sing 334 n n 
N9 C8 SAM sing 335 n y 
N9 C4 SAM sing 336 n y 
C8 N7 SAM doub 337 n y 
C8 H8 SAM sing 338 n n 
N7 C5 SAM sing 339 n y 
C5 C6 SAM sing 340 n y 
C5 C4 SAM doub 341 n y 
C6 N6 SAM sing 342 n n 
C6 N1 SAM doub 343 n y 
N6 HN61 SAM sing 344 n n 
N6 HN62 SAM sing 345 n n 
N1 C2 SAM sing 346 n y 
C2 N3 SAM doub 347 n y 
C2 H2 SAM sing 348 n n 
N3 C4 SAM sing 349 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 N N SAM . . . H 3 -3.245 40.039 -4.665 1 51.11 ? N SAM 1000 C 1 
HETATM 2 C CA SAM . . . H 3 -4.266 39.318 -5.435 1 51.04 ? CA SAM 1000 C 1 
HETATM 3 C C SAM . . . H 3 -4.916 40.234 -6.455 1 50.78 ? C SAM 1000 C 1 
HETATM 4 O O SAM . . . H 3 -4.413 41.32 -6.675 1 50.76 ? O SAM 1000 C 1 
HETATM 5 O OXT SAM . . . H 3 -5.938 39.929 -7.066 1 50.67 -1 OXT SAM 1000 C 1 
HETATM 6 C CB SAM . . . H 3 -5.344 38.712 -4.546 1 50.91 ? CB SAM 1000 C 1 
HETATM 7 C CG SAM . . . H 3 -5.587 39.491 -3.258 1 51.39 ? CG SAM 1000 C 1 
HETATM 8 S SD SAM . . . H 3 -6.586 40.985 -3.514 1 51.12 ? SD SAM 1000 C 1 
HETATM 9 C CE SAM . . . H 3 -6.783 41.466 -1.764 1 49.93 ? CE SAM 1000 C 1 
HETATM 10 C C5' SAM . . . H 3 -8.164 40.182 -3.928 1 46.78 ? C5' SAM 1000 C 1 
HETATM 11 C C4' SAM . . . H 3 -9.321 40.976 -3.34 1 45.46 ? C4' SAM 1000 C 1 
HETATM 12 O O4' SAM . . . H 3 -9.232 42.297 -3.831 1 44.64 ? O4' SAM 1000 C 1 
HETATM 13 C C3' SAM . . . H 3 -10.694 40.476 -3.731 1 44.54 ? C3' SAM 1000 C 1 
HETATM 14 O O3' SAM . . . H 3 -11.421 40.141 -2.578 1 43.67 ? O3' SAM 1000 C 1 
HETATM 15 C C2' SAM . . . H 3 -11.352 41.653 -4.404 1 44.34 ? C2' SAM 1000 C 1 
HETATM 16 O O2' SAM . . . H 3 -12.708 41.709 -4.031 1 44.46 ? O2' SAM 1000 C 1 
HETATM 17 C C1' SAM . . . H 3 -10.516 42.835 -3.925 1 44.09 ? C1' SAM 1000 C 1 
HETATM 18 N N9 SAM . . . H 3 -10.475 43.917 -4.913 1 43.99 ? N9 SAM 1000 C 1 
HETATM 19 C C8 SAM . . . H 3 -10.315 43.735 -6.254 1 43.86 ? C8 SAM 1000 C 1 
HETATM 20 N N7 SAM . . . H 3 -10.337 44.938 -6.841 1 43.89 ? N7 SAM 1000 C 1 
HETATM 21 C C5 SAM . . . H 3 -10.516 45.886 -5.906 1 43.49 ? C5 SAM 1000 C 1 
HETATM 22 C C6 SAM . . . H 3 -10.619 47.27 -6.01 1 43.86 ? C6 SAM 1000 C 1 
HETATM 23 N N6 SAM . . . H 3 -10.53 47.858 -7.205 1 42.79 ? N6 SAM 1000 C 1 
HETATM 24 N N1 SAM . . . H 3 -10.799 48.013 -4.86 1 43.99 ? N1 SAM 1000 C 1 
HETATM 25 C C2 SAM . . . H 3 -10.884 47.363 -3.632 1 43.57 ? C2 SAM 1000 C 1 
HETATM 26 N N3 SAM . . . H 3 -10.785 45.983 -3.552 1 42.38 ? N3 SAM 1000 C 1 
HETATM 27 C C4 SAM . . . H 3 -10.602 45.259 -4.676 1 42.92 ? C4 SAM 1000 C 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#