data_3NVK
#
_model_server_result.job_id            1S9iCUiTGFHD4E0ANX9n5Q 
_model_server_result.datetime_utc      '2024-11-04 22:43:02' 
_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          3nvk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":228}' 
#
_entry.id    3NVK 
#
_exptl.entry_id    3NVK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              398.437 
_entity.id                          6 
_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            3NVK 
_cell.length_a            330.039 
_cell.length_b            94.548 
_cell.length_c            97.729 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NVK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    decameric 
_pdbx_struct_assembly.oligomeric_count      10 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 6 K N N 
? 6 L 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
hydrog 'G-C PAIR' hydrog1 G N2 G 10 K G 2 1_555 H N3 C 4 G C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 G N3 C 11 K C 3 1_555 H N1 G 3 G G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 G N4 C 11 K C 3 1_555 H O6 G 3 G G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 G O2 C 11 K C 3 1_555 H N2 G 3 G G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 G N3 C 13 K C 5 1_555 G N1 G 31 K G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 G N4 C 13 K C 5 1_555 G O6 G 31 K G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 G O2 C 13 K C 5 1_555 G N2 G 31 K G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-A MISPAIR' hydrog8 G N4 C 13 K C 5 1_555 G N7 A 32 K A 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_28_PAIR hydrog9 G N3 U 14 K U 6 1_555 G O6 G 31 K G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_28_PAIR hydrog10 G O2 U 14 K U 6 1_555 G N1 G 31 K G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_11_PAIR hydrog11 G N2 G 15 K G 7 1_555 G N7 A 29 K A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_11_PAIR hydrog12 G N3 G 15 K G 7 1_555 G N6 A 29 K A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'G-U MISPAIR' hydrog13 G N2 G 15 K G 7 1_555 G O4 U 30 K U 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_11_PAIR hydrog14 G N6 A 16 K A 8 1_555 G N3 G 28 K G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_11_PAIR hydrog15 G N7 A 16 K A 8 1_555 G N2 G 28 K G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-C MISPAIR' hydrog16 G N4 C 17 K C 9 1_555 G N3 C 25 K C 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_11_PAIR hydrog17 G N2 G 19 K G 11 1_555 G N7 A 22 K A 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_11_PAIR hydrog18 G N3 G 19 K G 11 1_555 G N6 A 22 K A 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-G PAIR' hydrog19 G O2 C 25 K C 17 1_555 G N2 G 26 K G 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'G-C PAIR' hydrog20 I N2 G 10 L G 2 1_555 J N3 C 4 S C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-G PAIR' hydrog21 I O2 C 11 L C 3 1_555 J N2 G 3 S G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 I N3 C 13 L C 5 1_555 I N1 G 31 L G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 I N4 C 13 L C 5 1_555 I O6 G 31 L G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog24 I O2 C 13 L C 5 1_555 I N2 G 31 L G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_16_PAIR hydrog25 I N3 U 14 L U 6 1_555 I O4 U 30 L U 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_16_PAIR hydrog26 I O2 U 14 L U 6 1_555 I N3 U 30 L U 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'G-A MISPAIR' hydrog27 I N3 G 15 L G 7 1_555 I N6 A 29 L A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'G-U MISPAIR' hydrog28 I N2 G 15 L G 7 1_555 I O4 U 30 L U 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'A-G MISPAIR' hydrog29 I N7 A 16 L A 8 1_555 I N2 G 28 L G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'REVERSED WATSON-CRICK' hydrog30 I N3 C 17 L C 9 1_555 I N2 G 24 L G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'REVERSED WATSON-CRICK' hydrog31 I O2 C 17 L C 9 1_555 I N1 G 24 L G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-C MISPAIR' hydrog32 I N4 C 17 L C 9 1_555 I O2 C 25 L C 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-G PAIR' hydrog33 I O2 C 25 L C 17 1_555 I N2 G 26 L G 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 390 n n 
N HN1 SAM sing 391 n n 
N HN2 SAM sing 392 n n 
CA C SAM sing 393 n n 
CA CB SAM sing 394 n n 
CA HA SAM sing 395 n n 
C O SAM doub 396 n n 
C OXT SAM sing 397 n n 
CB CG SAM sing 398 n n 
CB HB1 SAM sing 399 n n 
CB HB2 SAM sing 400 n n 
CG SD SAM sing 401 n n 
CG HG1 SAM sing 402 n n 
CG HG2 SAM sing 403 n n 
SD CE SAM sing 404 n n 
SD C5' SAM sing 405 n n 
CE HE1 SAM sing 406 n n 
CE HE2 SAM sing 407 n n 
CE HE3 SAM sing 408 n n 
C5' C4' SAM sing 409 n n 
C5' "H5'1" SAM sing 410 n n 
C5' "H5'2" SAM sing 411 n n 
C4' O4' SAM sing 412 n n 
C4' C3' SAM sing 413 n n 
C4' H4' SAM sing 414 n n 
O4' C1' SAM sing 415 n n 
C3' O3' SAM sing 416 n n 
C3' C2' SAM sing 417 n n 
C3' H3' SAM sing 418 n n 
O3' HO3' SAM sing 419 n n 
C2' O2' SAM sing 420 n n 
C2' C1' SAM sing 421 n n 
C2' H2' SAM sing 422 n n 
O2' HO2' SAM sing 423 n n 
C1' N9 SAM sing 424 n n 
C1' H1' SAM sing 425 n n 
N9 C8 SAM sing 426 n y 
N9 C4 SAM sing 427 n y 
C8 N7 SAM doub 428 n y 
C8 H8 SAM sing 429 n n 
N7 C5 SAM sing 430 n y 
C5 C6 SAM sing 431 n y 
C5 C4 SAM doub 432 n y 
C6 N6 SAM sing 433 n n 
C6 N1 SAM doub 434 n y 
N6 HN61 SAM sing 435 n n 
N6 HN62 SAM sing 436 n n 
N1 C2 SAM sing 437 n y 
C2 N3 SAM doub 438 n y 
C2 H2 SAM sing 439 n n 
N3 C4 SAM sing 440 n y 
#
_atom_sites.entry_id                     3NVK 
_atom_sites.fract_transf_matrix[1][1]    0.00303 
_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]    0.010577 
_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]    0.010232 
_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
K 6 SAM I 1 228 1 SAM SAM . 
L 6 SAM J 1 228 1 SAM SAM . 
#
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 . . . L 6 -61.502 16.154 -67.114 1 118.85 ? N SAM 228 J 1 
HETATM 2 C CA SAM . . . L 6 -62.413 15.637 -68.141 1 128.71 ? CA SAM 228 J 1 
HETATM 3 C C SAM . . . L 6 -62.932 16.738 -69.091 1 116.01 ? C SAM 228 J 1 
HETATM 4 O O SAM . . . L 6 -62.293 17.111 -70.082 1 94.88 ? O SAM 228 J 1 
HETATM 5 C CB SAM . . . L 6 -63.557 14.835 -67.494 1 117.27 ? CB SAM 228 J 1 
HETATM 6 C CG SAM . . . L 6 -63.13 13.579 -66.726 1 110.46 ? CG SAM 228 J 1 
HETATM 7 S SD SAM . . . L 6 -63.259 12.097 -67.763 1 109.99 ? SD SAM 228 J 1 
HETATM 8 C CE SAM . . . L 6 -64.457 12.883 -68.864 1 99.64 ? CE SAM 228 J 1 
HETATM 9 C C5' SAM . . . L 6 -64.498 11.074 -66.917 1 93.19 ? C5' SAM 228 J 1 
HETATM 10 C C4' SAM . . . L 6 -64.199 9.769 -66.151 1 82.39 ? C4' SAM 228 J 1 
HETATM 11 O O4' SAM . . . L 6 -64.101 8.586 -66.904 1 73.19 ? O4' SAM 228 J 1 
HETATM 12 C C3' SAM . . . L 6 -63.027 9.706 -65.182 1 83.93 ? C3' SAM 228 J 1 
HETATM 13 O O3' SAM . . . L 6 -63.461 10.247 -63.957 1 82.58 ? O3' SAM 228 J 1 
HETATM 14 C C2' SAM . . . L 6 -62.796 8.206 -65.05 1 81.95 ? C2' SAM 228 J 1 
HETATM 15 O O2' SAM . . . L 6 -62.879 7.746 -63.719 1 78.02 ? O2' SAM 228 J 1 
HETATM 16 C C1' SAM . . . L 6 -63.948 7.653 -65.859 1 74.97 ? C1' SAM 228 J 1 
HETATM 17 N N9 SAM . . . L 6 -63.783 6.286 -66.349 1 75.22 ? N9 SAM 228 J 1 
HETATM 18 C C8 SAM . . . L 6 -62.66 5.731 -66.893 1 77.78 ? C8 SAM 228 J 1 
HETATM 19 N N7 SAM . . . L 6 -62.974 4.457 -67.226 1 82.46 ? N7 SAM 228 J 1 
HETATM 20 C C5 SAM . . . L 6 -64.268 4.195 -66.904 1 77.25 ? C5 SAM 228 J 1 
HETATM 21 C C6 SAM . . . L 6 -65.08 3.068 -67.036 1 71.47 ? C6 SAM 228 J 1 
HETATM 22 N N6 SAM . . . L 6 -64.597 1.944 -67.564 1 69.18 ? N6 SAM 228 J 1 
HETATM 23 N N1 SAM . . . L 6 -66.392 3.12 -66.621 1 65.8 ? N1 SAM 228 J 1 
HETATM 24 C C2 SAM . . . L 6 -66.885 4.274 -66.067 1 68.95 ? C2 SAM 228 J 1 
HETATM 25 N N3 SAM . . . L 6 -66.073 5.381 -65.941 1 72.21 ? N3 SAM 228 J 1 
HETATM 26 C C4 SAM . . . L 6 -64.787 5.348 -66.353 1 73.22 ? C4 SAM 228 J 1 
#
_model_server_stats.io_time_ms              45 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#