data_2NV4
#
_model_server_result.job_id            C679uFNTtxGIMai5tDEh-Q 
_model_server_result.datetime_utc      '2024-11-01 12:30:37' 
_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          2nv4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":201}' 
#
_entry.id    2NV4 
#
_exptl.entry_id    2NV4 
_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            2NV4 
_cell.length_a            48.812 
_cell.length_b            73.496 
_cell.length_c            78.545 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2NV4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_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
? 3 D N N 
? 3 E 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
disulf ? disulf1 A SG CYS 130 A CYS 130 1_555 B SG CYS 130 B CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
covale ? covale1 A C MSE 1 A MSE 1 1_555 A N ILE 2 A ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 A C TRP 56 A TRP 56 1_555 A N MSE 57 A MSE 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale3 A C MSE 57 A MSE 57 1_555 A N ASP 58 A ASP 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale4 B C MSE 1 B MSE 1 1_555 B N ILE 2 B ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale5 B C TRP 56 B TRP 56 1_555 B N MSE 57 B MSE 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale6 B C MSE 57 B MSE 57 1_555 B N ASP 58 B ASP 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
#
_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 302 n n 
N HN1 SAM sing 303 n n 
N HN2 SAM sing 304 n n 
CA C SAM sing 305 n n 
CA CB SAM sing 306 n n 
CA HA SAM sing 307 n n 
C O SAM doub 308 n n 
C OXT SAM sing 309 n n 
CB CG SAM sing 310 n n 
CB HB1 SAM sing 311 n n 
CB HB2 SAM sing 312 n n 
CG SD SAM sing 313 n n 
CG HG1 SAM sing 314 n n 
CG HG2 SAM sing 315 n n 
SD CE SAM sing 316 n n 
SD C5' SAM sing 317 n n 
CE HE1 SAM sing 318 n n 
CE HE2 SAM sing 319 n n 
CE HE3 SAM sing 320 n n 
C5' C4' SAM sing 321 n n 
C5' "H5'1" SAM sing 322 n n 
C5' "H5'2" SAM sing 323 n n 
C4' O4' SAM sing 324 n n 
C4' C3' SAM sing 325 n n 
C4' H4' SAM sing 326 n n 
O4' C1' SAM sing 327 n n 
C3' O3' SAM sing 328 n n 
C3' C2' SAM sing 329 n n 
C3' H3' SAM sing 330 n n 
O3' HO3' SAM sing 331 n n 
C2' O2' SAM sing 332 n n 
C2' C1' SAM sing 333 n n 
C2' H2' SAM sing 334 n n 
O2' HO2' SAM sing 335 n n 
C1' N9 SAM sing 336 n n 
C1' H1' SAM sing 337 n n 
N9 C8 SAM sing 338 n y 
N9 C4 SAM sing 339 n y 
C8 N7 SAM doub 340 n y 
C8 H8 SAM sing 341 n n 
N7 C5 SAM sing 342 n y 
C5 C6 SAM sing 343 n y 
C5 C4 SAM doub 344 n y 
C6 N6 SAM sing 345 n n 
C6 N1 SAM doub 346 n y 
N6 HN61 SAM sing 347 n n 
N6 HN62 SAM sing 348 n n 
N1 C2 SAM sing 349 n y 
C2 N3 SAM doub 350 n y 
C2 H2 SAM sing 351 n n 
N3 C4 SAM sing 352 n y 
#
_atom_sites.entry_id                     2NV4 
_atom_sites.fract_transf_matrix[1][1]    0.020487 
_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]    0.013606 
_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]    0.012732 
_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 ACT A 1 148 1 ACT ACY . 
D 3 SAM A 1 201 201 SAM SAM . 
E 3 SAM B 1 202 202 SAM SAM . 
F 4 HOH A 1 202 2 HOH TIP . 
F 4 HOH A 2 203 5 HOH TIP . 
F 4 HOH A 3 204 6 HOH TIP . 
F 4 HOH A 4 205 7 HOH TIP . 
F 4 HOH A 5 206 9 HOH TIP . 
F 4 HOH A 6 207 10 HOH TIP . 
F 4 HOH A 7 208 11 HOH TIP . 
F 4 HOH A 8 209 20 HOH TIP . 
F 4 HOH A 9 210 21 HOH TIP . 
F 4 HOH A 10 211 22 HOH TIP . 
F 4 HOH A 11 212 23 HOH TIP . 
F 4 HOH A 12 213 28 HOH TIP . 
F 4 HOH A 13 214 29 HOH TIP . 
F 4 HOH A 14 215 32 HOH TIP . 
F 4 HOH A 15 216 33 HOH TIP . 
F 4 HOH A 16 217 34 HOH TIP . 
F 4 HOH A 17 218 39 HOH TIP . 
F 4 HOH A 18 219 41 HOH TIP . 
F 4 HOH A 19 220 43 HOH TIP . 
F 4 HOH A 20 221 47 HOH TIP . 
F 4 HOH A 21 222 49 HOH TIP . 
F 4 HOH A 22 223 50 HOH TIP . 
F 4 HOH A 23 224 52 HOH TIP . 
G 4 HOH B 1 203 1 HOH TIP . 
G 4 HOH B 2 204 3 HOH TIP . 
G 4 HOH B 3 205 4 HOH TIP . 
G 4 HOH B 4 206 8 HOH TIP . 
G 4 HOH B 5 207 12 HOH TIP . 
G 4 HOH B 6 208 13 HOH TIP . 
G 4 HOH B 7 209 14 HOH TIP . 
G 4 HOH B 8 210 15 HOH TIP . 
G 4 HOH B 9 211 16 HOH TIP . 
G 4 HOH B 10 212 17 HOH TIP . 
G 4 HOH B 11 213 18 HOH TIP . 
G 4 HOH B 12 214 19 HOH TIP . 
G 4 HOH B 13 215 24 HOH TIP . 
G 4 HOH B 14 216 25 HOH TIP . 
G 4 HOH B 15 217 26 HOH TIP . 
G 4 HOH B 16 218 27 HOH TIP . 
G 4 HOH B 17 219 30 HOH TIP . 
G 4 HOH B 18 220 31 HOH TIP . 
G 4 HOH B 19 221 35 HOH TIP . 
G 4 HOH B 20 222 36 HOH TIP . 
G 4 HOH B 21 223 37 HOH TIP . 
G 4 HOH B 22 224 38 HOH TIP . 
G 4 HOH B 23 225 40 HOH TIP . 
G 4 HOH B 24 226 42 HOH TIP . 
G 4 HOH B 25 227 44 HOH TIP . 
G 4 HOH B 26 228 45 HOH TIP . 
G 4 HOH B 27 229 46 HOH TIP . 
G 4 HOH B 28 230 48 HOH TIP . 
G 4 HOH B 29 231 51 HOH TIP . 
#
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 . . . D 3 18.082 38.802 26.747 1 52.08 ? N SAM 201 A 1 
HETATM 2 C CA SAM . . . D 3 17.424 39.38 25.567 1 51.75 ? CA SAM 201 A 1 
HETATM 3 C C SAM . . . D 3 17.827 38.622 24.359 1 53.07 ? C SAM 201 A 1 
HETATM 4 O O SAM . . . D 3 17.379 38.95 23.276 1 53.8 ? O SAM 201 A 1 
HETATM 5 O OXT SAM . . . D 3 18.586 37.688 24.445 1 57.67 ? OXT SAM 201 A 1 
HETATM 6 C CB SAM . . . D 3 17.85 40.808 25.356 1 51.03 ? CB SAM 201 A 1 
HETATM 7 C CG SAM . . . D 3 17.405 41.654 26.513 1 46.97 ? CG SAM 201 A 1 
HETATM 8 S SD SAM . . . D 3 17.904 43.341 26.158 1 42.95 ? SD SAM 201 A 1 
HETATM 9 C CE SAM . . . D 3 19.69 43.247 26.493 1 40.53 ? CE SAM 201 A 1 
HETATM 10 C C5' SAM . . . D 3 17.202 44.268 27.526 1 40.36 ? C5' SAM 201 A 1 
HETATM 11 C C4' SAM . . . D 3 17.503 45.716 27.252 1 37.87 ? C4' SAM 201 A 1 
HETATM 12 O O4' SAM . . . D 3 16.952 46.077 25.953 1 34.02 ? O4' SAM 201 A 1 
HETATM 13 C C3' SAM . . . D 3 16.919 46.628 28.337 1 36.59 ? C3' SAM 201 A 1 
HETATM 14 O O3' SAM . . . D 3 17.912 47.259 29.151 1 40.63 ? O3' SAM 201 A 1 
HETATM 15 C C2' SAM . . . D 3 16.024 47.637 27.567 1 35.81 ? C2' SAM 201 A 1 
HETATM 16 O O2' SAM . . . D 3 16.487 48.979 27.772 1 39.35 ? O2' SAM 201 A 1 
HETATM 17 C C1' SAM . . . D 3 16.11 47.247 26.056 1 33.12 ? C1' SAM 201 A 1 
HETATM 18 N N9 SAM . . . D 3 14.733 47.024 25.502 1 28.51 ? N9 SAM 201 A 1 
HETATM 19 C C8 SAM . . . D 3 13.741 46.205 25.995 1 25 ? C8 SAM 201 A 1 
HETATM 20 N N7 SAM . . . D 3 12.672 46.294 25.254 1 22.29 ? N7 SAM 201 A 1 
HETATM 21 C C5 SAM . . . D 3 12.887 47.159 24.245 1 24.04 ? C5 SAM 201 A 1 
HETATM 22 C C6 SAM . . . D 3 12.112 47.662 23.155 1 24.12 ? C6 SAM 201 A 1 
HETATM 23 N N6 SAM . . . D 3 10.806 47.261 22.958 1 26.69 ? N6 SAM 201 A 1 
HETATM 24 N N1 SAM . . . D 3 12.685 48.554 22.306 1 23.93 ? N1 SAM 201 A 1 
HETATM 25 C C2 SAM . . . D 3 13.948 48.968 22.473 1 24.97 ? C2 SAM 201 A 1 
HETATM 26 N N3 SAM . . . D 3 14.696 48.53 23.48 1 25.97 ? N3 SAM 201 A 1 
HETATM 27 C C4 SAM . . . D 3 14.219 47.639 24.379 1 25.22 ? C4 SAM 201 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#