data_7DN9
#
_model_server_result.job_id            Zo_uG-btHvPwKh9YpJ5C6Q 
_model_server_result.datetime_utc      '2024-10-25 20:27:28' 
_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          7dn9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":401}' 
#
_entry.id    7DN9 
#
_exptl.entry_id    7DN9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              663.425 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            NICOTINAMIDE-ADENINE-DINUCLEOTIDE 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          104.8 
_cell.angle_gamma         90 
_cell.entry_id            7DN9 
_cell.length_a            104.711 
_cell.length_b            105.576 
_cell.length_c            105.839 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7DN9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
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 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K 1 1 
C,D,L,M,N 2 1 
E,F,O,P,Q 3 1 
G,H,R,S,T 4 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 I N N 
? 3 L N N 
? 3 O N N 
? 3 R 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 B OG1 THR 32 B THR 48 1_555 J MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? 
metalc ? metalc2 J MG MG . B MG 201 1_555 K O1B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc3 M MG MG . D MG 201 1_555 N O1B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc4 F OG1 THR 32 F THR 48 1_555 P MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? 
metalc ? metalc5 P MG MG . F MG 201 1_555 Q O1B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
metalc ? metalc6 H OG1 THR 32 H THR 48 1_555 S MG MG . H MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? 
metalc ? metalc7 S MG MG . H MG 201 1_555 T O3B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? 
metalc ? metalc8 S MG MG . H MG 201 1_555 T O1B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
#
_chem_comp.formula           'C21 H27 N7 O14 P2' 
_chem_comp.formula_weight    663.425 
_chem_comp.id                NAD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              NICOTINAMIDE-ADENINE-DINUCLEOTIDE 
_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
PA O1A NAD doub 280 n n 
PA O2A NAD sing 281 n n 
PA O5B NAD sing 282 n n 
PA O3 NAD sing 283 n n 
O2A HOA2 NAD sing 284 n n 
O5B C5B NAD sing 285 n n 
C5B C4B NAD sing 286 n n 
C5B H51A NAD sing 287 n n 
C5B H52A NAD sing 288 n n 
C4B O4B NAD sing 289 n n 
C4B C3B NAD sing 290 n n 
C4B H4B NAD sing 291 n n 
O4B C1B NAD sing 292 n n 
C3B O3B NAD sing 293 n n 
C3B C2B NAD sing 294 n n 
C3B H3B NAD sing 295 n n 
O3B HO3A NAD sing 296 n n 
C2B O2B NAD sing 297 n n 
C2B C1B NAD sing 298 n n 
C2B H2B NAD sing 299 n n 
O2B HO2A NAD sing 300 n n 
C1B N9A NAD sing 301 n n 
C1B H1B NAD sing 302 n n 
N9A C8A NAD sing 303 n y 
N9A C4A NAD sing 304 n y 
C8A N7A NAD doub 305 n y 
C8A H8A NAD sing 306 n n 
N7A C5A NAD sing 307 n y 
C5A C6A NAD sing 308 n y 
C5A C4A NAD doub 309 n y 
C6A N6A NAD sing 310 n n 
C6A N1A NAD doub 311 n y 
N6A H61A NAD sing 312 n n 
N6A H62A NAD sing 313 n n 
N1A C2A NAD sing 314 n y 
C2A N3A NAD doub 315 n y 
C2A H2A NAD sing 316 n n 
N3A C4A NAD sing 317 n y 
O3 PN NAD sing 318 n n 
PN O1N NAD doub 319 n n 
PN O2N NAD sing 320 n n 
PN O5D NAD sing 321 n n 
O5D C5D NAD sing 322 n n 
C5D C4D NAD sing 323 n n 
C5D H51N NAD sing 324 n n 
C5D H52N NAD sing 325 n n 
C4D O4D NAD sing 326 n n 
C4D C3D NAD sing 327 n n 
C4D H4D NAD sing 328 n n 
O4D C1D NAD sing 329 n n 
C3D O3D NAD sing 330 n n 
C3D C2D NAD sing 331 n n 
C3D H3D NAD sing 332 n n 
O3D HO3N NAD sing 333 n n 
C2D O2D NAD sing 334 n n 
C2D C1D NAD sing 335 n n 
C2D H2D NAD sing 336 n n 
O2D HO2N NAD sing 337 n n 
C1D N1N NAD sing 338 n n 
C1D H1D NAD sing 339 n n 
N1N C2N NAD sing 340 n y 
N1N C6N NAD doub 341 n y 
C2N C3N NAD doub 342 n y 
C2N H2N NAD sing 343 n n 
C3N C7N NAD sing 344 n n 
C3N C4N NAD sing 345 n y 
C7N O7N NAD doub 346 n n 
C7N N7N NAD sing 347 n n 
N7N H71N NAD sing 348 n n 
N7N H72N NAD sing 349 n n 
C4N C5N NAD doub 350 n y 
C4N H4N NAD sing 351 n n 
C5N C6N NAD sing 352 n y 
C5N H5N NAD sing 353 n n 
C6N H6N NAD sing 354 n n 
#
_atom_sites.entry_id                     7DN9 
_atom_sites.fract_transf_matrix[1][1]    0.00955 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002524 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009472 
_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]    0.009773 
_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
I 3 NAD A 1 401 401 NAD NAD . 
J 4 MG B 1 201 201 MG MG . 
K 5 GDP B 1 202 202 GDP GDP . 
L 3 NAD C 1 401 401 NAD NAD . 
M 4 MG D 1 201 201 MG MG . 
N 5 GDP D 1 202 202 GDP GDP . 
O 3 NAD E 1 401 401 NAD NAD . 
P 4 MG F 1 201 201 MG MG . 
Q 5 GDP F 1 202 202 GDP GDP . 
R 3 NAD G 1 401 401 NAD NAD . 
S 4 MG H 1 201 201 MG MG . 
T 5 GDP H 1 202 202 GDP GDP . 
#
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 P PA NAD . . . L 3 -0.426 16.094 -22.233 1 90.02 ? PA NAD 401 C 1 
HETATM 2 O O1A NAD . . . L 3 0.19 16.603 -23.495 1 67.81 ? O1A NAD 401 C 1 
HETATM 3 O O2A NAD . . . L 3 0.216 14.925 -21.563 1 76.05 ? O2A NAD 401 C 1 
HETATM 4 O O5B NAD . . . L 3 -1.976 15.772 -22.484 1 69 ? O5B NAD 401 C 1 
HETATM 5 C C5B NAD . . . L 3 -2.376 14.402 -22.735 1 61.35 ? C5B NAD 401 C 1 
HETATM 6 C C4B NAD . . . L 3 -3.467 14.033 -21.76 1 74.86 ? C4B NAD 401 C 1 
HETATM 7 O O4B NAD . . . L 3 -4.041 12.761 -22.163 1 85.87 ? O4B NAD 401 C 1 
HETATM 8 C C3B NAD . . . L 3 -3.018 13.828 -20.305 1 77.33 ? C3B NAD 401 C 1 
HETATM 9 O O3B NAD . . . L 3 -4.066 14.185 -19.413 1 82.23 ? O3B NAD 401 C 1 
HETATM 10 C C2B NAD . . . L 3 -2.81 12.312 -20.259 1 72.63 ? C2B NAD 401 C 1 
HETATM 11 O O2B NAD . . . L 3 -2.782 11.773 -18.955 1 66.69 ? O2B NAD 401 C 1 
HETATM 12 C C1B NAD . . . L 3 -4.024 11.877 -21.068 1 77.33 ? C1B NAD 401 C 1 
HETATM 13 N N9A NAD . . . L 3 -3.942 10.514 -21.577 1 76.64 ? N9A NAD 401 C 1 
HETATM 14 C C8A NAD . . . L 3 -2.799 9.808 -21.857 1 67.67 ? C8A NAD 401 C 1 
HETATM 15 N N7A NAD . . . L 3 -3.033 8.601 -22.309 1 67.95 ? N7A NAD 401 C 1 
HETATM 16 C C5A NAD . . . L 3 -4.417 8.504 -22.332 1 74.58 ? C5A NAD 401 C 1 
HETATM 17 C C6A NAD . . . L 3 -5.288 7.465 -22.714 1 80.36 ? C6A NAD 401 C 1 
HETATM 18 N N6A NAD . . . L 3 -4.877 6.282 -23.164 1 77.41 ? N6A NAD 401 C 1 
HETATM 19 N N1A NAD . . . L 3 -6.618 7.696 -22.613 1 82.2 ? N1A NAD 401 C 1 
HETATM 20 C C2A NAD . . . L 3 -7.027 8.888 -22.161 1 81.28 ? C2A NAD 401 C 1 
HETATM 21 N N3A NAD . . . L 3 -6.304 9.934 -21.774 1 84.38 ? N3A NAD 401 C 1 
HETATM 22 C C4A NAD . . . L 3 -4.99 9.678 -21.883 1 80.16 ? C4A NAD 401 C 1 
HETATM 23 O O3 NAD . . . L 3 -0.543 17.291 -21.171 1 78.92 ? O3 NAD 401 C 1 
HETATM 24 P PN NAD . . . L 3 0.332 17.703 -19.891 1 71.51 ? PN NAD 401 C 1 
HETATM 25 O O1N NAD . . . L 3 0.658 16.461 -19.129 1 60.79 ? O1N NAD 401 C 1 
HETATM 26 O O2N NAD . . . L 3 -0.368 18.813 -19.177 1 55.68 ? O2N NAD 401 C 1 
HETATM 27 O O5D NAD . . . L 3 1.664 18.271 -20.579 1 68.67 ? O5D NAD 401 C 1 
HETATM 28 C C5D NAD . . . L 3 1.544 19.296 -21.598 1 70.59 ? C5D NAD 401 C 1 
HETATM 29 C C4D NAD . . . L 3 2.873 19.458 -22.292 1 55.33 ? C4D NAD 401 C 1 
HETATM 30 O O4D NAD . . . L 3 3.926 19.493 -21.31 1 46.76 ? O4D NAD 401 C 1 
HETATM 31 C C3D NAD . . . L 3 3.298 18.337 -23.247 1 50.92 ? C3D NAD 401 C 1 
HETATM 32 O O3D NAD . . . L 3 2.652 18.418 -24.512 1 56.84 ? O3D NAD 401 C 1 
HETATM 33 C C2D NAD . . . L 3 4.812 18.566 -23.309 1 52.69 ? C2D NAD 401 C 1 
HETATM 34 O O2D NAD . . . L 3 5.161 19.48 -24.335 1 55.24 ? O2D NAD 401 C 1 
HETATM 35 C C1D NAD . . . L 3 5.161 19.158 -21.941 1 52.39 ? C1D NAD 401 C 1 
HETATM 36 N N1N NAD . . . L 3 5.867 18.169 -21.075 1 55.06 ? N1N NAD 401 C 1 
HETATM 37 C C2N NAD . . . L 3 5.147 17.341 -20.247 1 49.77 ? C2N NAD 401 C 1 
HETATM 38 C C3N NAD . . . L 3 5.799 16.418 -19.439 1 49.46 ? C3N NAD 401 C 1 
HETATM 39 C C7N NAD . . . L 3 4.983 15.56 -18.504 1 46.41 ? C7N NAD 401 C 1 
HETATM 40 O O7N NAD . . . L 3 5.557 14.816 -17.712 1 44.11 ? O7N NAD 401 C 1 
HETATM 41 N N7N NAD . . . L 3 3.663 15.65 -18.581 1 48.81 ? N7N NAD 401 C 1 
HETATM 42 C C4N NAD . . . L 3 7.182 16.306 -19.519 1 49.63 ? C4N NAD 401 C 1 
HETATM 43 C C5N NAD . . . L 3 7.89 17.141 -20.354 1 53.06 ? C5N NAD 401 C 1 
HETATM 44 C C6N NAD . . . L 3 7.217 18.075 -21.109 1 53.93 ? C6N NAD 401 C 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           44 
#