data_6KDY
#
_model_server_result.job_id            2zz5cUGE0rY-VkO-Vc_FwQ 
_model_server_result.datetime_utc      '2024-12-21 12:16:07' 
_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          6kdy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":401}' 
#
_entry.id    6KDY 
#
_exptl.entry_id    6KDY 
_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          100.31 
_cell.angle_gamma         90 
_cell.entry_id            6KDY 
_cell.length_a            99.46 
_cell.length_b            162.979 
_cell.length_c            114.407 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6KDY 
_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 1 1 
C,D,K,L,M 2 1 
E,F,N,O 3 1 
G,H,P,Q 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 K N N 
? 3 N N N 
? 3 P N N 
#
_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 300 n n 
PA O2A NAD sing 301 n n 
PA O5B NAD sing 302 n n 
PA O3 NAD sing 303 n n 
O2A HOA2 NAD sing 304 n n 
O5B C5B NAD sing 305 n n 
C5B C4B NAD sing 306 n n 
C5B H51A NAD sing 307 n n 
C5B H52A NAD sing 308 n n 
C4B O4B NAD sing 309 n n 
C4B C3B NAD sing 310 n n 
C4B H4B NAD sing 311 n n 
O4B C1B NAD sing 312 n n 
C3B O3B NAD sing 313 n n 
C3B C2B NAD sing 314 n n 
C3B H3B NAD sing 315 n n 
O3B HO3A NAD sing 316 n n 
C2B O2B NAD sing 317 n n 
C2B C1B NAD sing 318 n n 
C2B H2B NAD sing 319 n n 
O2B HO2A NAD sing 320 n n 
C1B N9A NAD sing 321 n n 
C1B H1B NAD sing 322 n n 
N9A C8A NAD sing 323 n y 
N9A C4A NAD sing 324 n y 
C8A N7A NAD doub 325 n y 
C8A H8A NAD sing 326 n n 
N7A C5A NAD sing 327 n y 
C5A C6A NAD sing 328 n y 
C5A C4A NAD doub 329 n y 
C6A N6A NAD sing 330 n n 
C6A N1A NAD doub 331 n y 
N6A H61A NAD sing 332 n n 
N6A H62A NAD sing 333 n n 
N1A C2A NAD sing 334 n y 
C2A N3A NAD doub 335 n y 
C2A H2A NAD sing 336 n n 
N3A C4A NAD sing 337 n y 
O3 PN NAD sing 338 n n 
PN O1N NAD doub 339 n n 
PN O2N NAD sing 340 n n 
PN O5D NAD sing 341 n n 
O5D C5D NAD sing 342 n n 
C5D C4D NAD sing 343 n n 
C5D H51N NAD sing 344 n n 
C5D H52N NAD sing 345 n n 
C4D O4D NAD sing 346 n n 
C4D C3D NAD sing 347 n n 
C4D H4D NAD sing 348 n n 
O4D C1D NAD sing 349 n n 
C3D O3D NAD sing 350 n n 
C3D C2D NAD sing 351 n n 
C3D H3D NAD sing 352 n n 
O3D HO3N NAD sing 353 n n 
C2D O2D NAD sing 354 n n 
C2D C1D NAD sing 355 n n 
C2D H2D NAD sing 356 n n 
O2D HO2N NAD sing 357 n n 
C1D N1N NAD sing 358 n n 
C1D H1D NAD sing 359 n n 
N1N C2N NAD sing 360 n y 
N1N C6N NAD doub 361 n y 
C2N C3N NAD doub 362 n y 
C2N H2N NAD sing 363 n n 
C3N C7N NAD sing 364 n n 
C3N C4N NAD sing 365 n y 
C7N O7N NAD doub 366 n n 
C7N N7N NAD sing 367 n n 
N7N H71N NAD sing 368 n n 
N7N H72N NAD sing 369 n n 
C4N C5N NAD doub 370 n y 
C4N H4N NAD sing 371 n n 
C5N C6N NAD sing 372 n y 
C5N H5N NAD sing 373 n n 
C6N H6N NAD sing 374 n n 
#
_atom_sites.entry_id                     6KDY 
_atom_sites.fract_transf_matrix[1][1]    0.010054 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001828 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006136 
_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]    0.008884 
_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 3 NAD NAD . 
J 4 PG4 B 1 401 2 PG4 PG4 . 
K 3 NAD C 1 401 2 NAD NAD . 
L 5 2PE D 1 401 1 2PE 2PE . 
M 4 PG4 D 1 402 1 PG4 PG4 . 
N 3 NAD E 1 401 1 NAD NAD . 
O 6 PE7 F 1 401 1 PE7 PE7 . 
P 3 NAD G 1 401 4 NAD NAD . 
Q 7 P6G H 1 401 1 P6G P6G . 
#
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 . . . K 3 30.164 -1.983 46.647 1 79.16 ? PA NAD 401 C 1 
HETATM 2 O O1A NAD . . . K 3 31.135 -0.936 46.187 1 65.14 ? O1A NAD 401 C 1 
HETATM 3 O O2A NAD . . . K 3 29.178 -2.352 45.574 1 84.65 ? O2A NAD 401 C 1 
HETATM 4 O O5B NAD . . . K 3 29.336 -1.276 47.873 1 83.68 ? O5B NAD 401 C 1 
HETATM 5 C C5B NAD . . . K 3 28.488 -2.195 48.499 1 78.46 ? C5B NAD 401 C 1 
HETATM 6 C C4B NAD . . . K 3 28 -1.511 49.81 1 74.85 ? C4B NAD 401 C 1 
HETATM 7 O O4B NAD . . . K 3 28.279 -0.2 49.764 1 80.6 ? O4B NAD 401 C 1 
HETATM 8 C C3B NAD . . . K 3 26.481 -1.634 49.689 1 73.3 ? C3B NAD 401 C 1 
HETATM 9 O O3B NAD . . . K 3 25.923 -1.455 50.946 1 78.24 ? O3B NAD 401 C 1 
HETATM 10 C C2B NAD . . . K 3 26.183 -0.456 48.734 1 81.48 ? C2B NAD 401 C 1 
HETATM 11 O O2B NAD . . . K 3 24.758 -0.015 48.746 1 104.45 ? O2B NAD 401 C 1 
HETATM 12 C C1B NAD . . . K 3 26.942 0.474 49.196 1 80.25 ? C1B NAD 401 C 1 
HETATM 13 N N9A NAD . . . K 3 27.354 1.548 48.26 1 82.31 ? N9A NAD 401 C 1 
HETATM 14 C C8A NAD . . . K 3 28.477 1.487 47.563 1 78.34 ? C8A NAD 401 C 1 
HETATM 15 N N7A NAD . . . K 3 28.593 2.555 46.807 1 74.16 ? N7A NAD 401 C 1 
HETATM 16 C C5A NAD . . . K 3 27.524 3.344 47.039 1 81.62 ? C5A NAD 401 C 1 
HETATM 17 C C6A NAD . . . K 3 27.135 4.566 46.528 1 83.01 ? C6A NAD 401 C 1 
HETATM 18 N N6A NAD . . . K 3 27.856 5.335 45.554 1 85.58 ? N6A NAD 401 C 1 
HETATM 19 N N1A NAD . . . K 3 26.005 5.135 46.935 1 80.19 ? N1A NAD 401 C 1 
HETATM 20 C C2A NAD . . . K 3 25.242 4.482 47.863 1 85.48 ? C2A NAD 401 C 1 
HETATM 21 N N3A NAD . . . K 3 25.598 3.303 48.362 1 81.54 ? N3A NAD 401 C 1 
HETATM 22 C C4A NAD . . . K 3 26.733 2.717 47.969 1 81.86 ? C4A NAD 401 C 1 
HETATM 23 O O3 NAD . . . K 3 30.851 -3.359 47.205 1 75.57 ? O3 NAD 401 C 1 
HETATM 24 P PN NAD . . . K 3 30.315 -4.864 46.889 1 76.15 ? PN NAD 401 C 1 
HETATM 25 O O1N NAD . . . K 3 28.862 -4.993 47.252 1 70.01 ? O1N NAD 401 C 1 
HETATM 26 O O2N NAD . . . K 3 31.149 -5.877 47.643 1 77.39 ? O2N NAD 401 C 1 
HETATM 27 O O5D NAD . . . K 3 30.533 -4.946 45.272 1 93.93 ? O5D NAD 401 C 1 
HETATM 28 C C5D NAD . . . K 3 29.841 -5.767 44.37 1 87.47 ? C5D NAD 401 C 1 
HETATM 29 C C4D NAD . . . K 3 30.549 -5.683 43.073 1 77.72 ? C4D NAD 401 C 1 
HETATM 30 O O4D NAD . . . K 3 31.123 -4.488 42.822 1 76 ? O4D NAD 401 C 1 
HETATM 31 C C3D NAD . . . K 3 31.778 -6.756 43.195 1 78.06 ? C3D NAD 401 C 1 
HETATM 32 O O3D NAD . . . K 3 31.602 -7.862 42.25 1 76.58 ? O3D NAD 401 C 1 
HETATM 33 C C2D NAD . . . K 3 32.863 -6.126 42.994 1 76.03 ? C2D NAD 401 C 1 
HETATM 34 O O2D NAD . . . K 3 33.778 -6.944 42.14 1 86.38 ? O2D NAD 401 C 1 
HETATM 35 C C1D NAD . . . K 3 32.493 -4.756 42.28 1 77.9 ? C1D NAD 401 C 1 
HETATM 36 N N1N NAD . . . K 3 33.326 -3.802 42.553 1 81.61 ? N1N NAD 401 C 1 
HETATM 37 C C2N NAD . . . K 3 33.825 -3.008 41.505 1 79.24 ? C2N NAD 401 C 1 
HETATM 38 C C3N NAD . . . K 3 34.823 -2.031 41.785 1 79.54 ? C3N NAD 401 C 1 
HETATM 39 C C7N NAD . . . K 3 35.397 -1.079 40.677 1 80.59 ? C7N NAD 401 C 1 
HETATM 40 O O7N NAD . . . K 3 36.019 -1.589 39.84 1 84.35 ? O7N NAD 401 C 1 
HETATM 41 N N7N NAD . . . K 3 35.211 0.398 40.574 1 73.15 ? N7N NAD 401 C 1 
HETATM 42 C C4N NAD . . . K 3 35.24 -1.888 43.047 1 78.62 ? C4N NAD 401 C 1 
HETATM 43 C C5N NAD . . . K 3 34.771 -2.666 44.04 1 76.81 ? C5N NAD 401 C 1 
HETATM 44 C C6N NAD . . . K 3 33.799 -3.628 43.809 1 80.83 ? C6N NAD 401 C 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    43 
_model_server_stats.query_time_ms           349 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           44 
#