data_4YR9
#
_model_server_result.job_id            5nXZjvU4fvkYPTihPp4L8Q 
_model_server_result.datetime_utc      '2025-03-09 02:32:00' 
_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          4yr9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1001}' 
#
_entry.id    4YR9 
#
_exptl.entry_id    4YR9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              663.425 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            NICOTINAMIDE-ADENINE-DINUCLEOTIDE 
_entity.pdbx_number_of_molecules    6 
_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            4YR9 
_cell.length_a            74.15 
_cell.length_b            160.13 
_cell.length_c            194.3 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YR9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 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,C,G,H,K,L,P,R 1 1 
B,D,I,J,M,Q,S 2 1 
E,F,N,O,T,U 3 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
? 2 G N N 
? 2 I N N 
? 2 K N N 
? 2 M N N 
? 2 N N N 
? 2 O 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 250 n n 
PA O2A NAD sing 251 n n 
PA O5B NAD sing 252 n n 
PA O3 NAD sing 253 n n 
O2A HOA2 NAD sing 254 n n 
O5B C5B NAD sing 255 n n 
C5B C4B NAD sing 256 n n 
C5B H51A NAD sing 257 n n 
C5B H52A NAD sing 258 n n 
C4B O4B NAD sing 259 n n 
C4B C3B NAD sing 260 n n 
C4B H4B NAD sing 261 n n 
O4B C1B NAD sing 262 n n 
C3B O3B NAD sing 263 n n 
C3B C2B NAD sing 264 n n 
C3B H3B NAD sing 265 n n 
O3B HO3A NAD sing 266 n n 
C2B O2B NAD sing 267 n n 
C2B C1B NAD sing 268 n n 
C2B H2B NAD sing 269 n n 
O2B HO2A NAD sing 270 n n 
C1B N9A NAD sing 271 n n 
C1B H1B NAD sing 272 n n 
N9A C8A NAD sing 273 n y 
N9A C4A NAD sing 274 n y 
C8A N7A NAD doub 275 n y 
C8A H8A NAD sing 276 n n 
N7A C5A NAD sing 277 n y 
C5A C6A NAD sing 278 n y 
C5A C4A NAD doub 279 n y 
C6A N6A NAD sing 280 n n 
C6A N1A NAD doub 281 n y 
N6A H61A NAD sing 282 n n 
N6A H62A NAD sing 283 n n 
N1A C2A NAD sing 284 n y 
C2A N3A NAD doub 285 n y 
C2A H2A NAD sing 286 n n 
N3A C4A NAD sing 287 n y 
O3 PN NAD sing 288 n n 
PN O1N NAD doub 289 n n 
PN O2N NAD sing 290 n n 
PN O5D NAD sing 291 n n 
O5D C5D NAD sing 292 n n 
C5D C4D NAD sing 293 n n 
C5D H51N NAD sing 294 n n 
C5D H52N NAD sing 295 n n 
C4D O4D NAD sing 296 n n 
C4D C3D NAD sing 297 n n 
C4D H4D NAD sing 298 n n 
O4D C1D NAD sing 299 n n 
C3D O3D NAD sing 300 n n 
C3D C2D NAD sing 301 n n 
C3D H3D NAD sing 302 n n 
O3D HO3N NAD sing 303 n n 
C2D O2D NAD sing 304 n n 
C2D C1D NAD sing 305 n n 
C2D H2D NAD sing 306 n n 
O2D HO2N NAD sing 307 n n 
C1D N1N NAD sing 308 n n 
C1D H1D NAD sing 309 n n 
N1N C2N NAD sing 310 n y 
N1N C6N NAD doub 311 n y 
C2N C3N NAD doub 312 n y 
C2N H2N NAD sing 313 n n 
C3N C7N NAD sing 314 n n 
C3N C4N NAD sing 315 n y 
C7N O7N NAD doub 316 n n 
C7N N7N NAD sing 317 n n 
N7N H71N NAD sing 318 n n 
N7N H72N NAD sing 319 n n 
C4N C5N NAD doub 320 n y 
C4N H4N NAD sing 321 n n 
C5N C6N NAD sing 322 n y 
C5N H5N NAD sing 323 n n 
C6N H6N NAD sing 324 n n 
#
_atom_sites.entry_id                     4YR9 
_atom_sites.fract_transf_matrix[1][1]    0.013486 
_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]    0.006245 
_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]    0.005147 
_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
G 2 NAD A 1 1001 1001 NAD NAD . 
H 3 GOL A 1 1002 6 GOL GOL . 
I 2 NAD B 1 1001 1001 NAD NAD . 
J 3 GOL B 1 1002 2 GOL GOL . 
K 2 NAD C 1 1001 1001 NAD NAD . 
L 3 GOL C 1 1002 5 GOL GOL . 
M 2 NAD D 1 1001 1001 NAD NAD . 
N 2 NAD E 1 1001 1001 NAD NAD . 
O 2 NAD F 1 1001 1001 NAD NAD . 
P 4 HOH A 1 1101 23 HOH HOH . 
P 4 HOH A 2 1102 6 HOH HOH . 
P 4 HOH A 3 1103 15 HOH HOH . 
P 4 HOH A 4 1104 22 HOH HOH . 
P 4 HOH A 5 1105 25 HOH HOH . 
P 4 HOH A 6 1106 28 HOH HOH . 
P 4 HOH A 7 1107 41 HOH HOH . 
P 4 HOH A 8 1108 42 HOH HOH . 
P 4 HOH A 9 1109 43 HOH HOH . 
P 4 HOH A 10 1110 45 HOH HOH . 
P 4 HOH A 11 1111 46 HOH HOH . 
P 4 HOH A 12 1112 47 HOH HOH . 
P 4 HOH A 13 1113 57 HOH HOH . 
P 4 HOH A 14 1114 81 HOH HOH . 
Q 4 HOH B 1 1101 24 HOH HOH . 
Q 4 HOH B 2 1102 33 HOH HOH . 
Q 4 HOH B 3 1103 18 HOH HOH . 
Q 4 HOH B 4 1104 4 HOH HOH . 
Q 4 HOH B 5 1105 10 HOH HOH . 
Q 4 HOH B 6 1106 13 HOH HOH . 
Q 4 HOH B 7 1107 37 HOH HOH . 
Q 4 HOH B 8 1108 39 HOH HOH . 
Q 4 HOH B 9 1109 48 HOH HOH . 
Q 4 HOH B 10 1110 49 HOH HOH . 
Q 4 HOH B 11 1111 50 HOH HOH . 
Q 4 HOH B 12 1112 51 HOH HOH . 
Q 4 HOH B 13 1113 52 HOH HOH . 
Q 4 HOH B 14 1114 53 HOH HOH . 
Q 4 HOH B 15 1115 54 HOH HOH . 
Q 4 HOH B 16 1116 55 HOH HOH . 
Q 4 HOH B 17 1117 56 HOH HOH . 
Q 4 HOH B 18 1118 58 HOH HOH . 
Q 4 HOH B 19 1119 60 HOH HOH . 
Q 4 HOH B 20 1120 61 HOH HOH . 
Q 4 HOH B 21 1121 62 HOH HOH . 
R 4 HOH C 1 1101 7 HOH HOH . 
R 4 HOH C 2 1102 8 HOH HOH . 
R 4 HOH C 3 1103 12 HOH HOH . 
R 4 HOH C 4 1104 14 HOH HOH . 
R 4 HOH C 5 1105 16 HOH HOH . 
R 4 HOH C 6 1106 17 HOH HOH . 
R 4 HOH C 7 1107 20 HOH HOH . 
R 4 HOH C 8 1108 30 HOH HOH . 
R 4 HOH C 9 1109 63 HOH HOH . 
R 4 HOH C 10 1110 64 HOH HOH . 
S 4 HOH D 1 1101 21 HOH HOH . 
S 4 HOH D 2 1102 68 HOH HOH . 
S 4 HOH D 3 1103 1 HOH HOH . 
S 4 HOH D 4 1104 2 HOH HOH . 
S 4 HOH D 5 1105 5 HOH HOH . 
S 4 HOH D 6 1106 27 HOH HOH . 
S 4 HOH D 7 1107 38 HOH HOH . 
S 4 HOH D 8 1108 66 HOH HOH . 
S 4 HOH D 9 1109 67 HOH HOH . 
S 4 HOH D 10 1110 69 HOH HOH . 
S 4 HOH D 11 1111 70 HOH HOH . 
S 4 HOH D 12 1112 71 HOH HOH . 
S 4 HOH D 13 1113 72 HOH HOH . 
S 4 HOH D 14 1114 73 HOH HOH . 
S 4 HOH D 15 1115 74 HOH HOH . 
S 4 HOH D 16 1116 75 HOH HOH . 
T 4 HOH E 1 1101 3 HOH HOH . 
T 4 HOH E 2 1102 11 HOH HOH . 
T 4 HOH E 3 1103 19 HOH HOH . 
T 4 HOH E 4 1104 35 HOH HOH . 
T 4 HOH E 5 1105 76 HOH HOH . 
T 4 HOH E 6 1106 78 HOH HOH . 
T 4 HOH E 7 1107 79 HOH HOH . 
U 4 HOH F 1 1101 36 HOH HOH . 
U 4 HOH F 2 1102 40 HOH HOH . 
U 4 HOH F 3 1103 80 HOH HOH . 
U 4 HOH F 4 1104 9 HOH HOH . 
U 4 HOH F 5 1105 26 HOH HOH . 
U 4 HOH F 6 1106 29 HOH HOH . 
U 4 HOH F 7 1107 77 HOH HOH . 
#
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 . . . I 2 -17.241 -25.909 99.823 1 29.44 ? PA NAD 1001 B 1 
HETATM 2 O O1A NAD . . . I 2 -18.411 -25.029 99.45 1 29.47 -1 O1A NAD 1001 B 1 
HETATM 3 O O2A NAD . . . I 2 -15.818 -25.499 99.535 1 28.94 ? O2A NAD 1001 B 1 
HETATM 4 O O5B NAD . . . I 2 -17.381 -26.18 101.401 1 30.13 ? O5B NAD 1001 B 1 
HETATM 5 C C5B NAD . . . I 2 -16.542 -27.11 102.089 1 31.14 ? C5B NAD 1001 B 1 
HETATM 6 C C4B NAD . . . I 2 -16.978 -27.149 103.547 1 31.88 ? C4B NAD 1001 B 1 
HETATM 7 O O4B NAD . . . I 2 -16.084 -27.951 104.326 1 32.05 ? O4B NAD 1001 B 1 
HETATM 8 C C3B NAD . . . I 2 -16.982 -25.75 104.156 1 32.21 ? C3B NAD 1001 B 1 
HETATM 9 O O3B NAD . . . I 2 -18.288 -25.466 104.67 1 32.09 ? O3B NAD 1001 B 1 
HETATM 10 C C2B NAD . . . I 2 -15.97 -25.809 105.276 1 32.2 ? C2B NAD 1001 B 1 
HETATM 11 O O2B NAD . . . I 2 -16.428 -25.061 106.403 1 33.8 ? O2B NAD 1001 B 1 
HETATM 12 C C1B NAD . . . I 2 -15.894 -27.298 105.582 1 32.18 ? C1B NAD 1001 B 1 
HETATM 13 N N9A NAD . . . I 2 -14.611 -27.689 106.223 1 32.31 ? N9A NAD 1001 B 1 
HETATM 14 C C8A NAD . . . I 2 -13.385 -27.195 105.958 1 32.09 ? C8A NAD 1001 B 1 
HETATM 15 N N7A NAD . . . I 2 -12.441 -27.779 106.738 1 31.75 ? N7A NAD 1001 B 1 
HETATM 16 C C5A NAD . . . I 2 -13.068 -28.671 107.528 1 31.98 ? C5A NAD 1001 B 1 
HETATM 17 C C6A NAD . . . I 2 -12.676 -29.633 108.59 1 31.7 ? C6A NAD 1001 B 1 
HETATM 18 N N6A NAD . . . I 2 -11.384 -29.765 108.975 1 31.68 ? N6A NAD 1001 B 1 
HETATM 19 N N1A NAD . . . I 2 -13.651 -30.378 109.161 1 31.78 ? N1A NAD 1001 B 1 
HETATM 20 C C2A NAD . . . I 2 -14.945 -30.272 108.795 1 31.98 ? C2A NAD 1001 B 1 
HETATM 21 N N3A NAD . . . I 2 -15.37 -29.419 107.845 1 32.45 ? N3A NAD 1001 B 1 
HETATM 22 C C4A NAD . . . I 2 -14.499 -28.606 107.186 1 32.25 ? C4A NAD 1001 B 1 
HETATM 23 O O3 NAD . . . I 2 -17.445 -27.38 99.197 1 30.13 ? O3 NAD 1001 B 1 
HETATM 24 P PN NAD . . . I 2 -18.521 -27.7 98.046 1 30.34 ? PN NAD 1001 B 1 
HETATM 25 O O1N NAD . . . I 2 -18.291 -26.729 96.91 1 30.84 -1 O1N NAD 1001 B 1 
HETATM 26 O O2N NAD . . . I 2 -19.89 -27.843 98.663 1 30.28 ? O2N NAD 1001 B 1 
HETATM 27 O O5D NAD . . . I 2 -18.044 -29.148 97.55 1 30.97 ? O5D NAD 1001 B 1 
HETATM 28 C C5D NAD . . . I 2 -18.079 -30.299 98.391 1 31.11 ? C5D NAD 1001 B 1 
HETATM 29 C C4D NAD . . . I 2 -17.223 -31.387 97.751 1 31.48 ? C4D NAD 1001 B 1 
HETATM 30 O O4D NAD . . . I 2 -17.497 -31.476 96.344 1 31.77 ? O4D NAD 1001 B 1 
HETATM 31 C C3D NAD . . . I 2 -15.74 -31.079 97.892 1 31.54 ? C3D NAD 1001 B 1 
HETATM 32 O O3D NAD . . . I 2 -15.049 -32.287 98.228 1 31.37 ? O3D NAD 1001 B 1 
HETATM 33 C C2D NAD . . . I 2 -15.307 -30.599 96.522 1 31.79 ? C2D NAD 1001 B 1 
HETATM 34 O O2D NAD . . . I 2 -13.955 -30.969 96.246 1 31.92 ? O2D NAD 1001 B 1 
HETATM 35 C C1D NAD . . . I 2 -16.283 -31.315 95.594 1 32.16 ? C1D NAD 1001 B 1 
HETATM 36 N N1N NAD . . . I 2 -16.488 -30.601 94.324 1 32.43 ? N1N NAD 1001 B 1 
HETATM 37 C C2N NAD . . . I 2 -17.211 -29.46 94.253 1 32.94 ? C2N NAD 1001 B 1 
HETATM 38 C C3N NAD . . . I 2 -17.39 -28.802 93.027 1 33.21 ? C3N NAD 1001 B 1 
HETATM 39 C C7N NAD . . . I 2 -18.19 -27.528 92.924 1 33.25 ? C7N NAD 1001 B 1 
HETATM 40 O O7N NAD . . . I 2 -17.86 -26.658 92.131 1 33.02 ? O7N NAD 1001 B 1 
HETATM 41 N N7N NAD . . . I 2 -19.256 -27.362 93.703 1 33.8 ? N7N NAD 1001 B 1 
HETATM 42 C C4N NAD . . . I 2 -16.813 -29.347 91.88 1 32.88 ? C4N NAD 1001 B 1 
HETATM 43 C C5N NAD . . . I 2 -16.071 -30.52 91.979 1 32.59 ? C5N NAD 1001 B 1 
HETATM 44 C C6N NAD . . . I 2 -15.928 -31.13 93.222 1 32.29 ? C6N NAD 1001 B 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           44 
#