data_7RGD
#
_model_server_result.job_id            ivqJbKRflg9lie6QTfpFpg 
_model_server_result.datetime_utc      '2024-11-23 12:12:46' 
_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          7rgd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"VA","auth_seq_id":605}' 
#
_entry.id    7RGD 
#
_exptl.entry_id    7RGD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              663.425 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            NICOTINAMIDE-ADENINE-DINUCLEOTIDE 
_entity.pdbx_number_of_molecules    8 
_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            7RGD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7RGD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA 
_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    ? 
_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
? 5 M N N 
? 5 R N N 
? 5 W N N 
? 5 BA N N 
? 5 GA N N 
? 5 LA N N 
? 5 QA N N 
? 5 VA 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 372 n n 
PA O2A NAD sing 373 n n 
PA O5B NAD sing 374 n n 
PA O3 NAD sing 375 n n 
O2A HOA2 NAD sing 376 n n 
O5B C5B NAD sing 377 n n 
C5B C4B NAD sing 378 n n 
C5B H51A NAD sing 379 n n 
C5B H52A NAD sing 380 n n 
C4B O4B NAD sing 381 n n 
C4B C3B NAD sing 382 n n 
C4B H4B NAD sing 383 n n 
O4B C1B NAD sing 384 n n 
C3B O3B NAD sing 385 n n 
C3B C2B NAD sing 386 n n 
C3B H3B NAD sing 387 n n 
O3B HO3A NAD sing 388 n n 
C2B O2B NAD sing 389 n n 
C2B C1B NAD sing 390 n n 
C2B H2B NAD sing 391 n n 
O2B HO2A NAD sing 392 n n 
C1B N9A NAD sing 393 n n 
C1B H1B NAD sing 394 n n 
N9A C8A NAD sing 395 n y 
N9A C4A NAD sing 396 n y 
C8A N7A NAD doub 397 n y 
C8A H8A NAD sing 398 n n 
N7A C5A NAD sing 399 n y 
C5A C6A NAD sing 400 n y 
C5A C4A NAD doub 401 n y 
C6A N6A NAD sing 402 n n 
C6A N1A NAD doub 403 n y 
N6A H61A NAD sing 404 n n 
N6A H62A NAD sing 405 n n 
N1A C2A NAD sing 406 n y 
C2A N3A NAD doub 407 n y 
C2A H2A NAD sing 408 n n 
N3A C4A NAD sing 409 n y 
O3 PN NAD sing 410 n n 
PN O1N NAD doub 411 n n 
PN O2N NAD sing 412 n n 
PN O5D NAD sing 413 n n 
O5D C5D NAD sing 414 n n 
C5D C4D NAD sing 415 n n 
C5D H51N NAD sing 416 n n 
C5D H52N NAD sing 417 n n 
C4D O4D NAD sing 418 n n 
C4D C3D NAD sing 419 n n 
C4D H4D NAD sing 420 n n 
O4D C1D NAD sing 421 n n 
C3D O3D NAD sing 422 n n 
C3D C2D NAD sing 423 n n 
C3D H3D NAD sing 424 n n 
O3D HO3N NAD sing 425 n n 
C2D O2D NAD sing 426 n n 
C2D C1D NAD sing 427 n n 
C2D H2D NAD sing 428 n n 
O2D HO2N NAD sing 429 n n 
C1D N1N NAD sing 430 n n 
C1D H1D NAD sing 431 n n 
N1N C2N NAD sing 432 n y 
N1N C6N NAD doub 433 n y 
C2N C3N NAD doub 434 n y 
C2N H2N NAD sing 435 n n 
C3N C7N NAD sing 436 n n 
C3N C4N NAD sing 437 n y 
C7N O7N NAD doub 438 n n 
C7N N7N NAD sing 439 n n 
N7N H71N NAD sing 440 n n 
N7N H72N NAD sing 441 n n 
C4N C5N NAD doub 442 n y 
C4N H4N NAD sing 443 n n 
C5N C6N NAD sing 444 n y 
C5N H5N NAD sing 445 n n 
C6N H6N NAD sing 446 n n 
#
_atom_sites.entry_id                     7RGD 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 2 GTP A 1 601 601 GTP GTP . 
J 2 GTP A 1 602 602 GTP GTP . 
K 3 ATP A 1 603 603 ATP ATP . 
L 4 IMP A 1 604 604 IMP IMP . 
M 5 NAD A 1 605 605 NAD NAD . 
N 2 GTP B 1 601 601 GTP GTP . 
O 2 GTP B 1 602 602 GTP GTP . 
P 3 ATP B 1 603 603 ATP ATP . 
Q 4 IMP B 1 604 604 IMP IMP . 
R 5 NAD B 1 605 605 NAD NAD . 
S 2 GTP C 1 601 601 GTP GTP . 
T 2 GTP C 1 602 602 GTP GTP . 
U 3 ATP C 1 603 603 ATP ATP . 
V 4 IMP C 1 604 604 IMP IMP . 
W 5 NAD C 1 605 605 NAD NAD . 
X 2 GTP D 1 601 601 GTP GTP . 
Y 2 GTP D 1 602 602 GTP GTP . 
Z 3 ATP D 1 603 603 ATP ATP . 
AA 4 IMP D 1 604 604 IMP IMP . 
BA 5 NAD D 1 605 605 NAD NAD . 
CA 2 GTP E 1 601 601 GTP GTP . 
DA 2 GTP E 1 602 602 GTP GTP . 
EA 3 ATP E 1 603 603 ATP ATP . 
FA 4 IMP E 1 604 604 IMP IMP . 
GA 5 NAD E 1 605 605 NAD NAD . 
HA 2 GTP F 1 601 601 GTP GTP . 
IA 2 GTP F 1 602 602 GTP GTP . 
JA 3 ATP F 1 603 603 ATP ATP . 
KA 4 IMP F 1 604 604 IMP IMP . 
LA 5 NAD F 1 605 605 NAD NAD . 
MA 2 GTP G 1 601 601 GTP GTP . 
NA 2 GTP G 1 602 602 GTP GTP . 
OA 3 ATP G 1 603 603 ATP ATP . 
PA 4 IMP G 1 604 604 IMP IMP . 
QA 5 NAD G 1 605 605 NAD NAD . 
RA 2 GTP H 1 601 601 GTP GTP . 
SA 2 GTP H 1 602 602 GTP GTP . 
TA 3 ATP H 1 603 603 ATP ATP . 
UA 4 IMP H 1 604 604 IMP IMP . 
VA 5 NAD H 1 605 605 NAD NAD . 
#
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 . . . VA 5 142.192 145.935 190.534 1 43.08 ? PA NAD 605 H 1 
HETATM 2 O O1A NAD . . . VA 5 142.552 145.639 191.933 1 43.08 ? O1A NAD 605 H 1 
HETATM 3 O O2A NAD . . . VA 5 141.367 144.937 189.822 1 43.08 ? O2A NAD 605 H 1 
HETATM 4 O O5B NAD . . . VA 5 141.359 147.307 190.535 1 43.08 ? O5B NAD 605 H 1 
HETATM 5 C C5B NAD . . . VA 5 139.974 147.316 190.263 1 43.08 ? C5B NAD 605 H 1 
HETATM 6 C C4B NAD . . . VA 5 139.207 148.483 190.901 1 43.08 ? C4B NAD 605 H 1 
HETATM 7 O O4B NAD . . . VA 5 137.981 147.964 191.399 1 43.08 ? O4B NAD 605 H 1 
HETATM 8 C C3B NAD . . . VA 5 139.845 149.146 192.12 1 43.08 ? C3B NAD 605 H 1 
HETATM 9 O O3B NAD . . . VA 5 139.215 150.41 192.283 1 43.08 ? O3B NAD 605 H 1 
HETATM 10 C C2B NAD . . . VA 5 139.493 148.139 193.221 1 43.08 ? C2B NAD 605 H 1 
HETATM 11 O O2B NAD . . . VA 5 139.433 148.719 194.518 1 43.08 ? O2B NAD 605 H 1 
HETATM 12 C C1B NAD . . . VA 5 138.123 147.621 192.77 1 43.08 ? C1B NAD 605 H 1 
HETATM 13 N N9A NAD . . . VA 5 137.875 146.169 192.977 1 43.08 ? N9A NAD 605 H 1 
HETATM 14 C C8A NAD . . . VA 5 138.746 145.105 192.997 1 43.08 ? C8A NAD 605 H 1 
HETATM 15 N N7A NAD . . . VA 5 138.195 143.959 193.302 1 43.08 ? N7A NAD 605 H 1 
HETATM 16 C C5A NAD . . . VA 5 136.856 144.303 193.502 1 43.08 ? C5A NAD 605 H 1 
HETATM 17 C C6A NAD . . . VA 5 135.695 143.596 193.89 1 43.08 ? C6A NAD 605 H 1 
HETATM 18 N N6A NAD . . . VA 5 135.641 142.316 194.191 1 43.08 ? N6A NAD 605 H 1 
HETATM 19 N N1A NAD . . . VA 5 134.518 144.208 193.99 1 43.08 ? N1A NAD 605 H 1 
HETATM 20 C C2A NAD . . . VA 5 134.475 145.507 193.746 1 43.08 ? C2A NAD 605 H 1 
HETATM 21 N N3A NAD . . . VA 5 135.475 146.301 193.397 1 43.08 ? N3A NAD 605 H 1 
HETATM 22 C C4A NAD . . . VA 5 136.654 145.628 193.291 1 43.08 ? C4A NAD 605 H 1 
HETATM 23 O O3 NAD . . . VA 5 143.506 146.007 189.671 1 43.08 ? O3 NAD 605 H 1 
HETATM 24 P PN NAD . . . VA 5 144.168 147.424 189.528 1 43.08 ? PN NAD 605 H 1 
HETATM 25 O O1N NAD . . . VA 5 144.573 147.937 190.843 1 43.08 ? O1N NAD 605 H 1 
HETATM 26 O O2N NAD . . . VA 5 143.387 148.264 188.598 1 43.08 ? O2N NAD 605 H 1 
HETATM 27 O O5D NAD . . . VA 5 145.504 146.992 188.738 1 43.08 ? O5D NAD 605 H 1 
HETATM 28 C C5D NAD . . . VA 5 145.394 146.484 187.414 1 43.08 ? C5D NAD 605 H 1 
HETATM 29 C C4D NAD . . . VA 5 146.677 145.853 186.862 1 43.08 ? C4D NAD 605 H 1 
HETATM 30 O O4D NAD . . . VA 5 147.702 146.822 186.697 1 43.08 ? O4D NAD 605 H 1 
HETATM 31 C C3D NAD . . . VA 5 147.253 144.756 187.751 1 43.08 ? C3D NAD 605 H 1 
HETATM 32 O O3D NAD . . . VA 5 147.97 143.86 186.924 1 43.08 ? O3D NAD 605 H 1 
HETATM 33 C C2D NAD . . . VA 5 148.199 145.543 188.656 1 43.08 ? C2D NAD 605 H 1 
HETATM 34 O O2D NAD . . . VA 5 149.281 144.77 189.17 1 43.08 ? O2D NAD 605 H 1 
HETATM 35 C C1D NAD . . . VA 5 148.677 146.667 187.72 1 43.08 ? C1D NAD 605 H 1 
HETATM 36 N N1N NAD . . . VA 5 148.952 147.939 188.448 1 43.08 ? N1N NAD 605 H 1 
HETATM 37 C C2N NAD . . . VA 5 149.984 147.995 189.335 1 43.08 ? C2N NAD 605 H 1 
HETATM 38 C C3N NAD . . . VA 5 150.298 149.185 190.033 1 43.08 ? C3N NAD 605 H 1 
HETATM 39 C C7N NAD . . . VA 5 151.356 149.273 190.971 1 43.08 ? C7N NAD 605 H 1 
HETATM 40 O O7N NAD . . . VA 5 151.937 150.328 191.184 1 43.08 ? O7N NAD 605 H 1 
HETATM 41 N N7N NAD . . . VA 5 151.683 148.203 191.655 1 43.08 ? N7N NAD 605 H 1 
HETATM 42 C C4N NAD . . . VA 5 149.543 150.339 189.765 1 43.08 ? C4N NAD 605 H 1 
HETATM 43 C C5N NAD . . . VA 5 148.485 150.266 188.848 1 43.08 ? C5N NAD 605 H 1 
HETATM 44 C C6N NAD . . . VA 5 148.197 149.047 188.213 1 43.08 ? C6N NAD 605 H 1 
HETATM 45 H H51A NAD . . . VA 5 139.533 146.385 190.619 1 43.08 ? H51A NAD 605 H 1 
HETATM 46 H H52A NAD . . . VA 5 139.837 147.364 189.183 1 43.08 ? H52A NAD 605 H 1 
HETATM 47 H H4B NAD . . . VA 5 139.02 149.235 190.134 1 43.08 ? H4B NAD 605 H 1 
HETATM 48 H H3B NAD . . . VA 5 140.923 149.265 192.009 1 43.08 ? H3B NAD 605 H 1 
HETATM 49 H HO3A NAD . . . VA 5 139.478 150.804 193.116 1 43.08 ? HO3A NAD 605 H 1 
HETATM 50 H H2B NAD . . . VA 5 140.227 147.334 193.198 1 43.08 ? H2B NAD 605 H 1 
HETATM 51 H HO2A NAD . . . VA 5 140.324 148.805 194.856 1 43.08 ? HO2A NAD 605 H 1 
HETATM 52 H H1B NAD . . . VA 5 137.366 148.17 193.329 1 43.08 ? H1B NAD 605 H 1 
HETATM 53 H H8A NAD . . . VA 5 139.8 145.203 192.783 1 43.08 ? H8A NAD 605 H 1 
HETATM 54 H H61A NAD . . . VA 5 136.476 141.749 194.186 1 43.08 ? H61A NAD 605 H 1 
HETATM 55 H H62A NAD . . . VA 5 134.75 141.947 194.489 1 43.08 ? H62A NAD 605 H 1 
HETATM 56 H H2A NAD . . . VA 5 133.509 145.979 193.842 1 43.08 ? H2A NAD 605 H 1 
HETATM 57 H H51N NAD . . . VA 5 145.1 147.295 186.748 1 43.08 ? H51N NAD 605 H 1 
HETATM 58 H H52N NAD . . . VA 5 144.61 145.73 187.374 1 43.08 ? H52N NAD 605 H 1 
HETATM 59 H H4D NAD . . . VA 5 146.427 145.425 185.892 1 43.08 ? H4D NAD 605 H 1 
HETATM 60 H H3D NAD . . . VA 5 146.478 144.243 188.319 1 43.08 ? H3D NAD 605 H 1 
HETATM 61 H HO3N NAD . . . VA 5 147.878 142.987 187.31 1 43.08 ? HO3N NAD 605 H 1 
HETATM 62 H H2D NAD . . . VA 5 147.624 145.966 189.479 1 43.08 ? H2D NAD 605 H 1 
HETATM 63 H HO2N NAD . . . VA 5 149.139 143.836 189.003 1 43.08 ? HO2N NAD 605 H 1 
HETATM 64 H H1D NAD . . . VA 5 149.596 146.332 187.241 1 43.08 ? H1D NAD 605 H 1 
HETATM 65 H H2N NAD . . . VA 5 150.555 147.089 189.47 1 43.08 ? H2N NAD 605 H 1 
HETATM 66 H H71N NAD . . . VA 5 152.448 148.29 192.307 1 43.08 ? H71N NAD 605 H 1 
HETATM 67 H H72N NAD . . . VA 5 151.206 147.323 191.527 1 43.08 ? H72N NAD 605 H 1 
HETATM 68 H H4N NAD . . . VA 5 149.758 151.267 190.273 1 43.08 ? H4N NAD 605 H 1 
HETATM 69 H H5N NAD . . . VA 5 147.872 151.134 188.66 1 43.08 ? H5N NAD 605 H 1 
HETATM 70 H H6N NAD . . . VA 5 147.357 148.969 187.539 1 43.08 ? H6N NAD 605 H 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    96 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           70 
#