data_5LDH
#
_model_server_result.job_id            uKBSe1wus2D-OqiyMt6AQQ 
_model_server_result.datetime_utc      '2024-11-08 09:06:39' 
_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          5ldh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":332}' 
#
_entry.id    5LDH 
#
_exptl.entry_id    5LDH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              765.514 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(3S)-5-(3-CARBOXY-3-HYDROXYPROPYL) NICOTINAMIDE-ADENINE-DINUCLEOTIDE' 
_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         120 
_cell.entry_id            5LDH 
_cell.length_a            133.6 
_cell.length_b            133.6 
_cell.length_c            113.5 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LDH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 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
covale ? covale1 A C ACE 1 A ACE 0 1_555 A N ALA 2 A ALA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale2 A NE2 HIS 187 A HIS 188 1_555 D O5 CIT . A CIT 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? 
covale ? covale3 A CD2 HIS 187 A HIS 188 1_555 D O4 CIT . A CIT 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? 
covale ? covale4 B C ACE 1 B ACE 0 1_555 B N ALA 2 B ALA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale5 B CD2 HIS 187 B HIS 188 1_555 F O4 CIT . B CIT 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? 
covale ? covale6 B NE2 HIS 187 B HIS 188 1_555 F O5 CIT . B CIT 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? 
#
_chem_comp.formula           'C25 H33 N7 O17 P2' 
_chem_comp.formula_weight    765.514 
_chem_comp.id                LNC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(3S)-5-(3-CARBOXY-3-HYDROXYPROPYL) NICOTINAMIDE-ADENINE-DINUCLEOTIDE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     S-LAC-NAD+ 
#
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
N7N C7N LNC sing 218 n n 
N7N HN71 LNC sing 219 n n 
N7N HN72 LNC sing 220 n n 
C7N O7N LNC doub 221 n n 
C7N C3N LNC sing 222 n n 
C3N C4N LNC doub 223 n y 
C3N C2N LNC sing 224 n y 
C4N C5N LNC sing 225 n y 
C4N H4 LNC sing 226 n n 
C5N CGS LNC sing 227 n n 
C5N C6N LNC doub 228 n y 
CGS CBS LNC sing 229 n n 
CGS HGS1 LNC sing 230 n n 
CGS HGS2 LNC sing 231 n n 
CBS CAS LNC sing 232 n n 
CBS HBS1 LNC sing 233 n n 
CBS HBS2 LNC sing 234 n n 
CAS OAS LNC sing 235 n n 
CAS CS LNC sing 236 n n 
CAS HAS LNC sing 237 n n 
OAS H1 LNC sing 238 n n 
CS O1S LNC doub 239 n n 
CS O2S LNC sing 240 n n 
O2S H2S LNC sing 241 n n 
C6N N1N LNC sing 242 n y 
C6N H6 LNC sing 243 n n 
N1N C2N LNC doub 244 n y 
N1N C1D LNC sing 245 n n 
C2N H2 LNC sing 246 n n 
C1D O4D LNC sing 247 n n 
C1D C2D LNC sing 248 n n 
C1D H1' LNC sing 249 n n 
O4D C4D LNC sing 250 n n 
C4D C5D LNC sing 251 n n 
C4D C3D LNC sing 252 n n 
C4D H4' LNC sing 253 n n 
C5D O5D LNC sing 254 n n 
C5D "H5'1" LNC sing 255 n n 
C5D "H5'2" LNC sing 256 n n 
O5D PN LNC sing 257 n n 
PN O1N LNC sing 258 n n 
PN O2N LNC doub 259 n n 
PN O3 LNC sing 260 n n 
O1N HO1 LNC sing 261 n n 
O3 PA LNC sing 262 n n 
PA O1A LNC sing 263 n n 
PA O2A LNC doub 264 n n 
PA O5B LNC sing 265 n n 
O5B C5B LNC sing 266 n n 
C5B C4B LNC sing 267 n n 
C5B H11 LNC sing 268 n n 
C5B H12 LNC sing 269 n n 
C4B O4B LNC sing 270 n n 
C4B C3B LNC sing 271 n n 
C4B H5 LNC sing 272 n n 
O4B C1B LNC sing 273 n n 
C1B C2B LNC sing 274 n n 
C1B N9A LNC sing 275 n n 
C1B H7 LNC sing 276 n n 
C2B O2B LNC sing 277 n n 
C2B C3B LNC sing 278 n n 
C2B H2' LNC sing 279 n n 
O2B H8 LNC sing 280 n n 
C3B O3B LNC sing 281 n n 
C3B H3' LNC sing 282 n n 
O3B H9 LNC sing 283 n n 
N9A C8A LNC sing 284 n y 
N9A C4A LNC sing 285 n y 
C8A N7A LNC doub 286 n y 
C8A H10 LNC sing 287 n n 
N7A C5A LNC sing 288 n y 
C5A C6A LNC sing 289 n y 
C5A C4A LNC doub 290 n y 
C6A N6A LNC sing 291 n n 
C6A N1A LNC doub 292 n y 
N6A HN61 LNC sing 293 n n 
N6A HN62 LNC sing 294 n n 
N1A C2A LNC sing 295 n y 
C2A N3A LNC doub 296 n y 
C2A H111 LNC sing 297 n n 
N3A C4A LNC sing 298 n y 
C3D O3D LNC sing 299 n n 
C3D C2D LNC sing 300 n n 
C3D H122 LNC sing 301 n n 
O3D H13 LNC sing 302 n n 
C2D O2D LNC sing 303 n n 
C2D H14 LNC sing 304 n n 
O2D H15 LNC sing 305 n n 
#
_atom_sites.entry_id                     5LDH 
_atom_sites.fract_transf_matrix[1][1]    0.007485 
_atom_sites.fract_transf_matrix[1][2]    0.004321 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008643 
_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]    0.008811 
_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 LNC A 1 332 1 LNC NAL . 
D 3 CIT A 1 333 2 CIT CIT . 
E 2 LNC B 1 332 1 LNC NAL . 
F 3 CIT B 1 333 2 CIT CIT . 
#
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 N7N LNC . . . E 2 -33.295 -59.597 24.183 1 0 ? N7N LNC 332 B 1 
HETATM 2 C C7N LNC . . . E 2 -32.932 -58.43 24.752 1 0 ? C7N LNC 332 B 1 
HETATM 3 O O7N LNC . . . E 2 -31.776 -58.065 24.592 1 0 ? O7N LNC 332 B 1 
HETATM 4 C C3N LNC . . . E 2 -33.881 -57.586 25.553 1 0 ? C3N LNC 332 B 1 
HETATM 5 C C4N LNC . . . E 2 -33.411 -56.546 26.257 1 0 ? C4N LNC 332 B 1 
HETATM 6 C C5N LNC . . . E 2 -34.311 -55.797 26.978 1 0 ? C5N LNC 332 B 1 
HETATM 7 C CGS LNC . . . E 2 -33.817 -54.626 27.776 1 0 ? CGS LNC 332 B 1 
HETATM 8 C CBS LNC . . . E 2 -32.444 -54.941 28.398 1 0 ? CBS LNC 332 B 1 
HETATM 9 C CAS LNC . . . E 2 -31.632 -55.827 27.468 1 0 ? CAS LNC 332 B 1 
HETATM 10 O OAS LNC . . . E 2 -31.185 -56.982 28.164 1 0 ? OAS LNC 332 B 1 
HETATM 11 C CS LNC . . . E 2 -30.435 -55.083 26.951 1 0 ? CS LNC 332 B 1 
HETATM 12 O O1S LNC . . . E 2 -29.259 -55.434 27.312 1 0 ? O1S LNC 332 B 1 
HETATM 13 O O2S LNC . . . E 2 -30.592 -54.099 26.148 1 0 ? O2S LNC 332 B 1 
HETATM 14 C C6N LNC . . . E 2 -35.642 -56.11 26.974 1 0 ? C6N LNC 332 B 1 
HETATM 15 N N1N LNC . . . E 2 -36.063 -57.167 26.251 1 0 ? N1N LNC 332 B 1 
HETATM 16 C C2N LNC . . . E 2 -35.25 -57.794 25.636 1 0 ? C2N LNC 332 B 1 
HETATM 17 C C1D LNC . . . E 2 -37.473 -57.561 26.199 1 0 ? C1D LNC 332 B 1 
HETATM 18 O O4D LNC . . . E 2 -38.094 -56.948 25.08 1 0 ? O4D LNC 332 B 1 
HETATM 19 C C4D LNC . . . E 2 -39.537 -56.978 25.277 1 0 ? C4D LNC 332 B 1 
HETATM 20 C C5D LNC . . . E 2 -40.152 -55.774 24.591 1 0 ? C5D LNC 332 B 1 
HETATM 21 O O5D LNC . . . E 2 -40.175 -54.651 25.493 1 0 ? O5D LNC 332 B 1 
HETATM 22 P PN LNC . . . E 2 -41.104 -53.396 25.145 1 0 ? PN LNC 332 B 1 
HETATM 23 O O1N LNC . . . E 2 -41.552 -52.749 26.398 1 0 ? O1N LNC 332 B 1 
HETATM 24 O O2N LNC . . . E 2 -40.412 -52.52 24.174 1 0 ? O2N LNC 332 B 1 
HETATM 25 O O3 LNC . . . E 2 -42.347 -54.109 24.434 1 0 ? O3 LNC 332 B 1 
HETATM 26 P PA LNC . . . E 2 -43.539 -53.735 25.433 1 0 ? PA LNC 332 B 1 
HETATM 27 O O1A LNC . . . E 2 -43.346 -54.437 26.723 1 0 ? O1A LNC 332 B 1 
HETATM 28 O O2A LNC . . . E 2 -43.684 -52.265 25.509 1 0 ? O2A LNC 332 B 1 
HETATM 29 O O5B LNC . . . E 2 -44.797 -54.36 24.666 1 0 ? O5B LNC 332 B 1 
HETATM 30 C C5B LNC . . . E 2 -45.563 -53.52 23.781 1 0 ? C5B LNC 332 B 1 
HETATM 31 C C4B LNC . . . E 2 -46.656 -54.331 23.115 1 0 ? C4B LNC 332 B 1 
HETATM 32 O O4B LNC . . . E 2 -46.727 -55.653 23.722 1 0 ? O4B LNC 332 B 1 
HETATM 33 C C1B LNC . . . E 2 -48.049 -56.158 23.61 1 0 ? C1B LNC 332 B 1 
HETATM 34 C C2B LNC . . . E 2 -48.928 -55.05 23.037 1 0 ? C2B LNC 332 B 1 
HETATM 35 O O2B LNC . . . E 2 -49.041 -55.291 21.646 1 0 ? O2B LNC 332 B 1 
HETATM 36 C C3B LNC . . . E 2 -48.081 -53.806 23.301 1 0 ? C3B LNC 332 B 1 
HETATM 37 O O3B LNC . . . E 2 -48.366 -52.736 22.416 1 0 ? O3B LNC 332 B 1 
HETATM 38 N N9A LNC . . . E 2 -48.481 -56.62 24.958 1 0 ? N9A LNC 332 B 1 
HETATM 39 C C8A LNC . . . E 2 -48.391 -55.961 26.15 1 0 ? C8A LNC 332 B 1 
HETATM 40 N N7A LNC . . . E 2 -48.858 -56.632 27.156 1 0 ? N7A LNC 332 B 1 
HETATM 41 C C5A LNC . . . E 2 -49.29 -57.825 26.593 1 0 ? C5A LNC 332 B 1 
HETATM 42 C C6A LNC . . . E 2 -49.896 -58.986 27.13 1 0 ? C6A LNC 332 B 1 
HETATM 43 N N6A LNC . . . E 2 -50.179 -59.131 28.433 1 0 ? N6A LNC 332 B 1 
HETATM 44 N N1A LNC . . . E 2 -50.194 -59.984 26.279 1 0 ? N1A LNC 332 B 1 
HETATM 45 C C2A LNC . . . E 2 -49.909 -59.833 24.987 1 0 ? C2A LNC 332 B 1 
HETATM 46 N N3A LNC . . . E 2 -49.353 -58.812 24.372 1 0 ? N3A LNC 332 B 1 
HETATM 47 C C4A LNC . . . E 2 -49.064 -57.826 25.247 1 0 ? C4A LNC 332 B 1 
HETATM 48 C C3D LNC . . . E 2 -39.708 -57.141 26.788 1 0 ? C3D LNC 332 B 1 
HETATM 49 O O3D LNC . . . E 2 -40.201 -58.442 27.055 1 0 ? O3D LNC 332 B 1 
HETATM 50 C C2D LNC . . . E 2 -38.299 -57.035 27.368 1 0 ? C2D LNC 332 B 1 
HETATM 51 O O2D LNC . . . E 2 -38.095 -57.772 28.562 1 0 ? O2D LNC 332 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           51 
#