data_7LNG
#
_model_server_result.job_id            5-oVyfh1MmWyfTvN8khpMA 
_model_server_result.datetime_utc      '2024-11-24 13:29:35' 
_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          7lng 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":101}' 
#
_entry.id    7LNG 
#
_exptl.entry_id    7LNG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              269.254 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-AMINO-1-[(1S,3R,4R,7S)-7-HYDROXY-1-(HYDROXYMETHYL)-2,5-DIOXABICYCLO[2.2.1]HEPT-3-YL]-5-METHYLPYRIMIDIN-2(1H)-ONE 
_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            7LNG 
_cell.length_a            45.165 
_cell.length_b            45.165 
_cell.length_c            82.831 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7LNG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,G,H,I,J,K,L,M,N 
_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    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
? 5 F N N 
? 5 J 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 P A 5 A A 5 1_555 D O3' LCG . A LCG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.646 ? 
covale ? covale2 A O3' C 13 A C 13 1_555 E P TG . A TG 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.634 ? 
covale ? covale3 C O3' LCC . A LCC 101 1_555 D P LCG . A LCG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? 
covale ? covale4 C P LCC . A LCC 101 1_555 K O3' LCC . B LCC 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.643 ? 
covale ? covale5 F O3' LKC . A LKC 104 1_555 G P LCC . A LCC 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.612 ? 
covale ? covale6 G O3' LCC . A LCC 105 1_555 H P LCC . A LCC 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.65 ? 
covale ? covale7 H O3' LCC . A LCC 106 1_555 M P LCG . B LCG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.684 ? 
covale ? covale8 B P A 5 B A 5 1_555 M O3' LCG . B LCG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.62 ? 
covale ? covale9 B O3' C 13 B C 13 1_555 N P TG . B TG 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? 
covale ? covale10 J O3' LKC . B LKC 101 1_555 K P LCC . B LCC 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.64 ? 
hydrog WATSON-CRICK hydrog1 A N1 A 5 A A 5 1_555 B N3 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N6 A 5 A A 5 1_555 B O4 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A N3 C 6 A C 6 1_555 B N1 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N4 C 6 A C 6 1_555 B O6 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A O2 C 6 A C 6 1_555 B N2 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A N3 U 7 A U 7 1_555 B N1 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A O4 U 7 A U 7 1_555 B N6 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N3 U 8 A U 8 1_555 B N1 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O4 U 8 A U 8 1_555 B N6 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 A 9 A A 9 1_555 B N3 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N6 A 9 A A 9 1_555 B O4 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N1 A 10 A A 10 1_555 B N3 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N6 A 10 A A 10 1_555 B O4 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N1 G 11 A G 11 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N2 G 11 A G 11 1_555 B O2 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A O6 G 11 A G 11 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N3 U 12 A U 12 1_555 B N1 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A O4 U 12 A U 12 1_555 B N6 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'C11 H15 N3 O5' 
_chem_comp.formula_weight    269.254 
_chem_comp.id                LKC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-AMINO-1-[(1S,3R,4R,7S)-7-HYDROXY-1-(HYDROXYMETHYL)-2,5-DIOXABICYCLO[2.2.1]HEPT-3-YL]-5-METHYLPYRIMIDIN-2(1H)-ONE 
_chem_comp.type              'rna linking' 
_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
N1 C2 LKC sing 282 n n 
N1 C6 LKC sing 283 n n 
N1 C1' LKC sing 284 n n 
C2 N3 LKC sing 285 n n 
C2 O2 LKC doub 286 n n 
N3 C4 LKC doub 287 n n 
C4 C5 LKC sing 288 n n 
C4 N4 LKC sing 289 n n 
C5 C6 LKC doub 290 n n 
C5 C5A LKC sing 291 n n 
C6 H6 LKC sing 292 n n 
N4 H41 LKC sing 293 n n 
N4 H42 LKC sing 294 n n 
C1' C2' LKC sing 295 n n 
C1' O4' LKC sing 296 n n 
C1' H1' LKC sing 297 n n 
C2' C3' LKC sing 298 n n 
C2' O2' LKC sing 299 n n 
C2' "H2'1" LKC sing 300 n n 
C3' C4' LKC sing 301 n n 
C3' O3' LKC sing 302 n n 
C3' H3' LKC sing 303 n n 
C4' O4' LKC sing 304 n n 
C4' C5' LKC sing 305 n n 
C4' C6' LKC sing 306 n n 
O3' H3T LKC sing 307 n n 
C5' O5' LKC sing 308 n n 
C5' "H5'1" LKC sing 309 n n 
C5' "H5'2" LKC sing 310 n n 
O5' H5T LKC sing 311 n n 
C5A H5M1 LKC sing 312 n n 
C5A H5M2 LKC sing 313 n n 
C5A H5M3 LKC sing 314 n n 
O2' C6' LKC sing 315 n n 
C6' "H6'1" LKC sing 316 n n 
C6' "H6'2" LKC sing 317 n n 
#
_atom_sites.entry_id                     7LNG 
_atom_sites.fract_transf_matrix[1][1]    0.022141 
_atom_sites.fract_transf_matrix[1][2]    0.012783 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.025566 
_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]    0.012073 
_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 LCC A 1 101 3 LCC LCC . 
D 3 LCG A 1 102 4 LCG LCG . 
E 4 TG A 1 103 14 TG TG . 
F 5 LKC A 1 104 1 LKC LCC . 
G 2 LCC A 1 105 2 LCC LCC . 
H 2 LCC A 1 106 3 LCC LCC . 
I 6 GP3 A 1 107 101 GP3 GP3 . 
J 5 LKC B 1 101 1 LKC LCC . 
K 2 LCC B 1 102 2 LCC LCC . 
L 6 GP3 B 1 103 101 GP3 GP3 . 
M 3 LCG B 1 104 4 LCG LCG . 
N 4 TG B 1 105 14 TG TG . 
#
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 N1 LKC . . . J 5 6.782 14.328 39.615 1 51.22 0 N1 LKC 101 B 1 
HETATM 2 C C2 LKC . . . J 5 8.078 14.019 39.846 1 59.16 0 C2 LKC 101 B 1 
HETATM 3 N N3 LKC . . . J 5 8.444 12.722 39.883 1 60.06 0 N3 LKC 101 B 1 
HETATM 4 C C4 LKC . . . J 5 7.542 11.727 39.73 1 62.72 0 C4 LKC 101 B 1 
HETATM 5 C C5 LKC . . . J 5 6.206 12.017 39.484 1 61.35 0 C5 LKC 101 B 1 
HETATM 6 C C6 LKC . . . J 5 5.826 13.34 39.428 1 53.53 0 C6 LKC 101 B 1 
HETATM 7 O O2 LKC . . . J 5 8.948 14.898 40.023 1 42.91 0 O2 LKC 101 B 1 
HETATM 8 N N4 LKC . . . J 5 7.867 10.433 39.769 1 60.42 0 N4 LKC 101 B 1 
HETATM 9 C C1' LKC . . . J 5 6.316 15.729 39.562 1 47.13 0 C1' LKC 101 B 1 
HETATM 10 C C2' LKC . . . J 5 6.659 16.446 38.248 1 42.76 0 C2' LKC 101 B 1 
HETATM 11 C C3' LKC . . . J 5 5.338 16.125 37.487 1 41.68 0 C3' LKC 101 B 1 
HETATM 12 C C4' LKC . . . J 5 4.566 16.85 38.549 1 41.08 0 C4' LKC 101 B 1 
HETATM 13 O O4' LKC . . . J 5 4.807 15.834 39.608 1 45.49 0 O4' LKC 101 B 1 
HETATM 14 O O3' LKC . . . J 5 5.189 16.632 36.11 1 43.53 0 O3' LKC 101 B 1 
HETATM 15 C C5' LKC . . . J 5 3.118 17.031 38.228 1 42.23 0 C5' LKC 101 B 1 
HETATM 16 O O5' LKC . . . J 5 2.628 15.644 38.179 1 38.14 0 O5' LKC 101 B 1 
HETATM 17 C C5A LKC . . . J 5 5.247 11.03 39.291 1 67.26 0 C5A LKC 101 B 1 
HETATM 18 O O2' LKC . . . J 5 6.676 17.914 38.451 1 40.37 0 O2' LKC 101 B 1 
HETATM 19 C C6' LKC . . . J 5 5.306 18.179 38.93 1 41.83 0 C6' LKC 101 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           188 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           19 
#