data_3F1J
#
_model_server_result.job_id            LcEkBYPShaRS4Lo7r17pVA 
_model_server_result.datetime_utc      '2025-03-09 04:21:46' 
_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          3f1j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":300}' 
#
_entry.id    3F1J 
#
_exptl.entry_id    3F1J 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              323.197 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            3F1J 
_cell.length_a            143.57 
_cell.length_b            143.57 
_cell.length_c            143.57 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3F1J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        211 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 3 2' 
#
_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    1,2,3,4 
#
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' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
3 'crystal symmetry operation' 21_555 z,y,-x 0 0 1 0 1 0 -1 0 0 0 0 0 
4 'crystal symmetry operation' 23_555 -z,y,x 0 0 -1 0 1 0 1 0 0 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 LEU 22 A LEU 22 1_555 A N MSE 23 A MSE 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale2 A C MSE 23 A MSE 23 1_555 A N LEU 24 A LEU 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale3 A C TYR 100 A TYR 100 1_555 A N MSE 101 A MSE 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale4 A C MSE 101 A MSE 101 1_555 A N PHE 102 A PHE 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
#
_chem_comp.formula           'C9 H14 N3 O8 P' 
_chem_comp.formula_weight    323.197 
_chem_comp.id                C5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-5'-MONOPHOSPHATE" 
_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
O3P P C5P sing 70 n n 
O3P HOP3 C5P sing 71 n n 
P O1P C5P doub 72 n n 
P O2P C5P sing 73 n n 
P O5' C5P sing 74 n n 
O2P HOP2 C5P sing 75 n n 
O5' C5' C5P sing 76 n n 
C5' C4' C5P sing 77 n n 
C5' "H5'1" C5P sing 78 n n 
C5' "H5'2" C5P sing 79 n n 
C4' O4' C5P sing 80 n n 
C4' C3' C5P sing 81 n n 
C4' H4' C5P sing 82 n n 
O4' C1' C5P sing 83 n n 
C3' O3' C5P sing 84 n n 
C3' C2' C5P sing 85 n n 
C3' H3' C5P sing 86 n n 
O3' HO3' C5P sing 87 n n 
C2' O2' C5P sing 88 n n 
C2' C1' C5P sing 89 n n 
C2' "H2'1" C5P sing 90 n n 
O2' HO2' C5P sing 91 n n 
C1' N1 C5P sing 92 n n 
C1' H1' C5P sing 93 n n 
N1 C2 C5P sing 94 n n 
N1 C6 C5P sing 95 n n 
C2 N3 C5P sing 96 n n 
C2 O2 C5P doub 97 n n 
N3 C4 C5P doub 98 n n 
C4 C5 C5P sing 99 n n 
C4 N4 C5P sing 100 n n 
C5 C6 C5P doub 101 n n 
C5 H5 C5P sing 102 n n 
C6 H6 C5P sing 103 n n 
N4 HN41 C5P sing 104 n n 
N4 HN42 C5P sing 105 n n 
#
_atom_sites.entry_id                     3F1J 
_atom_sites.fract_transf_matrix[1][1]    0.006965 
_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]    0.006965 
_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]    0.006965 
_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
B 2 C5P A 1 300 300 C5P CYT . 
C 3 SO4 A 1 301 301 SO4 SO4 . 
D 3 SO4 A 1 302 302 SO4 SO4 . 
E 3 SO4 A 1 303 303 SO4 SO4 . 
F 4 HOH A 1 201 201 HOH HOH . 
F 4 HOH A 2 202 202 HOH HOH . 
F 4 HOH A 3 203 203 HOH HOH . 
F 4 HOH A 4 204 204 HOH HOH . 
F 4 HOH A 5 205 205 HOH HOH . 
F 4 HOH A 6 206 206 HOH HOH . 
F 4 HOH A 7 207 207 HOH HOH . 
F 4 HOH A 8 208 208 HOH HOH . 
F 4 HOH A 9 209 209 HOH HOH . 
F 4 HOH A 10 210 210 HOH HOH . 
F 4 HOH A 11 211 211 HOH HOH . 
F 4 HOH A 12 212 212 HOH HOH . 
F 4 HOH A 13 213 213 HOH HOH . 
F 4 HOH A 14 214 214 HOH HOH . 
F 4 HOH A 15 215 215 HOH HOH . 
F 4 HOH A 16 216 216 HOH HOH . 
F 4 HOH A 17 217 217 HOH HOH . 
F 4 HOH A 18 218 218 HOH HOH . 
F 4 HOH A 19 219 219 HOH HOH . 
F 4 HOH A 20 220 220 HOH HOH . 
F 4 HOH A 21 221 221 HOH HOH . 
F 4 HOH A 22 222 222 HOH HOH . 
F 4 HOH A 23 223 223 HOH HOH . 
F 4 HOH A 24 224 224 HOH HOH . 
F 4 HOH A 25 225 225 HOH HOH . 
F 4 HOH A 26 226 226 HOH HOH . 
F 4 HOH A 27 227 227 HOH HOH . 
F 4 HOH A 28 228 228 HOH HOH . 
F 4 HOH A 29 229 229 HOH HOH . 
F 4 HOH A 30 230 230 HOH HOH . 
F 4 HOH A 31 231 231 HOH HOH . 
F 4 HOH A 32 232 232 HOH HOH . 
F 4 HOH A 33 233 233 HOH HOH . 
F 4 HOH A 34 234 234 HOH HOH . 
F 4 HOH A 35 235 235 HOH HOH . 
F 4 HOH A 36 236 236 HOH HOH . 
F 4 HOH A 37 237 237 HOH HOH . 
F 4 HOH A 38 238 238 HOH HOH . 
F 4 HOH A 39 239 239 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 O O3P C5P . . . B 2 4.418 44.175 -0.242 1 98.48 ? O3P C5P 300 A 1 
HETATM 2 P P C5P . . . B 2 3.874 42.749 -0.271 1 99.47 ? P C5P 300 A 1 
HETATM 3 O O1P C5P . . . B 2 2.565 42.652 -1.044 1 99.2 ? O1P C5P 300 A 1 
HETATM 4 O O2P C5P . . . B 2 4.919 41.711 -0.67 1 98.55 ? O2P C5P 300 A 1 
HETATM 5 O O5' C5P . . . B 2 3.475 42.378 1.264 1 97.56 ? O5' C5P 300 A 1 
HETATM 6 C C5' C5P . . . B 2 3.531 41.017 1.743 1 91.4 ? C5' C5P 300 A 1 
HETATM 7 C C4' C5P . . . B 2 4.108 40.992 3.136 1 86.98 ? C4' C5P 300 A 1 
HETATM 8 O O4' C5P . . . B 2 5.48 41.461 3.081 1 84.57 ? O4' C5P 300 A 1 
HETATM 9 C C3' C5P . . . B 2 3.442 41.947 4.114 1 85.97 ? C3' C5P 300 A 1 
HETATM 10 O O3' C5P . . . B 2 2.224 41.443 4.67 1 87.58 ? O3' C5P 300 A 1 
HETATM 11 C C2' C5P . . . B 2 4.534 42.165 5.149 1 84.76 ? C2' C5P 300 A 1 
HETATM 12 O O2' C5P . . . B 2 4.631 41.08 6.053 1 88.18 ? O2' C5P 300 A 1 
HETATM 13 C C1' C5P . . . B 2 5.784 42.172 4.268 1 81.41 ? C1' C5P 300 A 1 
HETATM 14 N N1 C5P . . . B 2 6.308 43.503 3.913 1 75.52 ? N1 C5P 300 A 1 
HETATM 15 C C2 C5P . . . B 2 6.886 44.279 4.917 1 72.3 ? C2 C5P 300 A 1 
HETATM 16 N N3 C5P . . . B 2 7.458 45.459 4.598 1 72.51 ? N3 C5P 300 A 1 
HETATM 17 C C4 C5P . . . B 2 7.446 45.886 3.336 1 71.36 ? C4 C5P 300 A 1 
HETATM 18 C C5 C5P . . . B 2 6.818 45.14 2.297 1 71.3 ? C5 C5P 300 A 1 
HETATM 19 C C6 C5P . . . B 2 6.265 43.963 2.627 1 72.49 ? C6 C5P 300 A 1 
HETATM 20 O O2 C5P . . . B 2 6.853 43.868 6.079 1 70.71 ? O2 C5P 300 A 1 
HETATM 21 N N4 C5P . . . B 2 8.053 47.041 3.068 1 69.14 ? N4 C5P 300 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           21 
#