data_5H5K
#
_model_server_result.job_id            maU5DZDkF39Gflhu-aFP8g 
_model_server_result.datetime_utc      '2024-11-24 08:59:48' 
_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          5h5k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":206}' 
#
_entry.id    5H5K 
#
_exptl.entry_id    5H5K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              323.197 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         92 
_cell.angle_beta          92.3 
_cell.angle_gamma         112.22 
_cell.entry_id            5H5K 
_cell.length_a            42.84 
_cell.length_b            51.863 
_cell.length_c            53.595 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5H5K 
_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        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 
_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 H N N 
? 5 K 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
metalc ? metalc1 A OG1 THR 14 A THR 14 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc2 C MG MG . A MG 201 1_555 D O1G ATP . A ATP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc3 C MG MG . A MG 201 1_555 D O1B ATP . A ATP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? 
metalc ? metalc4 C MG MG . A MG 201 1_555 L O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
metalc ? metalc5 C MG MG . A MG 201 1_555 L O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc6 B OG1 THR 14 B THR 14 1_555 I MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
metalc ? metalc7 I MG MG . B MG 201 1_555 J O1G ATP . B ATP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc8 I MG MG . B MG 201 1_555 J O1B ATP . B ATP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc9 I MG MG . B MG 201 1_555 K O1P C5P . B C5P 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.829 ? 
#
_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 119 n n 
O3P HOP3 C5P sing 120 n n 
P O1P C5P doub 121 n n 
P O2P C5P sing 122 n n 
P O5' C5P sing 123 n n 
O2P HOP2 C5P sing 124 n n 
O5' C5' C5P sing 125 n n 
C5' C4' C5P sing 126 n n 
C5' "H5'1" C5P sing 127 n n 
C5' "H5'2" C5P sing 128 n n 
C4' O4' C5P sing 129 n n 
C4' C3' C5P sing 130 n n 
C4' H4' C5P sing 131 n n 
O4' C1' C5P sing 132 n n 
C3' O3' C5P sing 133 n n 
C3' C2' C5P sing 134 n n 
C3' H3' C5P sing 135 n n 
O3' HO3' C5P sing 136 n n 
C2' O2' C5P sing 137 n n 
C2' C1' C5P sing 138 n n 
C2' "H2'1" C5P sing 139 n n 
O2' HO2' C5P sing 140 n n 
C1' N1 C5P sing 141 n n 
C1' H1' C5P sing 142 n n 
N1 C2 C5P sing 143 n n 
N1 C6 C5P sing 144 n n 
C2 N3 C5P sing 145 n n 
C2 O2 C5P doub 146 n n 
N3 C4 C5P doub 147 n n 
C4 C5 C5P sing 148 n n 
C4 N4 C5P sing 149 n n 
C5 C6 C5P doub 150 n n 
C5 H5 C5P sing 151 n n 
C6 H6 C5P sing 152 n n 
N4 HN41 C5P sing 153 n n 
N4 HN42 C5P sing 154 n n 
#
_atom_sites.entry_id                     5H5K 
_atom_sites.fract_transf_matrix[1][1]    0.023343 
_atom_sites.fract_transf_matrix[1][2]    0.009537 
_atom_sites.fract_transf_matrix[1][3]    0.001457 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020829 
_atom_sites.fract_transf_matrix[2][3]    0.001128 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.018701 
_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 MG A 1 201 3 MG MG . 
D 3 ATP A 1 202 1 ATP ATP . 
E 4 EDO A 1 203 1 EDO EDO . 
F 4 EDO A 1 204 2 EDO EDO . 
G 4 EDO A 1 205 3 EDO EDO . 
H 5 C5P A 1 206 1 C5P C5P . 
I 2 MG B 1 201 4 MG MG . 
J 3 ATP B 1 202 2 ATP ATP . 
K 5 C5P B 1 203 2 C5P C5P . 
L 6 HOH A 1 301 66 HOH HOH . 
L 6 HOH A 2 302 9 HOH HOH . 
L 6 HOH A 3 303 6 HOH HOH . 
L 6 HOH A 4 304 77 HOH HOH . 
L 6 HOH A 5 305 12 HOH HOH . 
L 6 HOH A 6 306 27 HOH HOH . 
L 6 HOH A 7 307 17 HOH HOH . 
L 6 HOH A 8 308 52 HOH HOH . 
L 6 HOH A 9 309 55 HOH HOH . 
L 6 HOH A 10 310 56 HOH HOH . 
L 6 HOH A 11 311 25 HOH HOH . 
L 6 HOH A 12 312 18 HOH HOH . 
L 6 HOH A 13 313 3 HOH HOH . 
L 6 HOH A 14 314 51 HOH HOH . 
L 6 HOH A 15 315 24 HOH HOH . 
L 6 HOH A 16 316 76 HOH HOH . 
L 6 HOH A 17 317 20 HOH HOH . 
L 6 HOH A 18 318 78 HOH HOH . 
L 6 HOH A 19 319 7 HOH HOH . 
L 6 HOH A 20 320 21 HOH HOH . 
L 6 HOH A 21 321 11 HOH HOH . 
L 6 HOH A 22 322 10 HOH HOH . 
L 6 HOH A 23 323 14 HOH HOH . 
L 6 HOH A 24 324 22 HOH HOH . 
L 6 HOH A 25 325 4 HOH HOH . 
L 6 HOH A 26 326 1 HOH HOH . 
L 6 HOH A 27 327 16 HOH HOH . 
L 6 HOH A 28 328 2 HOH HOH . 
L 6 HOH A 29 329 19 HOH HOH . 
L 6 HOH A 30 330 68 HOH HOH . 
L 6 HOH A 31 331 8 HOH HOH . 
L 6 HOH A 32 332 5 HOH HOH . 
L 6 HOH A 33 333 80 HOH HOH . 
L 6 HOH A 34 334 23 HOH HOH . 
L 6 HOH A 35 335 57 HOH HOH . 
L 6 HOH A 36 336 13 HOH HOH . 
L 6 HOH A 37 337 35 HOH HOH . 
L 6 HOH A 38 338 64 HOH HOH . 
L 6 HOH A 39 339 36 HOH HOH . 
L 6 HOH A 40 340 74 HOH HOH . 
M 6 HOH B 1 301 61 HOH HOH . 
M 6 HOH B 2 302 71 HOH HOH . 
M 6 HOH B 3 303 41 HOH HOH . 
M 6 HOH B 4 304 43 HOH HOH . 
M 6 HOH B 5 305 75 HOH HOH . 
M 6 HOH B 6 306 31 HOH HOH . 
M 6 HOH B 7 307 40 HOH HOH . 
M 6 HOH B 8 308 42 HOH HOH . 
M 6 HOH B 9 309 67 HOH HOH . 
M 6 HOH B 10 310 45 HOH HOH . 
M 6 HOH B 11 311 44 HOH HOH . 
M 6 HOH B 12 312 79 HOH HOH . 
M 6 HOH B 13 313 54 HOH HOH . 
M 6 HOH B 14 314 53 HOH HOH . 
M 6 HOH B 15 315 73 HOH HOH . 
M 6 HOH B 16 316 60 HOH HOH . 
M 6 HOH B 17 317 15 HOH HOH . 
M 6 HOH B 18 318 46 HOH HOH . 
M 6 HOH B 19 319 38 HOH HOH . 
M 6 HOH B 20 320 32 HOH HOH . 
M 6 HOH B 21 321 39 HOH HOH . 
M 6 HOH B 22 322 49 HOH HOH . 
M 6 HOH B 23 323 50 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 . . . H 5 10.55 7.219 4.153 1 82.51 ? O3P C5P 206 A 1 
HETATM 2 P P C5P . . . H 5 11.888 6.526 4.046 1 76.37 ? P C5P 206 A 1 
HETATM 3 O O1P C5P . . . H 5 11.911 5.297 3.163 1 81.33 ? O1P C5P 206 A 1 
HETATM 4 O O2P C5P . . . H 5 12.539 6.368 5.382 1 73.17 ? O2P C5P 206 A 1 
HETATM 5 O O5' C5P . . . H 5 12.809 7.639 3.318 1 75.42 ? O5' C5P 206 A 1 
HETATM 6 C C5' C5P . . . H 5 14.026 7.386 2.604 1 73.16 ? C5' C5P 206 A 1 
HETATM 7 C C4' C5P . . . H 5 15.149 8.317 3.092 1 71.01 ? C4' C5P 206 A 1 
HETATM 8 O O4' C5P . . . H 5 14.757 9.681 3.384 1 67.16 ? O4' C5P 206 A 1 
HETATM 9 C C3' C5P . . . H 5 15.736 7.792 4.4 1 72.89 ? C3' C5P 206 A 1 
HETATM 10 O O3' C5P . . . H 5 16.947 7.045 4.153 1 73.08 ? O3' C5P 206 A 1 
HETATM 11 C C2' C5P . . . H 5 15.951 9.013 5.298 1 69.62 ? C2' C5P 206 A 1 
HETATM 12 O O2' C5P . . . H 5 17.29 9.006 5.825 1 64.88 ? O2' C5P 206 A 1 
HETATM 13 C C1' C5P . . . H 5 15.636 10.233 4.405 1 70.27 ? C1' C5P 206 A 1 
HETATM 14 N N1 C5P . . . H 5 15.082 11.447 5.105 1 70.11 ? N1 C5P 206 A 1 
HETATM 15 C C2 C5P . . . H 5 15.868 12.641 5.36 1 69.8 ? C2 C5P 206 A 1 
HETATM 16 N N3 C5P . . . H 5 15.305 13.707 5.984 1 71.93 ? N3 C5P 206 A 1 
HETATM 17 C C4 C5P . . . H 5 14.012 13.698 6.386 1 73.82 ? C4 C5P 206 A 1 
HETATM 18 C C5 C5P . . . H 5 13.214 12.568 6.156 1 73.09 ? C5 C5P 206 A 1 
HETATM 19 C C6 C5P . . . H 5 13.776 11.453 5.503 1 73.18 ? C6 C5P 206 A 1 
HETATM 20 O O2 C5P . . . H 5 17.072 12.806 5.036 1 67.14 ? O2 C5P 206 A 1 
HETATM 21 N N4 C5P . . . H 5 13.536 14.804 6.997 1 74.86 ? N4 C5P 206 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           21 
#