data_4BER
#
_model_server_result.job_id            -hUW-9Q3v4oBvnrdNfzfcg 
_model_server_result.datetime_utc      '2024-11-06 22:48:40' 
_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          4ber 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1000}' 
#
_entry.id    4BER 
#
_exptl.entry_id    4BER 
_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    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         90 
_cell.entry_id            4BER 
_cell.length_a            58.33 
_cell.length_b            103.56 
_cell.length_c            224.1 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4BER 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        17 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,J 1 1 
B,G,H,I,K 2 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
? 2 C N N 
? 2 G N N 
#
_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                     4BER 
_atom_sites.fract_transf_matrix[1][1]    0.017144 
_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]    0.009656 
_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]    0.004462 
_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 C5P A 1 1000 1000 C5P C5P . 
D 3 PO4 A 1 2000 2000 PO4 PO4 . 
E 3 PO4 A 1 2001 2001 PO4 PO4 . 
F 4 GOL A 1 3000 3000 GOL GOL . 
G 2 C5P B 1 1000 1000 C5P C5P . 
H 3 PO4 B 1 2000 2000 PO4 PO4 . 
I 3 PO4 B 1 2001 2001 PO4 PO4 . 
J 5 HOH A 1 3001 3001 HOH HOH . 
J 5 HOH A 2 3002 3002 HOH HOH . 
J 5 HOH A 3 3003 3003 HOH HOH . 
J 5 HOH A 4 3004 3004 HOH HOH . 
J 5 HOH A 5 3005 3005 HOH HOH . 
J 5 HOH A 6 3006 3006 HOH HOH . 
J 5 HOH A 7 3007 3007 HOH HOH . 
J 5 HOH A 8 3008 3008 HOH HOH . 
J 5 HOH A 9 3009 3009 HOH HOH . 
J 5 HOH A 10 3010 3010 HOH HOH . 
J 5 HOH A 11 3011 3011 HOH HOH . 
J 5 HOH A 12 3012 3012 HOH HOH . 
J 5 HOH A 13 3013 3013 HOH HOH . 
J 5 HOH A 14 3014 3014 HOH HOH . 
J 5 HOH A 15 3015 3015 HOH HOH . 
J 5 HOH A 16 3016 3016 HOH HOH . 
J 5 HOH A 17 3017 3017 HOH HOH . 
J 5 HOH A 18 3018 3018 HOH HOH . 
J 5 HOH A 19 3019 3019 HOH HOH . 
J 5 HOH A 20 3020 3020 HOH HOH . 
J 5 HOH A 21 3021 3021 HOH HOH . 
J 5 HOH A 22 3022 3022 HOH HOH . 
J 5 HOH A 23 3023 3023 HOH HOH . 
J 5 HOH A 24 3024 3024 HOH HOH . 
J 5 HOH A 25 3025 3025 HOH HOH . 
J 5 HOH A 26 3026 3026 HOH HOH . 
J 5 HOH A 27 3027 3027 HOH HOH . 
J 5 HOH A 28 3028 3028 HOH HOH . 
J 5 HOH A 29 3029 3029 HOH HOH . 
J 5 HOH A 30 3030 3030 HOH HOH . 
J 5 HOH A 31 3031 3031 HOH HOH . 
J 5 HOH A 32 3032 3032 HOH HOH . 
J 5 HOH A 33 3033 3033 HOH HOH . 
J 5 HOH A 34 3034 3034 HOH HOH . 
J 5 HOH A 35 3035 3035 HOH HOH . 
J 5 HOH A 36 3036 3036 HOH HOH . 
K 5 HOH B 1 3001 3001 HOH HOH . 
K 5 HOH B 2 3002 3002 HOH HOH . 
K 5 HOH B 3 3003 3003 HOH HOH . 
K 5 HOH B 4 3004 3004 HOH HOH . 
K 5 HOH B 5 3005 3005 HOH HOH . 
K 5 HOH B 6 3006 3006 HOH HOH . 
K 5 HOH B 7 3007 3007 HOH HOH . 
K 5 HOH B 8 3008 3008 HOH HOH . 
K 5 HOH B 9 3009 3009 HOH HOH . 
K 5 HOH B 10 3010 3010 HOH HOH . 
K 5 HOH B 11 3011 3011 HOH HOH . 
K 5 HOH B 12 3012 3012 HOH HOH . 
K 5 HOH B 13 3013 3013 HOH HOH . 
K 5 HOH B 14 3014 3014 HOH HOH . 
K 5 HOH B 15 3015 3015 HOH HOH . 
K 5 HOH B 16 3016 3016 HOH HOH . 
K 5 HOH B 17 3017 3017 HOH HOH . 
K 5 HOH B 18 3018 3018 HOH HOH . 
K 5 HOH B 19 3019 3019 HOH HOH . 
K 5 HOH B 20 3020 3020 HOH HOH . 
K 5 HOH B 21 3021 3021 HOH HOH . 
K 5 HOH B 22 3022 3022 HOH HOH . 
K 5 HOH B 23 3023 3023 HOH HOH . 
K 5 HOH B 24 3024 3024 HOH HOH . 
K 5 HOH B 25 3025 3025 HOH HOH . 
K 5 HOH B 26 3026 3026 HOH HOH . 
K 5 HOH B 27 3027 3027 HOH HOH . 
K 5 HOH B 28 3028 3028 HOH HOH . 
K 5 HOH B 29 3029 3029 HOH HOH . 
K 5 HOH B 30 3030 3030 HOH HOH . 
K 5 HOH B 31 3031 3031 HOH HOH . 
K 5 HOH B 32 3032 3032 HOH HOH . 
K 5 HOH B 33 3033 3033 HOH HOH . 
K 5 HOH B 34 3034 3034 HOH HOH . 
K 5 HOH B 35 3035 3035 HOH HOH . 
K 5 HOH B 36 3036 3036 HOH HOH . 
K 5 HOH B 37 3037 3037 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 . . . G 2 -14.369 95.243 26.922 1 64.22 ? O3P C5P 1000 B 1 
HETATM 2 P P C5P . . . G 2 -13.691 96.485 27.539 1 63.89 ? P C5P 1000 B 1 
HETATM 3 O O1P C5P . . . G 2 -14.424 97.78 27.237 1 64.58 ? O1P C5P 1000 B 1 
HETATM 4 O O2P C5P . . . G 2 -13.531 96.239 29.021 1 64.01 ? O2P C5P 1000 B 1 
HETATM 5 O O5' C5P . . . G 2 -12.211 96.515 26.978 1 61.31 ? O5' C5P 1000 B 1 
HETATM 6 C C5' C5P . . . G 2 -10.991 96.898 27.643 1 61.06 ? C5' C5P 1000 B 1 
HETATM 7 C C4' C5P . . . G 2 -10.358 98.031 26.877 1 61.86 ? C4' C5P 1000 B 1 
HETATM 8 O O4' C5P . . . G 2 -11.251 99.165 26.86 1 63.22 ? O4' C5P 1000 B 1 
HETATM 9 C C3' C5P . . . G 2 -9.057 98.561 27.464 1 61.65 ? C3' C5P 1000 B 1 
HETATM 10 O O3' C5P . . . G 2 -7.949 97.778 27.034 1 62.68 ? O3' C5P 1000 B 1 
HETATM 11 C C2' C5P . . . G 2 -9.022 99.993 26.93 1 60.4 ? C2' C5P 1000 B 1 
HETATM 12 O O2' C5P . . . G 2 -8.537 100.07 25.595 1 57.84 ? O2' C5P 1000 B 1 
HETATM 13 C C1' C5P . . . G 2 -10.511 100.371 26.948 1 62.86 ? C1' C5P 1000 B 1 
HETATM 14 N N1 C5P . . . G 2 -10.942 101.125 28.155 1 64.2 ? N1 C5P 1000 B 1 
HETATM 15 C C2 C5P . . . G 2 -10.479 102.442 28.312 1 63.24 ? C2 C5P 1000 B 1 
HETATM 16 N N3 C5P . . . G 2 -10.894 103.159 29.395 1 64.67 ? N3 C5P 1000 B 1 
HETATM 17 C C4 C5P . . . G 2 -11.737 102.621 30.293 1 65.32 ? C4 C5P 1000 B 1 
HETATM 18 C C5 C5P . . . G 2 -12.228 101.287 30.149 1 65.62 ? C5 C5P 1000 B 1 
HETATM 19 C C6 C5P . . . G 2 -11.807 100.578 29.087 1 64.81 ? C6 C5P 1000 B 1 
HETATM 20 O O2 C5P . . . G 2 -9.722 102.917 27.461 1 60.36 ? O2 C5P 1000 B 1 
HETATM 21 N N4 C5P . . . G 2 -12.092 103.355 31.345 1 65.14 ? N4 C5P 1000 B 1 
HETATM 22 H HOP3 C5P . . . G 2 -15.107 95.203 26.258 1 64.27 ? HOP3 C5P 1000 B 1 
HETATM 23 H HOP2 C5P . . . G 2 -13.314 95.341 29.382 1 63.96 ? HOP2 C5P 1000 B 1 
HETATM 24 H "H5'1" C5P . . . G 2 -10.312 96.046 27.662 1 61.27 ? "H5'1" C5P 1000 B 1 
HETATM 25 H "H5'2" C5P . . . G 2 -11.263 97.182 28.658 1 61 ? "H5'2" C5P 1000 B 1 
HETATM 26 H H4' C5P . . . G 2 -10.229 97.75 25.833 1 62.01 ? H4' C5P 1000 B 1 
HETATM 27 H H3' C5P . . . G 2 -9.077 98.558 28.553 1 61.98 ? H3' C5P 1000 B 1 
HETATM 28 H HO3' C5P . . . G 2 -7.341 97.665 27.811 1 62.82 ? HO3' C5P 1000 B 1 
HETATM 29 H "H2'1" C5P . . . G 2 -8.43 100.599 27.615 1 60.34 ? "H2'1" C5P 1000 B 1 
HETATM 30 H HO2' C5P . . . G 2 -7.656 100.522 25.66 1 57.55 ? HO2' C5P 1000 B 1 
HETATM 31 H H1' C5P . . . G 2 -10.742 100.962 26.063 1 62.86 ? H1' C5P 1000 B 1 
HETATM 32 H H5 C5P . . . G 2 -12.929 100.845 30.857 1 65.81 ? H5 C5P 1000 B 1 
HETATM 33 H H6 C5P . . . G 2 -12.15 99.553 28.957 1 64.86 ? H6 C5P 1000 B 1 
HETATM 34 H HN41 C5P . . . G 2 -11.769 104.308 31.48 1 65.13 ? HN41 C5P 1000 B 1 
HETATM 35 H HN42 C5P . . . G 2 -12.696 102.984 32.07 1 65.04 ? HN42 C5P 1000 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           35 
#