data_1RO8
#
_model_server_result.job_id            dxDJuktGUTawJItyBi2TnQ 
_model_server_result.datetime_utc      '2024-10-19 11:45:22' 
_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          1ro8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1001}' 
#
_entry.id    1RO8 
#
_exptl.entry_id    1RO8 
_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            1RO8 
_cell.length_a            115.434 
_cell.length_b            115.434 
_cell.length_c            41.059 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RO8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        75 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 4' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 author_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,E 1 1,2,3,4 
B,D,F 2 1,5,6,7 
#
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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 
5 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 115.434 115.434 0 
6 'crystal symmetry operation' 3_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 115.434 0 0 
7 'crystal symmetry operation' 4_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 115.434 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 D 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 HIS 3 A HIS -1 1_555 A N MSE 4 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale2 A C MSE 4 A MSE 1 1_555 A N LYS 5 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale3 A C ILE 79 A ILE 76 1_555 A N MSE 80 A MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale4 A C MSE 80 A MSE 77 1_555 A N CYS 81 A CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale5 A C TYR 138 A TYR 135 1_555 A N MSE 139 A MSE 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale6 A C MSE 139 A MSE 136 1_555 A N CYS 140 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale7 B C MSE 4 B MSE 1 1_555 B N LYS 5 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale8 B C ILE 79 B ILE 76 1_555 B N MSE 80 B MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale9 B C MSE 80 B MSE 77 1_555 B N CYS 81 B CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale10 B C TYR 138 B TYR 135 1_555 B N MSE 139 B MSE 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale11 B C MSE 139 B MSE 136 1_555 B N CYS 140 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
#
_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                     1RO8 
_atom_sites.fract_transf_matrix[1][1]    0.008663 
_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]    0.008663 
_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]    0.024355 
_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 2001 2001 C5P C . 
D 2 C5P B 1 1001 1001 C5P C . 
E 3 HOH A 1 2002 6 HOH WAT . 
E 3 HOH A 2 2003 8 HOH WAT . 
E 3 HOH A 3 2004 9 HOH WAT . 
E 3 HOH A 4 2005 10 HOH WAT . 
E 3 HOH A 5 2006 11 HOH WAT . 
E 3 HOH A 6 2007 12 HOH WAT . 
E 3 HOH A 7 2008 13 HOH WAT . 
E 3 HOH A 8 2009 14 HOH WAT . 
E 3 HOH A 9 2010 15 HOH WAT . 
E 3 HOH A 10 2011 16 HOH WAT . 
E 3 HOH A 11 2012 17 HOH WAT . 
E 3 HOH A 12 2013 19 HOH WAT . 
E 3 HOH A 13 2014 20 HOH WAT . 
E 3 HOH A 14 2015 21 HOH WAT . 
E 3 HOH A 15 2016 22 HOH WAT . 
E 3 HOH A 16 2017 23 HOH WAT . 
E 3 HOH A 17 2018 27 HOH WAT . 
E 3 HOH A 18 2019 30 HOH WAT . 
E 3 HOH A 19 2020 31 HOH WAT . 
E 3 HOH A 20 2021 32 HOH WAT . 
E 3 HOH A 21 2022 33 HOH WAT . 
E 3 HOH A 22 2023 35 HOH WAT . 
E 3 HOH A 23 2024 36 HOH WAT . 
E 3 HOH A 24 2025 37 HOH WAT . 
E 3 HOH A 25 2026 38 HOH WAT . 
E 3 HOH A 26 2027 40 HOH WAT . 
E 3 HOH A 27 2028 41 HOH WAT . 
E 3 HOH A 28 2029 43 HOH WAT . 
E 3 HOH A 29 2030 44 HOH WAT . 
E 3 HOH A 30 2031 45 HOH WAT . 
E 3 HOH A 31 2032 50 HOH WAT . 
E 3 HOH A 32 2033 51 HOH WAT . 
E 3 HOH A 33 2034 52 HOH WAT . 
E 3 HOH A 34 2035 56 HOH WAT . 
E 3 HOH A 35 2036 58 HOH WAT . 
E 3 HOH A 36 2037 60 HOH WAT . 
E 3 HOH A 37 2038 65 HOH WAT . 
F 3 HOH B 1 1002 1 HOH WAT . 
F 3 HOH B 2 1003 2 HOH WAT . 
F 3 HOH B 3 1004 3 HOH WAT . 
F 3 HOH B 4 1005 4 HOH WAT . 
F 3 HOH B 5 1006 5 HOH WAT . 
F 3 HOH B 6 1007 7 HOH WAT . 
F 3 HOH B 7 1008 18 HOH WAT . 
F 3 HOH B 8 1009 24 HOH WAT . 
F 3 HOH B 9 1010 25 HOH WAT . 
F 3 HOH B 10 1011 26 HOH WAT . 
F 3 HOH B 11 1012 28 HOH WAT . 
F 3 HOH B 12 1013 29 HOH WAT . 
F 3 HOH B 13 1014 34 HOH WAT . 
F 3 HOH B 14 1015 39 HOH WAT . 
F 3 HOH B 15 1016 42 HOH WAT . 
F 3 HOH B 16 1017 46 HOH WAT . 
F 3 HOH B 17 1018 47 HOH WAT . 
F 3 HOH B 18 1019 48 HOH WAT . 
F 3 HOH B 19 1020 53 HOH WAT . 
F 3 HOH B 20 1021 54 HOH WAT . 
F 3 HOH B 21 1022 55 HOH WAT . 
F 3 HOH B 22 1023 57 HOH WAT . 
F 3 HOH B 23 1024 59 HOH WAT . 
F 3 HOH B 24 1025 63 HOH WAT . 
F 3 HOH B 25 1026 67 HOH WAT . 
F 3 HOH B 26 1027 76 HOH WAT . 
F 3 HOH B 27 1028 82 HOH WAT . 
#
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 . . . D 2 63.955 26.377 19.657 1 58.11 ? O3P C5P 1001 B 1 
HETATM 2 P P C5P . . . D 2 63.652 24.859 19.392 1 55.42 ? P C5P 1001 B 1 
HETATM 3 O O1P C5P . . . D 2 62.158 24.505 19.211 1 57.33 ? O1P C5P 1001 B 1 
HETATM 4 O O2P C5P . . . D 2 64.437 24.391 18.168 1 57.98 ? O2P C5P 1001 B 1 
HETATM 5 O O5' C5P . . . D 2 64.062 23.856 20.376 1 55.48 ? O5' C5P 1001 B 1 
HETATM 6 C C5' C5P . . . D 2 64.113 24.42 21.707 1 52 ? C5' C5P 1001 B 1 
HETATM 7 C C4' C5P . . . D 2 65.303 24.691 22.499 1 51.48 ? C4' C5P 1001 B 1 
HETATM 8 O O4' C5P . . . D 2 65.783 23.4 22.735 1 51.62 ? O4' C5P 1001 B 1 
HETATM 9 C C3' C5P . . . D 2 66.414 25.462 21.82 1 51.27 ? C3' C5P 1001 B 1 
HETATM 10 O O3' C5P . . . D 2 66.242 26.854 22.102 1 53.39 ? O3' C5P 1001 B 1 
HETATM 11 C C2' C5P . . . D 2 67.616 24.862 22.534 1 50.75 ? C2' C5P 1001 B 1 
HETATM 12 O O2' C5P . . . D 2 67.922 25.401 23.836 1 46.73 ? O2' C5P 1001 B 1 
HETATM 13 C C1' C5P . . . D 2 67.211 23.405 22.541 1 51.65 ? C1' C5P 1001 B 1 
HETATM 14 N N1 C5P . . . D 2 67.375 22.126 21.77 1 51.18 ? N1 C5P 1001 B 1 
HETATM 15 C C2 C5P . . . D 2 68.645 21.386 21.827 1 51.96 ? C2 C5P 1001 B 1 
HETATM 16 N N3 C5P . . . D 2 68.887 20.357 20.944 1 52.26 ? N3 C5P 1001 B 1 
HETATM 17 C C4 C5P . . . D 2 67.951 19.919 19.971 1 52.01 ? C4 C5P 1001 B 1 
HETATM 18 C C5 C5P . . . D 2 66.723 20.564 19.907 1 51.48 ? C5 C5P 1001 B 1 
HETATM 19 C C6 C5P . . . D 2 66.348 21.475 20.825 1 51.5 ? C6 C5P 1001 B 1 
HETATM 20 O O2 C5P . . . D 2 69.585 21.686 22.708 1 52.98 ? O2 C5P 1001 B 1 
HETATM 21 N N4 C5P . . . D 2 68.253 18.904 19.139 1 52.89 ? N4 C5P 1001 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           21 
#