data_2VBV
#
_model_server_result.job_id            lXKWUp2i7yZ561b6eFWQDg 
_model_server_result.datetime_utc      '2024-11-16 23:23:40' 
_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          2vbv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1135}' 
#
_entry.id    2VBV 
#
_exptl.entry_id    2VBV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-DIPHOSPHATE" 
_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            2VBV 
_cell.length_a            41.482 
_cell.length_b            73.299 
_cell.length_c            104.907 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VBV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 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
PQS monomeric 1 author_and_software_defined_assembly 1 
PQS 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,G,J 1 1 
B,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 I 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 43 A THR 43 1_555 D MG MG . A MG 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc2 A O THR 43 A THR 43 1_555 D MG MG . A MG 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc3 A OD1 ASN 45 A ASN 45 1_555 D MG MG . A MG 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc4 C O2B CDP . A CDP 1135 1_555 D MG MG . A MG 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc5 C O1A CDP . A CDP 1135 1_555 D MG MG . A MG 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc6 D MG MG . A MG 1136 1_555 G O1P FMN . A FMN 1140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc7 B OG1 THR 43 B THR 43 1_555 H MG MG . B MG 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
metalc ? metalc8 B O THR 43 B THR 43 1_555 H MG MG . B MG 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
metalc ? metalc9 B OD1 ASN 45 B ASN 45 1_555 H MG MG . B MG 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc10 H MG MG . B MG 1136 1_555 I O2B CDP . B CDP 1137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
metalc ? metalc11 H MG MG . B MG 1136 1_555 I O1A CDP . B CDP 1137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc12 H MG MG . B MG 1136 1_555 K O HOH . B HOH 2010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
#
_chem_comp.formula           'C9 H15 N3 O11 P2' 
_chem_comp.formula_weight    403.176 
_chem_comp.id                CDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-5'-DIPHOSPHATE" 
_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
O3B PB CDP sing 70 n n 
PB O1B CDP doub 71 n n 
PB O2B CDP sing 72 n n 
PB O3A CDP sing 73 n n 
O3A PA CDP sing 74 n n 
PA O1A CDP doub 75 n n 
PA O2A CDP sing 76 n n 
PA O5' CDP sing 77 n n 
O5' C5' CDP sing 78 n n 
C5' C4' CDP sing 79 n n 
C5' "H5'1" CDP sing 80 n n 
C5' "H5'2" CDP sing 81 n n 
C4' O4' CDP sing 82 n n 
C4' C3' CDP sing 83 n n 
C4' H4' CDP sing 84 n n 
O4' C1' CDP sing 85 n n 
C3' O3' CDP sing 86 n n 
C3' C2' CDP sing 87 n n 
C3' H3' CDP sing 88 n n 
O3' HA CDP sing 89 n n 
C2' O2' CDP sing 90 n n 
C2' C1' CDP sing 91 n n 
C2' H2' CDP sing 92 n n 
O2' HB CDP sing 93 n n 
C1' N1 CDP sing 94 n n 
C1' H1' CDP sing 95 n n 
N1 C2 CDP sing 96 n n 
N1 C6 CDP sing 97 n n 
C2 O2 CDP doub 98 n n 
C2 N3 CDP sing 99 n n 
N3 C4 CDP doub 100 n n 
C4 N4 CDP sing 101 n n 
C4 C5 CDP sing 102 n n 
N4 H4N1 CDP sing 103 n n 
N4 H4N2 CDP sing 104 n n 
C5 C6 CDP doub 105 n n 
C5 H5 CDP sing 106 n n 
C6 H6 CDP sing 107 n n 
HO1 O2A CDP sing 108 n n 
HO2 O2B CDP sing 109 n n 
HO3 O3B CDP sing 110 n n 
#
_atom_sites.entry_id                     2VBV 
_atom_sites.fract_transf_matrix[1][1]    0.024107 
_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]    0.013643 
_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]    0.009532 
_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 CDP A 1 1135 1135 CDP CDP . 
D 3 MG A 1 1136 1136 MG MG . 
E 4 IOD A 1 1138 1138 IOD IOD . 
F 5 CL A 1 1139 1139 CL CL . 
G 6 FMN A 1 1140 1140 FMN FMN . 
H 3 MG B 1 1136 1136 MG MG . 
I 2 CDP B 1 1137 1137 CDP CDP . 
J 7 HOH A 1 2001 2001 HOH HOH . 
J 7 HOH A 2 2002 2002 HOH HOH . 
J 7 HOH A 3 2003 2003 HOH HOH . 
J 7 HOH A 4 2004 2004 HOH HOH . 
J 7 HOH A 5 2005 2005 HOH HOH . 
J 7 HOH A 6 2006 2006 HOH HOH . 
J 7 HOH A 7 2007 2007 HOH HOH . 
J 7 HOH A 8 2008 2008 HOH HOH . 
J 7 HOH A 9 2009 2009 HOH HOH . 
J 7 HOH A 10 2010 2010 HOH HOH . 
J 7 HOH A 11 2011 2011 HOH HOH . 
J 7 HOH A 12 2012 2012 HOH HOH . 
J 7 HOH A 13 2013 2013 HOH HOH . 
J 7 HOH A 14 2014 2014 HOH HOH . 
J 7 HOH A 15 2015 2015 HOH HOH . 
J 7 HOH A 16 2016 2016 HOH HOH . 
J 7 HOH A 17 2017 2017 HOH HOH . 
J 7 HOH A 18 2018 2018 HOH HOH . 
J 7 HOH A 19 2019 2019 HOH HOH . 
J 7 HOH A 20 2020 2020 HOH HOH . 
J 7 HOH A 21 2021 2021 HOH HOH . 
J 7 HOH A 22 2022 2022 HOH HOH . 
J 7 HOH A 23 2023 2023 HOH HOH . 
J 7 HOH A 24 2024 2024 HOH HOH . 
J 7 HOH A 25 2025 2025 HOH HOH . 
J 7 HOH A 26 2026 2026 HOH HOH . 
J 7 HOH A 27 2027 2027 HOH HOH . 
J 7 HOH A 28 2028 2028 HOH HOH . 
J 7 HOH A 29 2029 2029 HOH HOH . 
J 7 HOH A 30 2030 2030 HOH HOH . 
J 7 HOH A 31 2031 2031 HOH HOH . 
J 7 HOH A 32 2032 2032 HOH HOH . 
J 7 HOH A 33 2033 2033 HOH HOH . 
J 7 HOH A 34 2034 2034 HOH HOH . 
J 7 HOH A 35 2035 2035 HOH HOH . 
J 7 HOH A 36 2036 2036 HOH HOH . 
J 7 HOH A 37 2037 2037 HOH HOH . 
J 7 HOH A 38 2038 2038 HOH HOH . 
J 7 HOH A 39 2039 2039 HOH HOH . 
J 7 HOH A 40 2040 2040 HOH HOH . 
J 7 HOH A 41 2041 2041 HOH HOH . 
J 7 HOH A 42 2042 2042 HOH HOH . 
J 7 HOH A 43 2043 2043 HOH HOH . 
J 7 HOH A 44 2044 2044 HOH HOH . 
J 7 HOH A 45 2045 2045 HOH HOH . 
J 7 HOH A 46 2046 2046 HOH HOH . 
J 7 HOH A 47 2047 2047 HOH HOH . 
J 7 HOH A 48 2048 2048 HOH HOH . 
J 7 HOH A 49 2049 2049 HOH HOH . 
J 7 HOH A 50 2050 2050 HOH HOH . 
K 7 HOH B 1 2001 2001 HOH HOH . 
K 7 HOH B 2 2002 2002 HOH HOH . 
K 7 HOH B 3 2003 2003 HOH HOH . 
K 7 HOH B 4 2004 2004 HOH HOH . 
K 7 HOH B 5 2005 2005 HOH HOH . 
K 7 HOH B 6 2006 2006 HOH HOH . 
K 7 HOH B 7 2007 2007 HOH HOH . 
K 7 HOH B 8 2008 2008 HOH HOH . 
K 7 HOH B 9 2009 2009 HOH HOH . 
K 7 HOH B 10 2010 2010 HOH HOH . 
K 7 HOH B 11 2011 2011 HOH HOH . 
K 7 HOH B 12 2012 2012 HOH HOH . 
K 7 HOH B 13 2013 2013 HOH HOH . 
K 7 HOH B 14 2014 2014 HOH HOH . 
K 7 HOH B 15 2015 2015 HOH HOH . 
K 7 HOH B 16 2016 2016 HOH HOH . 
K 7 HOH B 17 2017 2017 HOH HOH . 
K 7 HOH B 18 2018 2018 HOH HOH . 
K 7 HOH B 19 2019 2019 HOH HOH . 
K 7 HOH B 20 2020 2020 HOH HOH . 
K 7 HOH B 21 2021 2021 HOH HOH . 
K 7 HOH B 22 2022 2022 HOH HOH . 
K 7 HOH B 23 2023 2023 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 O3B CDP . . . C 2 -16.281 -11.378 5.648 1 24.19 ? O3B CDP 1135 A 1 
HETATM 2 P PB CDP . . . C 2 -15.615 -10.074 5.942 1 28.88 ? PB CDP 1135 A 1 
HETATM 3 O O1B CDP . . . C 2 -15.946 -9.461 7.283 1 24.8 ? O1B CDP 1135 A 1 
HETATM 4 O O2B CDP . . . C 2 -15.74 -9.063 4.826 1 26.61 ? O2B CDP 1135 A 1 
HETATM 5 O O3A CDP . . . C 2 -14.102 -10.444 6.005 1 23.57 ? O3A CDP 1135 A 1 
HETATM 6 P PA CDP . . . C 2 -13.074 -10.087 4.827 1 29.05 ? PA CDP 1135 A 1 
HETATM 7 O O1A CDP . . . C 2 -13.841 -9.722 3.569 1 25.7 ? O1A CDP 1135 A 1 
HETATM 8 O O2A CDP . . . C 2 -12.002 -11.09 4.838 1 22.68 ? O2A CDP 1135 A 1 
HETATM 9 O O5' CDP . . . C 2 -12.336 -8.736 5.264 1 32.49 ? O5' CDP 1135 A 1 
HETATM 10 C C5' CDP . . . C 2 -11.367 -8.669 6.303 1 30.74 ? C5' CDP 1135 A 1 
HETATM 11 C C4' CDP . . . C 2 -11.82 -7.58 7.213 1 28.42 ? C4' CDP 1135 A 1 
HETATM 12 O O4' CDP . . . C 2 -11.409 -6.435 6.583 1 28.79 ? O4' CDP 1135 A 1 
HETATM 13 C C3' CDP . . . C 2 -13.319 -7.389 7.274 1 32.67 ? C3' CDP 1135 A 1 
HETATM 14 O O3' CDP . . . C 2 -13.592 -6.785 8.542 1 32.88 ? O3' CDP 1135 A 1 
HETATM 15 C C2' CDP . . . C 2 -13.683 -6.396 6.167 1 33.07 ? C2' CDP 1135 A 1 
HETATM 16 O O2' CDP . . . C 2 -14.932 -5.705 6.43 1 34.21 ? O2' CDP 1135 A 1 
HETATM 17 C C1' CDP . . . C 2 -12.479 -5.524 6.286 1 29.83 ? C1' CDP 1135 A 1 
HETATM 18 N N1 CDP . . . C 2 -11.927 -4.864 5.135 1 30.13 ? N1 CDP 1135 A 1 
HETATM 19 C C2 CDP . . . C 2 -11.574 -3.535 5.231 1 30.06 ? C2 CDP 1135 A 1 
HETATM 20 O O2 CDP . . . C 2 -11.837 -2.958 6.284 1 29.76 ? O2 CDP 1135 A 1 
HETATM 21 N N3 CDP . . . C 2 -11.014 -2.889 4.187 1 27.51 ? N3 CDP 1135 A 1 
HETATM 22 C C4 CDP . . . C 2 -10.719 -3.551 3.07 1 27.04 ? C4 CDP 1135 A 1 
HETATM 23 N N4 CDP . . . C 2 -10.153 -2.931 2.041 1 26.83 ? N4 CDP 1135 A 1 
HETATM 24 C C5 CDP . . . C 2 -11.028 -4.871 2.962 1 26.73 ? C5 CDP 1135 A 1 
HETATM 25 C C6 CDP . . . C 2 -11.614 -5.518 4.028 1 30.91 ? C6 CDP 1135 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           300 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           25 
#