data_2VP9
#
_model_server_result.job_id            kzAwaKe8PFR0p6f89GJ46Q 
_model_server_result.datetime_utc      '2024-11-15 05:42:52' 
_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          2vp9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":1210}' 
#
_entry.id    2VP9 
#
_exptl.entry_id    2VP9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              291.198 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.1 
_cell.angle_gamma         90 
_cell.entry_id            2VP9 
_cell.length_a            70.5 
_cell.length_b            70.82 
_cell.length_c            226.032 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VP9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PQS dimeric 2 author_and_software_defined_assembly 2 
PQS dimeric 2 author_and_software_defined_assembly 3 
PQS dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K,L,M,Z,AA 1 1 
C,D,N,O,P,Q,BA,CA 2 1 
E,F,R,S,T,U,DA,EA 3 1 
G,H,V,W,X,Y,FA,GA 4 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
? 3 K N N 
? 3 M N N 
? 3 O N N 
? 3 Q N N 
? 3 S N N 
? 3 U N N 
? 3 W N N 
? 3 Y N N 
#
_chem_comp.formula           'C9 H14 N3 O6 P' 
_chem_comp.formula_weight    291.198 
_chem_comp.id                DOC 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              'dna linking' 
_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
N1 C2 DOC sing 83 n n 
N1 C6 DOC sing 84 n n 
N1 C1' DOC sing 85 n n 
C2 N3 DOC sing 86 n n 
C2 O2 DOC doub 87 n n 
N3 C4 DOC doub 88 n n 
C4 C5 DOC sing 89 n n 
C4 N4 DOC sing 90 n n 
C5 C6 DOC doub 91 n n 
C5 H5 DOC sing 92 n n 
C6 H6 DOC sing 93 n n 
N4 HN41 DOC sing 94 n n 
N4 HN42 DOC sing 95 n n 
C1' C2' DOC sing 96 n n 
C1' O4' DOC sing 97 n n 
C1' H1' DOC sing 98 n n 
C2' C3' DOC sing 99 n n 
C2' H2' DOC sing 100 n n 
C2' "H2''" DOC sing 101 n n 
C3' C4' DOC sing 102 n n 
C3' "H3'1" DOC sing 103 n n 
C3' "H3'2" DOC sing 104 n n 
C4' O4' DOC sing 105 n n 
C4' C5' DOC sing 106 n n 
C4' H4' DOC sing 107 n n 
C5' O5' DOC sing 108 n n 
C5' H5' DOC sing 109 n n 
C5' "H5''" DOC sing 110 n n 
O5' P DOC sing 111 n n 
P OP1 DOC doub 112 n n 
P OP2 DOC sing 113 n n 
P OP3 DOC sing 114 n n 
OP2 HOP2 DOC sing 115 n n 
OP3 HOP3 DOC sing 116 n n 
#
_atom_sites.entry_id                     2VP9 
_atom_sites.fract_transf_matrix[1][1]    0.014184 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000025 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01412 
_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]    0.004424 
_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
I 2 SO4 A 1 1209 1209 SO4 SO4 . 
J 2 SO4 A 1 1210 1210 SO4 SO4 . 
K 3 DOC A 1 1211 1211 DOC DOC . 
L 2 SO4 B 1 1209 1209 SO4 SO4 . 
M 3 DOC B 1 1210 1210 DOC DOC . 
N 2 SO4 C 1 1209 1209 SO4 SO4 . 
O 3 DOC C 1 1210 1210 DOC DOC . 
P 2 SO4 D 1 1209 1209 SO4 SO4 . 
Q 3 DOC D 1 1210 1210 DOC DOC . 
R 2 SO4 E 1 1209 1209 SO4 SO4 . 
S 3 DOC E 1 1210 1210 DOC DOC . 
T 2 SO4 F 1 1209 1209 SO4 SO4 . 
U 3 DOC F 1 1210 1210 DOC DOC . 
V 2 SO4 G 1 1209 1209 SO4 SO4 . 
W 3 DOC G 1 1210 1210 DOC DOC . 
X 2 SO4 H 1 1209 1209 SO4 SO4 . 
Y 3 DOC H 1 1210 1210 DOC DOC . 
Z 4 HOH A 1 2001 2001 HOH HOH . 
Z 4 HOH A 2 2002 2002 HOH HOH . 
Z 4 HOH A 3 2003 2003 HOH HOH . 
Z 4 HOH A 4 2004 2004 HOH HOH . 
Z 4 HOH A 5 2005 2005 HOH HOH . 
Z 4 HOH A 6 2006 2006 HOH HOH . 
Z 4 HOH A 7 2007 2007 HOH HOH . 
Z 4 HOH A 8 2008 2008 HOH HOH . 
Z 4 HOH A 9 2009 2009 HOH HOH . 
Z 4 HOH A 10 2010 2010 HOH HOH . 
Z 4 HOH A 11 2011 2011 HOH HOH . 
Z 4 HOH A 12 2012 2012 HOH HOH . 
Z 4 HOH A 13 2013 2013 HOH HOH . 
Z 4 HOH A 14 2014 2014 HOH HOH . 
Z 4 HOH A 15 2015 2015 HOH HOH . 
Z 4 HOH A 16 2016 2016 HOH HOH . 
Z 4 HOH A 17 2017 2017 HOH HOH . 
Z 4 HOH A 18 2018 2018 HOH HOH . 
Z 4 HOH A 19 2019 2019 HOH HOH . 
Z 4 HOH A 20 2020 2020 HOH HOH . 
Z 4 HOH A 21 2021 2021 HOH HOH . 
AA 4 HOH B 1 2001 2001 HOH HOH . 
AA 4 HOH B 2 2002 2002 HOH HOH . 
AA 4 HOH B 3 2003 2003 HOH HOH . 
AA 4 HOH B 4 2004 2004 HOH HOH . 
AA 4 HOH B 5 2005 2005 HOH HOH . 
AA 4 HOH B 6 2006 2006 HOH HOH . 
AA 4 HOH B 7 2007 2007 HOH HOH . 
AA 4 HOH B 8 2008 2008 HOH HOH . 
AA 4 HOH B 9 2009 2009 HOH HOH . 
AA 4 HOH B 10 2010 2010 HOH HOH . 
AA 4 HOH B 11 2011 2011 HOH HOH . 
BA 4 HOH C 1 2001 2001 HOH HOH . 
BA 4 HOH C 2 2002 2002 HOH HOH . 
BA 4 HOH C 3 2003 2003 HOH HOH . 
BA 4 HOH C 4 2004 2004 HOH HOH . 
BA 4 HOH C 5 2005 2005 HOH HOH . 
BA 4 HOH C 6 2006 2006 HOH HOH . 
BA 4 HOH C 7 2007 2007 HOH HOH . 
BA 4 HOH C 8 2008 2008 HOH HOH . 
BA 4 HOH C 9 2009 2009 HOH HOH . 
CA 4 HOH D 1 2001 2001 HOH HOH . 
CA 4 HOH D 2 2002 2002 HOH HOH . 
CA 4 HOH D 3 2003 2003 HOH HOH . 
CA 4 HOH D 4 2004 2004 HOH HOH . 
CA 4 HOH D 5 2005 2005 HOH HOH . 
CA 4 HOH D 6 2006 2006 HOH HOH . 
CA 4 HOH D 7 2007 2007 HOH HOH . 
CA 4 HOH D 8 2008 2008 HOH HOH . 
CA 4 HOH D 9 2009 2009 HOH HOH . 
CA 4 HOH D 10 2010 2010 HOH HOH . 
CA 4 HOH D 11 2011 2011 HOH HOH . 
CA 4 HOH D 12 2012 2012 HOH HOH . 
CA 4 HOH D 13 2013 2013 HOH HOH . 
DA 4 HOH E 1 2001 2001 HOH HOH . 
DA 4 HOH E 2 2002 2002 HOH HOH . 
DA 4 HOH E 3 2003 2003 HOH HOH . 
DA 4 HOH E 4 2004 2004 HOH HOH . 
DA 4 HOH E 5 2005 2005 HOH HOH . 
DA 4 HOH E 6 2006 2006 HOH HOH . 
DA 4 HOH E 7 2007 2007 HOH HOH . 
DA 4 HOH E 8 2008 2008 HOH HOH . 
DA 4 HOH E 9 2009 2009 HOH HOH . 
DA 4 HOH E 10 2010 2010 HOH HOH . 
DA 4 HOH E 11 2011 2011 HOH HOH . 
DA 4 HOH E 12 2012 2012 HOH HOH . 
DA 4 HOH E 13 2013 2013 HOH HOH . 
DA 4 HOH E 14 2014 2014 HOH HOH . 
DA 4 HOH E 15 2015 2015 HOH HOH . 
DA 4 HOH E 16 2016 2016 HOH HOH . 
EA 4 HOH F 1 2001 2001 HOH HOH . 
EA 4 HOH F 2 2002 2002 HOH HOH . 
EA 4 HOH F 3 2003 2003 HOH HOH . 
EA 4 HOH F 4 2004 2004 HOH HOH . 
EA 4 HOH F 5 2005 2005 HOH HOH . 
EA 4 HOH F 6 2006 2006 HOH HOH . 
EA 4 HOH F 7 2007 2007 HOH HOH . 
EA 4 HOH F 8 2008 2008 HOH HOH . 
EA 4 HOH F 9 2009 2009 HOH HOH . 
EA 4 HOH F 10 2010 2010 HOH HOH . 
EA 4 HOH F 11 2011 2011 HOH HOH . 
FA 4 HOH G 1 2001 2001 HOH HOH . 
FA 4 HOH G 2 2002 2002 HOH HOH . 
FA 4 HOH G 3 2003 2003 HOH HOH . 
FA 4 HOH G 4 2004 2004 HOH HOH . 
FA 4 HOH G 5 2005 2005 HOH HOH . 
FA 4 HOH G 6 2006 2006 HOH HOH . 
FA 4 HOH G 7 2007 2007 HOH HOH . 
FA 4 HOH G 8 2008 2008 HOH HOH . 
FA 4 HOH G 9 2009 2009 HOH HOH . 
GA 4 HOH H 1 2001 2001 HOH HOH . 
GA 4 HOH H 2 2002 2002 HOH HOH . 
GA 4 HOH H 3 2003 2003 HOH HOH . 
GA 4 HOH H 4 2004 2004 HOH HOH . 
GA 4 HOH H 5 2005 2005 HOH HOH . 
GA 4 HOH H 6 2006 2006 HOH HOH . 
GA 4 HOH H 7 2007 2007 HOH HOH . 
GA 4 HOH H 8 2008 2008 HOH HOH . 
GA 4 HOH H 9 2009 2009 HOH HOH . 
GA 4 HOH H 10 2010 2010 HOH HOH . 
GA 4 HOH H 11 2011 2011 HOH HOH . 
GA 4 HOH H 12 2012 2012 HOH HOH . 
GA 4 HOH H 13 2013 2013 HOH HOH . 
GA 4 HOH H 14 2014 2014 HOH HOH . 
GA 4 HOH H 15 2015 2015 HOH HOH . 
GA 4 HOH H 16 2016 2016 HOH HOH . 
GA 4 HOH H 17 2017 2017 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 N N1 DOC . . . O 3 49.894 37.621 103.191 1 31.79 ? N1 DOC 1210 C 1 
HETATM 2 C C2 DOC . . . O 3 49.571 36.644 102.212 1 28.84 ? C2 DOC 1210 C 1 
HETATM 3 N N3 DOC . . . O 3 50.501 35.864 101.644 1 28.1 ? N3 DOC 1210 C 1 
HETATM 4 C C4 DOC . . . O 3 51.789 36.028 102.035 1 32.41 ? C4 DOC 1210 C 1 
HETATM 5 C C5 DOC . . . O 3 52.181 36.986 103.003 1 31.5 ? C5 DOC 1210 C 1 
HETATM 6 C C6 DOC . . . O 3 51.189 37.784 103.577 1 32.22 ? C6 DOC 1210 C 1 
HETATM 7 O O2 DOC . . . O 3 48.395 36.491 101.879 1 29.92 ? O2 DOC 1210 C 1 
HETATM 8 N N4 DOC . . . O 3 52.738 35.236 101.468 1 33.45 ? N4 DOC 1210 C 1 
HETATM 9 C C1' DOC . . . O 3 48.781 38.448 103.76 1 32.29 ? C1' DOC 1210 C 1 
HETATM 10 C C2' DOC . . . O 3 48.503 38.12 105.236 1 31.82 ? C2' DOC 1210 C 1 
HETATM 11 C C3' DOC . . . O 3 48.066 39.431 105.869 1 29.21 ? C3' DOC 1210 C 1 
HETATM 12 C C4' DOC . . . O 3 48.465 40.503 104.874 1 27.55 ? C4' DOC 1210 C 1 
HETATM 13 O O4' DOC . . . O 3 48.913 39.893 103.657 1 28.28 ? O4' DOC 1210 C 1 
HETATM 14 C C5' DOC . . . O 3 49.634 41.201 105.516 1 27.81 ? C5' DOC 1210 C 1 
HETATM 15 O O5' DOC . . . O 3 50.778 40.656 104.869 1 27.42 ? O5' DOC 1210 C 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#