data_2JJ8
#
_model_server_result.job_id            DgZQyMZQeyDXZ4NqYq6RhA 
_model_server_result.datetime_utc      '2024-11-24 11:45:04' 
_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          2jj8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1211}' 
#
_entry.id    2JJ8 
#
_exptl.entry_id    2JJ8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              267.241 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "3'-azido-3'-deoxythymidine" 
_entity.pdbx_number_of_molecules    4 
_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            2JJ8 
_cell.length_a            140.031 
_cell.length_b            111.868 
_cell.length_c            71.1 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2JJ8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
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 dimeric 2 software_defined_assembly 1 
PISA dimeric 2 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,B,E,F,G,H,I,J,Q,R 1 1 
C,D,K,L,M,N,O,P,S,T 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
? 3 G N N 
? 3 J N N 
? 3 M N N 
? 3 P N N 
#
_chem_comp.formula           'C10 H13 N5 O4' 
_chem_comp.formula_weight    267.241 
_chem_comp.id                AZZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "3'-azido-3'-deoxythymidine" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Azidothymidine;Zidovudine 
#
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
O5' C5' AZZ sing 70 n n 
C5' C4' AZZ sing 71 n n 
C4' O4' AZZ sing 72 n n 
C4' C3' AZZ sing 73 n n 
O4' C1' AZZ sing 74 n n 
C3' N3' AZZ sing 75 n n 
C3' C2' AZZ sing 76 n n 
N3' N4' AZZ doub 77 n n 
N4' N5' AZZ doub 78 n n 
C2' C1' AZZ sing 79 n n 
C1' N1 AZZ sing 80 n n 
N1 C2 AZZ sing 81 n n 
N1 C6 AZZ sing 82 n n 
C2 O2 AZZ doub 83 n n 
C2 N3 AZZ sing 84 n n 
N3 C4 AZZ sing 85 n n 
C4 O4 AZZ doub 86 n n 
C4 C5 AZZ sing 87 n n 
C5 C5A AZZ sing 88 n n 
C5 C6 AZZ doub 89 n n 
O5' HO5' AZZ sing 90 n n 
C5' H5' AZZ sing 91 n n 
C5' "H5'A" AZZ sing 92 n n 
C4' H4' AZZ sing 93 n n 
C3' H3' AZZ sing 94 n n 
C2' H2' AZZ sing 95 n n 
C2' "H2'A" AZZ sing 96 n n 
C1' H1' AZZ sing 97 n n 
N3 HN3 AZZ sing 98 n n 
C5A H5A AZZ sing 99 n n 
C5A H5AA AZZ sing 100 n n 
C5A H5AB AZZ sing 101 n n 
C6 H6 AZZ sing 102 n n 
#
_atom_sites.entry_id                     2JJ8 
_atom_sites.fract_transf_matrix[1][1]    0.007141 
_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]    0.008939 
_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]    0.014065 
_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
E 2 SO4 A 1 1209 1209 SO4 SO4 . 
F 2 SO4 A 1 1210 1210 SO4 SO4 . 
G 3 AZZ A 1 1211 1211 AZZ AZZ . 
H 2 SO4 B 1 1209 1209 SO4 SO4 . 
I 2 SO4 B 1 1210 1210 SO4 SO4 . 
J 3 AZZ B 1 1211 1211 AZZ AZZ . 
K 2 SO4 C 1 1209 1209 SO4 SO4 . 
L 2 SO4 C 1 1210 1210 SO4 SO4 . 
M 3 AZZ C 1 1211 1211 AZZ AZZ . 
N 2 SO4 D 1 1209 1209 SO4 SO4 . 
O 2 SO4 D 1 1210 1210 SO4 SO4 . 
P 3 AZZ D 1 1211 1211 AZZ AZZ . 
Q 4 HOH A 1 2001 2001 HOH HOH . 
Q 4 HOH A 2 2002 2002 HOH HOH . 
Q 4 HOH A 3 2003 2003 HOH HOH . 
Q 4 HOH A 4 2004 2004 HOH HOH . 
Q 4 HOH A 5 2005 2005 HOH HOH . 
Q 4 HOH A 6 2006 2006 HOH HOH . 
Q 4 HOH A 7 2007 2007 HOH HOH . 
Q 4 HOH A 8 2008 2008 HOH HOH . 
Q 4 HOH A 9 2009 2009 HOH HOH . 
Q 4 HOH A 10 2010 2010 HOH HOH . 
Q 4 HOH A 11 2011 2011 HOH HOH . 
Q 4 HOH A 12 2012 2012 HOH HOH . 
R 4 HOH B 1 2001 2001 HOH HOH . 
R 4 HOH B 2 2002 2002 HOH HOH . 
R 4 HOH B 3 2003 2003 HOH HOH . 
R 4 HOH B 4 2004 2004 HOH HOH . 
R 4 HOH B 5 2005 2005 HOH HOH . 
R 4 HOH B 6 2006 2006 HOH HOH . 
R 4 HOH B 7 2007 2007 HOH HOH . 
R 4 HOH B 8 2008 2008 HOH HOH . 
R 4 HOH B 9 2009 2009 HOH HOH . 
R 4 HOH B 10 2010 2010 HOH HOH . 
R 4 HOH B 11 2011 2011 HOH HOH . 
R 4 HOH B 12 2012 2012 HOH HOH . 
R 4 HOH B 13 2013 2013 HOH HOH . 
R 4 HOH B 14 2014 2014 HOH HOH . 
R 4 HOH B 15 2015 2015 HOH HOH . 
S 4 HOH C 1 2001 2001 HOH HOH . 
S 4 HOH C 2 2002 2002 HOH HOH . 
S 4 HOH C 3 2003 2003 HOH HOH . 
S 4 HOH C 4 2004 2004 HOH HOH . 
S 4 HOH C 5 2005 2005 HOH HOH . 
S 4 HOH C 6 2006 2006 HOH HOH . 
S 4 HOH C 7 2007 2007 HOH HOH . 
S 4 HOH C 8 2008 2008 HOH HOH . 
S 4 HOH C 9 2009 2009 HOH HOH . 
S 4 HOH C 10 2010 2010 HOH HOH . 
S 4 HOH C 11 2011 2011 HOH HOH . 
S 4 HOH C 12 2012 2012 HOH HOH . 
S 4 HOH C 13 2013 2013 HOH HOH . 
S 4 HOH C 14 2014 2014 HOH HOH . 
T 4 HOH D 1 2001 2001 HOH HOH . 
T 4 HOH D 2 2002 2002 HOH HOH . 
T 4 HOH D 3 2003 2003 HOH HOH . 
T 4 HOH D 4 2004 2004 HOH HOH . 
T 4 HOH D 5 2005 2005 HOH HOH . 
T 4 HOH D 6 2006 2006 HOH HOH . 
T 4 HOH D 7 2007 2007 HOH HOH . 
T 4 HOH D 8 2008 2008 HOH HOH . 
T 4 HOH D 9 2009 2009 HOH HOH . 
T 4 HOH D 10 2010 2010 HOH HOH . 
T 4 HOH D 11 2011 2011 HOH HOH . 
T 4 HOH D 12 2012 2012 HOH HOH . 
T 4 HOH D 13 2013 2013 HOH HOH . 
T 4 HOH D 14 2014 2014 HOH HOH . 
T 4 HOH D 15 2015 2015 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 O5' AZZ . . . J 3 8.407 -20.5 -6.118 1 42.94 ? O5' AZZ 1211 B 1 
HETATM 2 C C5' AZZ . . . J 3 7.394 -19.776 -6.839 1 40.58 ? C5' AZZ 1211 B 1 
HETATM 3 C C4' AZZ . . . J 3 8.049 -19.17 -8.073 1 37.85 ? C4' AZZ 1211 B 1 
HETATM 4 O O4' AZZ . . . J 3 8.913 -18.092 -7.726 1 35.26 ? O4' AZZ 1211 B 1 
HETATM 5 C C3' AZZ . . . J 3 8.917 -20.226 -8.724 1 37.86 ? C3' AZZ 1211 B 1 
HETATM 6 N N3' AZZ . . . J 3 8.336 -20.375 -10.029 1 24.16 ? N3' AZZ 1211 B 1 
HETATM 7 N N4' AZZ . . . J 3 7.416 -21.099 -10.464 1 35.18 ? N4' AZZ 1211 B 1 
HETATM 8 N N5' AZZ . . . J 3 6.613 -21.731 -10.842 1 41.81 ? N5' AZZ 1211 B 1 
HETATM 9 C C2' AZZ . . . J 3 10.348 -19.695 -8.763 1 36 ? C2' AZZ 1211 B 1 
HETATM 10 C C1' AZZ . . . J 3 10.221 -18.24 -8.315 1 32.1 ? C1' AZZ 1211 B 1 
HETATM 11 N N1 AZZ . . . J 3 11.271 -17.696 -7.41 1 29.39 ? N1 AZZ 1211 B 1 
HETATM 12 C C2 AZZ . . . J 3 12.184 -16.739 -7.925 1 29.13 ? C2 AZZ 1211 B 1 
HETATM 13 O O2 AZZ . . . J 3 12.111 -16.397 -9.131 1 29.52 ? O2 AZZ 1211 B 1 
HETATM 14 N N3 AZZ . . . J 3 13.139 -16.171 -7.178 1 28.72 ? N3 AZZ 1211 B 1 
HETATM 15 C C4 AZZ . . . J 3 13.282 -16.491 -5.894 1 29.74 ? C4 AZZ 1211 B 1 
HETATM 16 O O4 AZZ . . . J 3 14.177 -15.952 -5.196 1 29.1 ? O4 AZZ 1211 B 1 
HETATM 17 C C5 AZZ . . . J 3 12.345 -17.488 -5.312 1 29.44 ? C5 AZZ 1211 B 1 
HETATM 18 C C5A AZZ . . . J 3 12.482 -17.864 -3.861 1 28.47 ? C5A AZZ 1211 B 1 
HETATM 19 C C6 AZZ . . . J 3 11.347 -18.044 -6.122 1 28.62 ? C6 AZZ 1211 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           220 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           19 
#