data_2YJ6
#
_model_server_result.job_id            GVuQlJdEWZ34GBRsws4W4Q 
_model_server_result.datetime_utc      '2024-11-15 15:33:04' 
_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          2yj6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1636}' 
#
_entry.id    2YJ6 
#
_exptl.entry_id    2YJ6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              656.328 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-O-[(S)-hydroxy{[(R)-hydroxy({(S)-hydroxy[(1S)-1-(2-nitrophenyl)ethoxy]phosphoryl}oxy)phosphoryl]oxy}phosphoryl]adenosine" 
_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          98.24 
_cell.angle_gamma         90 
_cell.entry_id            2YJ6 
_cell.length_a            69.56 
_cell.length_b            53.9 
_cell.length_c            78.95 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YJ6 
_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
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,F 1 1 
B,D,E,G 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 D N N 
#
_chem_comp.formula           'C18 H23 N6 O15 P3' 
_chem_comp.formula_weight    656.328 
_chem_comp.id                A99 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-O-[(S)-hydroxy{[(R)-hydroxy({(S)-hydroxy[(1S)-1-(2-nitrophenyl)ethoxy]phosphoryl}oxy)phosphoryl]oxy}phosphoryl]adenosine" 
_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
C' O2G A99 sing 1 n n 
C' C3' A99 sing 2 n n 
C' CM' A99 sing 3 n n 
N1 C2 A99 doub 4 n y 
N1 C6 A99 sing 5 n y 
C2 N3 A99 sing 6 n y 
N3 C4 A99 doub 7 n y 
C4 C5 A99 sing 8 n y 
C4 N9 A99 sing 9 n y 
C5 C6 A99 doub 10 n y 
C5 N7 A99 sing 11 n y 
C6 N6 A99 sing 12 n n 
N7 C8 A99 doub 13 n y 
C8 N9 A99 sing 14 n y 
N9 C1B A99 sing 15 n n 
PA O1A A99 doub 16 n n 
PA O2A A99 sing 17 n n 
PA O3A A99 sing 18 n n 
PA O5' A99 sing 19 n n 
PB O1B A99 doub 20 n n 
PB O2B A99 sing 21 n n 
PB O3A A99 sing 22 n n 
PB O3B A99 sing 23 n n 
PG O1G A99 sing 24 n n 
PG O2G A99 sing 25 n n 
PG O3B A99 sing 26 n n 
PG O3G A99 doub 27 n n 
"O'L" N2' A99 sing 28 n n 
"O'M" N2' A99 doub 29 n n 
C1' C2' A99 doub 30 n y 
C1' C6' A99 sing 31 n y 
C1B C2B A99 sing 32 n n 
C1B O4' A99 sing 33 n n 
C2' N2' A99 sing 34 n n 
C2' C3' A99 sing 35 n y 
O2' C2B A99 sing 36 n n 
C2B C3B A99 sing 37 n n 
C3' C4' A99 doub 38 n y 
O3' C3B A99 sing 39 n n 
C3B C4B A99 sing 40 n n 
C4' C5' A99 sing 41 n y 
O4' C4B A99 sing 42 n n 
C4B C5B A99 sing 43 n n 
C5' C6' A99 doub 44 n y 
O5' C5B A99 sing 45 n n 
C' H' A99 sing 46 n n 
C2 H2 A99 sing 47 n n 
N6 HN6 A99 sing 48 n n 
N6 HN6A A99 sing 49 n n 
C8 H8 A99 sing 50 n n 
C1' H1' A99 sing 51 n n 
C1B H1B A99 sing 52 n n 
O2' HO2' A99 sing 53 n n 
C2B H2B A99 sing 54 n n 
O3' HO3' A99 sing 55 n n 
C3B H3B A99 sing 56 n n 
C4' H4' A99 sing 57 n n 
C4B H4B A99 sing 58 n n 
C5' H5' A99 sing 59 n n 
C5B H5B A99 sing 60 n n 
C5B H5BA A99 sing 61 n n 
C6' H6' A99 sing 62 n n 
CM' HM' A99 sing 63 n n 
CM' "HM'A" A99 sing 64 n n 
CM' "HM'B" A99 sing 65 n n 
O2A H2A A99 sing 66 n n 
O2B HBB A99 sing 67 n n 
O1G H1G A99 sing 68 n n 
#
_atom_sites.entry_id                     2YJ6 
_atom_sites.fract_transf_matrix[1][1]    0.014376 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002082 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018553 
_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]    0.012798 
_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 A99 A 1 1636 1636 A99 A99 . 
D 2 A99 B 1 1636 1636 A99 A99 . 
E 3 PO4 B 1 1637 1637 PO4 PO4 . 
F 4 HOH A 1 2001 2001 HOH HOH . 
F 4 HOH A 2 2002 2002 HOH HOH . 
F 4 HOH A 3 2003 2003 HOH HOH . 
F 4 HOH A 4 2004 2004 HOH HOH . 
F 4 HOH A 5 2005 2005 HOH HOH . 
F 4 HOH A 6 2006 2006 HOH HOH . 
F 4 HOH A 7 2007 2007 HOH HOH . 
F 4 HOH A 8 2008 2008 HOH HOH . 
F 4 HOH A 9 2009 2009 HOH HOH . 
F 4 HOH A 10 2010 2010 HOH HOH . 
F 4 HOH A 11 2011 2011 HOH HOH . 
F 4 HOH A 12 2012 2012 HOH HOH . 
F 4 HOH A 13 2013 2013 HOH HOH . 
F 4 HOH A 14 2014 2014 HOH HOH . 
G 4 HOH B 1 2001 2001 HOH HOH . 
G 4 HOH B 2 2002 2002 HOH HOH . 
G 4 HOH B 3 2003 2003 HOH HOH . 
G 4 HOH B 4 2004 2004 HOH HOH . 
G 4 HOH B 5 2005 2005 HOH HOH . 
G 4 HOH B 6 2006 2006 HOH HOH . 
G 4 HOH B 7 2007 2007 HOH HOH . 
G 4 HOH B 8 2008 2008 HOH HOH . 
G 4 HOH B 9 2009 2009 HOH HOH . 
G 4 HOH B 10 2010 2010 HOH HOH . 
G 4 HOH B 11 2011 2011 HOH HOH . 
G 4 HOH B 12 2012 2012 HOH HOH . 
G 4 HOH B 13 2013 2013 HOH HOH . 
G 4 HOH B 14 2014 2014 HOH HOH . 
G 4 HOH B 15 2015 2015 HOH HOH . 
G 4 HOH B 16 2016 2016 HOH HOH . 
G 4 HOH B 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 C C' A99 . . . D 2 3.232 -15.048 13.312 1 54.86 ? C' A99 1636 B 1 
HETATM 2 N N1 A99 . . . D 2 -5.8 -14.877 15.431 1 36.85 ? N1 A99 1636 B 1 
HETATM 3 C C2 A99 . . . D 2 -5.379 -15.888 16.2 1 38.34 ? C2 A99 1636 B 1 
HETATM 4 N N3 A99 . . . D 2 -4.427 -15.75 17.13 1 40.4 ? N3 A99 1636 B 1 
HETATM 5 C C4 A99 . . . D 2 -3.845 -14.541 17.339 1 42.53 ? C4 A99 1636 B 1 
HETATM 6 C C5 A99 . . . D 2 -4.239 -13.384 16.533 1 40.73 ? C5 A99 1636 B 1 
HETATM 7 C C6 A99 . . . D 2 -5.307 -13.614 15.519 1 45.19 ? C6 A99 1636 B 1 
HETATM 8 N N6 A99 . . . D 2 -5.772 -12.615 14.708 1 33.86 ? N6 A99 1636 B 1 
HETATM 9 N N7 A99 . . . D 2 -3.491 -12.357 16.974 1 40.67 ? N7 A99 1636 B 1 
HETATM 10 C C8 A99 . . . D 2 -2.681 -12.813 17.965 1 45.78 ? C8 A99 1636 B 1 
HETATM 11 N N9 A99 . . . D 2 -2.901 -14.12 18.175 1 45.08 ? N9 A99 1636 B 1 
HETATM 12 P PA A99 . . . D 2 1.243 -11.3 18.887 1 61.74 ? PA A99 1636 B 1 
HETATM 13 P PB A99 . . . D 2 3.321 -12.208 17.212 1 58.67 ? PB A99 1636 B 1 
HETATM 14 P PG A99 . . . D 2 3.55 -14.705 16.008 1 60.13 ? PG A99 1636 B 1 
HETATM 15 O "O'L" A99 . . . D 2 5.305 -14.639 9.924 1 48.19 ? "O'L" A99 1636 B 1 
HETATM 16 O "O'M" A99 . . . D 2 6.296 -14.291 11.75 1 61.05 ? "O'M" A99 1636 B 1 
HETATM 17 C C1' A99 . . . D 2 5.441 -17.363 11.06 1 49.11 ? C1' A99 1636 B 1 
HETATM 18 O O1A A99 . . . D 2 2.194 -10.739 19.915 1 62.79 ? O1A A99 1636 B 1 
HETATM 19 C C1B A99 . . . D 2 -2.259 -15.031 19.149 1 46.7 ? C1B A99 1636 B 1 
HETATM 20 O O1B A99 . . . D 2 3.285 -10.802 16.668 1 58.3 ? O1B A99 1636 B 1 
HETATM 21 O O1G A99 . . . D 2 5.052 -14.666 15.955 1 58.31 ? O1G A99 1636 B 1 
HETATM 22 C C2' A99 . . . D 2 4.968 -16.161 11.586 1 48.17 ? C2' A99 1636 B 1 
HETATM 23 N N2' A99 . . . D 2 5.543 -14.982 11.074 1 51.79 ? N2' A99 1636 B 1 
HETATM 24 O O2' A99 . . . D 2 -1.055 -17.058 18.96 1 44.75 ? O2' A99 1636 B 1 
HETATM 25 O O2A A99 . . . D 2 0.581 -10.407 17.864 1 59.04 ? O2A A99 1636 B 1 
HETATM 26 C C2B A99 . . . D 2 -1.141 -15.742 18.42 1 46.17 ? C2B A99 1636 B 1 
HETATM 27 O O2B A99 . . . D 2 4.511 -12.733 17.972 1 67.18 ? O2B A99 1636 B 1 
HETATM 28 O O2G A99 . . . D 2 2.945 -15.396 14.681 1 48.49 ? O2G A99 1636 B 1 
HETATM 29 C C3' A99 . . . D 2 3.895 -16.212 12.639 1 48.98 ? C3' A99 1636 B 1 
HETATM 30 O O3' A99 . . . D 2 1.209 -15.85 18.78 1 47.45 ? O3' A99 1636 B 1 
HETATM 31 O O3A A99 . . . D 2 2.009 -12.46 18.093 1 52.92 ? O3A A99 1636 B 1 
HETATM 32 C C3B A99 . . . D 2 0.092 -14.96 18.793 1 47.74 ? C3B A99 1636 B 1 
HETATM 33 O O3B A99 . . . D 2 3.047 -13.187 15.969 1 61.07 ? O3B A99 1636 B 1 
HETATM 34 O O3G A99 . . . D 2 2.845 -15.366 17.16 1 56.2 ? O3G A99 1636 B 1 
HETATM 35 C C4' A99 . . . D 2 3.428 -17.467 13.024 1 51.54 ? C4' A99 1636 B 1 
HETATM 36 O O4' A99 . . . D 2 -1.665 -14.32 20.238 1 50.63 ? O4' A99 1636 B 1 
HETATM 37 C C4B A99 . . . D 2 -0.24 -14.468 20.199 1 46.75 ? C4B A99 1636 B 1 
HETATM 38 C C5' A99 . . . D 2 3.941 -18.638 12.469 1 52.32 ? C5' A99 1636 B 1 
HETATM 39 O O5' A99 . . . D 2 0.104 -12.158 19.621 1 54.18 ? O5' A99 1636 B 1 
HETATM 40 C C5B A99 . . . D 2 0.458 -13.159 20.567 1 50.25 ? C5B A99 1636 B 1 
HETATM 41 C C6' A99 . . . D 2 4.934 -18.586 11.493 1 44.49 ? C6' A99 1636 B 1 
HETATM 42 C CM' A99 . . . D 2 3.98 -13.722 13.197 1 60.41 ? CM' A99 1636 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          16 
_model_server_stats.element_count           42 
#