data_2YJ6
#
_model_server_result.job_id            rMYCmdF8nZZ4NAPw66IzYQ 
_model_server_result.datetime_utc      '2024-11-15 15:21:54' 
_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":"C","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 . . . C 2 1.221 8.843 26.295 1 72.87 ? C' A99 1636 A 1 
HETATM 2 N N1 A99 . . . C 2 -6.333 7.978 20.57 1 53.02 ? N1 A99 1636 A 1 
HETATM 3 C C2 A99 . . . C 2 -5.745 9.058 20.021 1 46.76 ? C2 A99 1636 A 1 
HETATM 4 N N3 A99 . . . C 2 -4.462 9.075 19.636 1 52.31 ? N3 A99 1636 A 1 
HETATM 5 C C4 A99 . . . C 2 -3.681 7.969 19.779 1 57.44 ? C4 A99 1636 A 1 
HETATM 6 C C5 A99 . . . C 2 -4.257 6.752 20.376 1 53.27 ? C5 A99 1636 A 1 
HETATM 7 C C6 A99 . . . C 2 -5.679 6.81 20.784 1 51.22 ? C6 A99 1636 A 1 
HETATM 8 N N6 A99 . . . C 2 -6.309 5.74 21.339 1 41.22 ? N6 A99 1636 A 1 
HETATM 9 N N7 A99 . . . C 2 -3.275 5.832 20.404 1 55.95 ? N7 A99 1636 A 1 
HETATM 10 C C8 A99 . . . C 2 -2.168 6.408 19.876 1 58.66 ? C8 A99 1636 A 1 
HETATM 11 N N9 A99 . . . C 2 -2.406 7.68 19.512 1 54.93 ? N9 A99 1636 A 1 
HETATM 12 P PA A99 . . . C 2 2.101 5.047 20.765 1 75.3 ? PA A99 1636 A 1 
HETATM 13 P PB A99 . . . C 2 2.617 5.956 23.357 1 89.35 ? PB A99 1636 A 1 
HETATM 14 P PG A99 . . . C 2 3.244 8.46 24.529 1 93.87 ? PG A99 1636 A 1 
HETATM 15 O "O'L" A99 . . . C 2 1.743 11.593 26.43 1 71.14 ? "O'L" A99 1636 A 1 
HETATM 16 O "O'M" A99 . . . C 2 1.441 12.568 28.286 1 60.72 ? "O'M" A99 1636 A 1 
HETATM 17 C C1' A99 . . . C 2 2.281 10.4 29.66 1 53.82 ? C1' A99 1636 A 1 
HETATM 18 O O1A A99 . . . C 2 3.524 5.493 20.517 1 85.77 ? O1A A99 1636 A 1 
HETATM 19 C C1B A99 . . . C 2 -1.43 8.596 18.885 1 56.92 ? C1B A99 1636 A 1 
HETATM 20 O O1B A99 . . . C 2 2.102 5.161 24.539 1 83.42 ? O1B A99 1636 A 1 
HETATM 21 O O1G A99 . . . C 2 4 7.588 25.508 1 86.33 ? O1G A99 1636 A 1 
HETATM 22 C C2' A99 . . . C 2 1.878 10.347 28.335 1 60.52 ? C2' A99 1636 A 1 
HETATM 23 N N2' A99 . . . C 2 1.68 11.55 27.649 1 64.64 ? N2' A99 1636 A 1 
HETATM 24 O O2' A99 . . . C 2 -0.464 10.693 19.516 1 53.86 ? O2' A99 1636 A 1 
HETATM 25 O O2A A99 . . . C 2 1.74 3.584 20.742 1 78.79 ? O2A A99 1636 A 1 
HETATM 26 C C2B A99 . . . C 2 -0.678 9.349 19.963 1 60.31 ? C2B A99 1636 A 1 
HETATM 27 O O2B A99 . . . C 2 4.049 5.793 22.891 1 82.64 ? O2B A99 1636 A 1 
HETATM 28 O O2G A99 . . . C 2 2.166 9.364 25.338 1 77.77 ? O2G A99 1636 A 1 
HETATM 29 C C3' A99 . . . C 2 1.668 9.018 27.702 1 65.35 ? C3' A99 1636 A 1 
HETATM 30 O O3' A99 . . . C 2 1.685 9.517 20.47 1 67.9 ? O3' A99 1636 A 1 
HETATM 31 O O3A A99 . . . C 2 1.599 5.662 22.153 1 73.26 ? O3A A99 1636 A 1 
HETATM 32 C C3B A99 . . . C 2 0.635 8.611 20.105 1 64 ? C3B A99 1636 A 1 
HETATM 33 O O3B A99 . . . C 2 2.31 7.526 23.602 1 82.32 ? O3B A99 1636 A 1 
HETATM 34 O O3G A99 . . . C 2 4.032 9.378 23.617 1 83.87 ? O3G A99 1636 A 1 
HETATM 35 C C4' A99 . . . C 2 1.87 7.879 28.47 1 64.77 ? C4' A99 1636 A 1 
HETATM 36 O O4' A99 . . . C 2 -0.463 7.819 18.162 1 60.56 ? O4' A99 1636 A 1 
HETATM 37 C C4B A99 . . . C 2 0.843 8.002 18.724 1 61.46 ? C4B A99 1636 A 1 
HETATM 38 C C5' A99 . . . C 2 2.284 7.985 29.791 1 58.36 ? C5' A99 1636 A 1 
HETATM 39 O O5' A99 . . . C 2 1.108 5.838 19.774 1 72.8 ? O5' A99 1636 A 1 
HETATM 40 C C5B A99 . . . C 2 1.624 6.691 18.751 1 70.19 ? C5B A99 1636 A 1 
HETATM 41 C C6' A99 . . . C 2 2.482 9.229 30.375 1 54.26 ? C6' A99 1636 A 1 
HETATM 42 C CM' A99 . . . C 2 0.895 7.368 26.074 1 68.2 ? CM' A99 1636 A 1 
#
_model_server_stats.io_time_ms              41 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           42 
#