data_4PYD
#
_model_server_result.job_id            b_RQKeV3fykRO6PBkUYAYw 
_model_server_result.datetime_utc      '2025-09-04 19:27:08' 
_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          4pyd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":201}' 
#
_entry.id    4PYD 
#
_exptl.entry_id    4PYD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              345.205 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "(2R,4AR,5AR,11AR,12AS)-8-AMINO-2-HYDROXY-4A,5A,9,11,11A,12A-HEXAHYDRO[1,3,2]DIOXAPHOSPHININO[4',5':5,6]PYRANO[3,2-G]PTERIDINE-10,12(4H,6H)-DIONE 2-OXIDE" 
_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            4PYD 
_cell.length_a            61.594 
_cell.length_b            97.213 
_cell.length_c            165.331 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PYD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 G N N 
? 2 H N N 
? 2 M N N 
? 2 N N N 
#
_chem_comp.formula           'C10 H12 N5 O7 P' 
_chem_comp.formula_weight    345.205 
_chem_comp.id                8CS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "(2R,4AR,5AR,11AR,12AS)-8-AMINO-2-HYDROXY-4A,5A,9,11,11A,12A-HEXAHYDRO[1,3,2]DIOXAPHOSPHININO[4',5':5,6]PYRANO[3,2-G]PTERIDINE-10,12(4H,6H)-DIONE 2-OXIDE" 
_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
O4' C4' 8CS doub 1 n n 
C4' N3' 8CS sing 2 n n 
C4' C4A 8CS sing 3 n n 
C4A N5' 8CS sing 4 n n 
C4A C4B 8CS doub 5 n n 
N5' C6' 8CS sing 6 n n 
N5' HN5' 8CS sing 7 n n 
N3' C2' 8CS sing 8 n n 
N3' HN3' 8CS sing 9 n n 
C2' N2' 8CS sing 10 n n 
C2' N1' 8CS doub 11 n n 
N2' "H2'1" 8CS sing 12 n n 
N2' "H2'2" 8CS sing 13 n n 
N1' C4B 8CS sing 14 n n 
C4B N8' 8CS sing 15 n n 
N8' C7 8CS sing 16 n n 
N8' HN8' 8CS sing 17 n n 
C7 C6' 8CS sing 18 n n 
C7 O9' 8CS sing 19 n n 
C7 H7 8CS sing 20 n n 
C6' C7' 8CS sing 21 n n 
C6' H6' 8CS sing 22 n n 
C7' C8' 8CS sing 23 n n 
C7' O10 8CS doub 24 n n 
C8' O3 8CS sing 25 n n 
C8' C9' 8CS sing 26 n n 
C8' H8' 8CS sing 27 n n 
O3 P 8CS sing 28 n n 
O9' C9' 8CS sing 29 n n 
C9' C10 8CS sing 30 n n 
C9' H9' 8CS sing 31 n n 
C10 O1 8CS sing 32 n n 
C10 H101 8CS sing 33 n n 
C10 H102 8CS sing 34 n n 
O1 P 8CS sing 35 n n 
P O2 8CS doub 36 n n 
P O4 8CS sing 37 n n 
O4 HO4 8CS sing 38 n n 
#
_atom_sites.entry_id                     4PYD 
_atom_sites.fract_transf_matrix[1][1]    0.016235 
_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]    0.010287 
_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]    0.006048 
_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
G 2 8CS A 1 201 2 8CS 8CS . 
H 2 8CS B 1 201 3 8CS 8CS . 
I 3 EDO C 1 201 3 EDO EDO . 
J 4 GOL C 1 202 1 GOL GOL . 
K 4 GOL D 1 201 2 GOL GOL . 
L 5 DTT D 1 202 1 DTT DTT . 
M 2 8CS E 1 201 1 8CS 8CS . 
N 2 8CS F 1 201 4 8CS 8CS . 
O 3 EDO F 1 202 1 EDO EDO . 
#
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 O4' 8CS . . . M 2 -2.168 -14.108 40.154 1 67.1 ? O4' 8CS 201 E 1 
HETATM 2 C C4' 8CS . . . M 2 -2.177 -13.764 38.949 1 67.22 ? C4' 8CS 201 E 1 
HETATM 3 C C4A 8CS . . . M 2 -1.652 -12.436 38.551 1 67.88 ? C4A 8CS 201 E 1 
HETATM 4 N N5' 8CS . . . M 2 -1.157 -11.532 39.433 1 68.2 ? N5' 8CS 201 E 1 
HETATM 5 N N3' 8CS . . . M 2 -2.658 -14.588 37.997 1 67.03 ? N3' 8CS 201 E 1 
HETATM 6 C C2' 8CS . . . M 2 -2.685 -14.25 36.693 1 67.16 ? C2' 8CS 201 E 1 
HETATM 7 N N2' 8CS . . . M 2 -3.189 -15.139 35.802 1 66.64 ? N2' 8CS 201 E 1 
HETATM 8 N N1' 8CS . . . M 2 -2.222 -13.045 36.251 1 67.68 ? N1' 8CS 201 E 1 
HETATM 9 C C4B 8CS . . . M 2 -1.708 -12.118 37.106 1 68.06 ? C4B 8CS 201 E 1 
HETATM 10 N N8' 8CS . . . M 2 -1.236 -10.917 36.69 1 68.44 ? N8' 8CS 201 E 1 
HETATM 11 C C7 8CS . . . M 2 -0.487 -10.096 37.626 1 68.95 ? C7 8CS 201 E 1 
HETATM 12 C C6' 8CS . . . M 2 -1.122 -10.137 39.015 1 68.69 ? C6' 8CS 201 E 1 
HETATM 13 C C7' 8CS . . . M 2 -0.295 -9.254 39.913 1 69.07 ? C7' 8CS 201 E 1 
HETATM 14 O O10 8CS . . . M 2 -0.819 -8.386 40.607 1 68.77 ? O10 8CS 201 E 1 
HETATM 15 C C8' 8CS . . . M 2 1.198 -9.459 39.929 1 69.44 ? C8' 8CS 201 E 1 
HETATM 16 O O3 8CS . . . M 2 1.49 -10.525 40.84 1 69.51 ? O3 8CS 201 E 1 
HETATM 17 O O9' 8CS . . . M 2 0.839 -10.612 37.749 1 69.27 ? O9' 8CS 201 E 1 
HETATM 18 C C9' 8CS . . . M 2 1.7 -9.733 38.497 1 69.84 ? C9' 8CS 201 E 1 
HETATM 19 C C10 8CS . . . M 2 3.124 -10.292 38.483 1 70.24 ? C10 8CS 201 E 1 
HETATM 20 O O1 8CS . . . M 2 3.187 -11.496 39.248 1 70.31 ? O1 8CS 201 E 1 
HETATM 21 P P 8CS . . . M 2 2.839 -11.424 40.819 1 70.5 ? P 8CS 201 E 1 
HETATM 22 O O2 8CS . . . M 2 2.449 -12.787 41.361 1 69.52 ? O2 8CS 201 E 1 
HETATM 23 O O4 8CS . . . M 2 3.989 -10.677 41.463 1 70.61 ? O4 8CS 201 E 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           4 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           23 
#