data_4X9L
#
_model_server_result.job_id            DXM6hfTKDqC06ndssYMJow 
_model_server_result.datetime_utc      '2024-12-30 20:34:37' 
_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          4x9l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
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_entry.id    4X9L 
#
_exptl.entry_id    4X9L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    1 
_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            4X9L 
_cell.length_a            116.87 
_cell.length_b            116.87 
_cell.length_c            105.34 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4X9L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C11 H18 N5 O12 P3' 
_chem_comp.formula_weight    505.208 
_chem_comp.id                ACP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" 
#
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
PG O1G ACP doub 1 n n 
PG O2G ACP sing 2 n n 
PG O3G ACP sing 3 n n 
PG C3B ACP sing 4 n n 
O2G HOG2 ACP sing 5 n n 
O3G HOG3 ACP sing 6 n n 
PB O1B ACP doub 7 n n 
PB O2B ACP sing 8 n n 
PB C3B ACP sing 9 n n 
PB O3A ACP sing 10 n n 
O2B HOB2 ACP sing 11 n n 
C3B H3B1 ACP sing 12 n n 
C3B H3B2 ACP sing 13 n n 
PA O1A ACP doub 14 n n 
PA O2A ACP sing 15 n n 
PA O3A ACP sing 16 n n 
PA O5' ACP sing 17 n n 
O2A HOA2 ACP sing 18 n n 
O5' C5' ACP sing 19 n n 
C5' C4' ACP sing 20 n n 
C5' "H5'1" ACP sing 21 n n 
C5' "H5'2" ACP sing 22 n n 
C4' O4' ACP sing 23 n n 
C4' C3' ACP sing 24 n n 
C4' H4' ACP sing 25 n n 
O4' C1' ACP sing 26 n n 
C3' O3' ACP sing 27 n n 
C3' C2' ACP sing 28 n n 
C3' H3' ACP sing 29 n n 
O3' HO3' ACP sing 30 n n 
C2' O2' ACP sing 31 n n 
C2' C1' ACP sing 32 n n 
C2' H2' ACP sing 33 n n 
O2' HO2' ACP sing 34 n n 
C1' N9 ACP sing 35 n n 
C1' H1' ACP sing 36 n n 
N9 C8 ACP sing 37 n y 
N9 C4 ACP sing 38 n y 
C8 N7 ACP doub 39 n y 
C8 H8 ACP sing 40 n n 
N7 C5 ACP sing 41 n y 
C5 C6 ACP sing 42 n y 
C5 C4 ACP doub 43 n y 
C6 N6 ACP sing 44 n n 
C6 N1 ACP doub 45 n y 
N6 HN61 ACP sing 46 n n 
N6 HN62 ACP sing 47 n n 
N1 C2 ACP sing 48 n y 
C2 N3 ACP doub 49 n y 
C2 H2 ACP sing 50 n n 
N3 C4 ACP sing 51 n y 
#
_atom_sites.entry_id                     4X9L 
_atom_sites.fract_transf_matrix[1][1]    0.008557 
_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]    0.008557 
_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]    0.009493 
_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
B 2 ACP A 1 301 1 ACP ACP . 
C 3 PG4 A 1 302 1 PG4 PG4 . 
D 4 HOH A 1 401 1 HOH HOH . 
D 4 HOH A 2 402 7 HOH HOH . 
D 4 HOH A 3 403 2 HOH HOH . 
D 4 HOH A 4 404 3 HOH HOH . 
D 4 HOH A 5 405 4 HOH HOH . 
D 4 HOH A 6 406 5 HOH HOH . 
D 4 HOH A 7 407 8 HOH HOH . 
D 4 HOH A 8 408 9 HOH HOH . 
D 4 HOH A 9 409 10 HOH HOH . 
D 4 HOH A 10 410 11 HOH HOH . 
D 4 HOH A 11 411 12 HOH HOH . 
D 4 HOH A 12 412 13 HOH HOH . 
D 4 HOH A 13 413 14 HOH HOH . 
D 4 HOH A 14 414 15 HOH HOH . 
D 4 HOH A 15 415 16 HOH HOH . 
D 4 HOH A 16 416 17 HOH HOH . 
D 4 HOH A 17 417 18 HOH HOH . 
D 4 HOH A 18 418 19 HOH HOH . 
D 4 HOH A 19 419 20 HOH HOH . 
D 4 HOH A 20 420 21 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 P PG ACP . . . B 2 21.399 12.16 6.588 1 135.85 ? PG ACP 301 A 1 
HETATM 2 O O1G ACP . . . B 2 22.347 11.684 5.51 1 127.74 ? O1G ACP 301 A 1 
HETATM 3 O O2G ACP . . . B 2 20.093 11.371 6.691 1 91.69 ? O2G ACP 301 A 1 
HETATM 4 O O3G ACP . . . B 2 22.137 12.473 7.869 1 114.6 ? O3G ACP 301 A 1 
HETATM 5 P PB ACP . . . B 2 20.322 14.795 7.495 1 159.24 ? PB ACP 301 A 1 
HETATM 6 O O1B ACP . . . B 2 19.703 16.012 6.842 1 136.67 ? O1B ACP 301 A 1 
HETATM 7 O O2B ACP . . . B 2 21.471 15.053 8.449 1 114.62 ? O2B ACP 301 A 1 
HETATM 8 C C3B ACP . . . B 2 20.907 13.824 6.072 1 134.01 ? C3B ACP 301 A 1 
HETATM 9 P PA ACP . . . B 2 19.093 13.465 9.798 1 108.4 ? PA ACP 301 A 1 
HETATM 10 O O1A ACP . . . B 2 18.04 12.394 10.011 1 120.79 ? O1A ACP 301 A 1 
HETATM 11 O O2A ACP . . . B 2 20.534 13.133 10.122 1 84.7 ? O2A ACP 301 A 1 
HETATM 12 O O3A ACP . . . B 2 19.12 13.967 8.245 1 146.34 ? O3A ACP 301 A 1 
HETATM 13 O O5' ACP . . . B 2 18.558 14.737 10.649 1 98.75 ? O5' ACP 301 A 1 
HETATM 14 C C5' ACP . . . B 2 17.498 15.566 10.16 1 98.33 ? C5' ACP 301 A 1 
HETATM 15 C C4' ACP . . . B 2 17.771 17.082 10.251 1 100.88 ? C4' ACP 301 A 1 
HETATM 16 O O4' ACP . . . B 2 18.222 17.53 11.54 1 87.62 ? O4' ACP 301 A 1 
HETATM 17 C C3' ACP . . . B 2 18.804 17.666 9.288 1 103.31 ? C3' ACP 301 A 1 
HETATM 18 O O3' ACP . . . B 2 18.319 17.824 7.955 1 104.69 ? O3' ACP 301 A 1 
HETATM 19 C C2' ACP . . . B 2 19.035 19.02 9.902 1 98.15 ? C2' ACP 301 A 1 
HETATM 20 O O2' ACP . . . B 2 17.909 19.86 9.625 1 87.09 ? O2' ACP 301 A 1 
HETATM 21 C C1' ACP . . . B 2 19.037 18.717 11.385 1 91.11 ? C1' ACP 301 A 1 
HETATM 22 N N9 ACP . . . B 2 20.456 18.54 11.828 1 89.64 ? N9 ACP 301 A 1 
HETATM 23 C C8 ACP . . . B 2 21.126 17.373 11.937 1 83.47 ? C8 ACP 301 A 1 
HETATM 24 N N7 ACP . . . B 2 22.398 17.57 12.38 1 84.17 ? N7 ACP 301 A 1 
HETATM 25 C C5 ACP . . . B 2 22.57 18.897 12.567 1 83.22 ? C5 ACP 301 A 1 
HETATM 26 C C6 ACP . . . B 2 23.673 19.79 13.022 1 70.65 ? C6 ACP 301 A 1 
HETATM 27 N N6 ACP . . . B 2 24.889 19.296 13.378 1 74.04 ? N6 ACP 301 A 1 
HETATM 28 N N1 ACP . . . B 2 23.423 21.122 13.071 1 69.83 ? N1 ACP 301 A 1 
HETATM 29 C C2 ACP . . . B 2 22.224 21.638 12.727 1 76.64 ? C2 ACP 301 A 1 
HETATM 30 N N3 ACP . . . B 2 21.184 20.888 12.309 1 87.37 ? N3 ACP 301 A 1 
HETATM 31 C C4 ACP . . . B 2 21.285 19.532 12.211 1 93.24 ? C4 ACP 301 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           702 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#