data_3CLY
#
_model_server_result.job_id            C22pWhNKcJFtOn_ePrxe5A 
_model_server_result.datetime_utc      '2024-11-16 16:19:43' 
_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          3cly 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1803}' 
#
_entry.id    3CLY 
#
_exptl.entry_id    3CLY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          3 
_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            3CLY 
_cell.length_a            55.437 
_cell.length_b            68.462 
_cell.length_c            85.711 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3CLY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PISA monomeric 1 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,C,D,E 1 1,2 
A,B,C,D,E 2 1 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_645 -x+1,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 55.437 -34.231 42.8555 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
covale ? covale1 A C ASP 211 A ASP 1655 1_555 A N PTR 212 A PTR 1656 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 A C PTR 212 A PTR 1656 1_555 A N PTR 213 A PTR 1657 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale3 A C PTR 213 A PTR 1657 1_555 A N LYS 214 A LYS 1658 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
metalc ? metalc1 A OD1 ASN 187 A ASN 1631 1_555 B MG MG . A MG 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? 
metalc ? metalc2 A OD2 ASP 200 A ASP 1644 1_555 B MG MG . A MG 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc3 B MG MG . A MG 1801 1_555 D O2A ACP . A ACP 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc4 B MG MG . A MG 1801 1_555 D O1G ACP . A ACP 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc5 B MG MG . A MG 1801 1_555 E O HOH . A HOH 1901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc6 B MG MG . A MG 1801 1_555 E O HOH . A HOH 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc7 C MG MG . A MG 1802 1_555 D O2B ACP . A ACP 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? 
#
_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                     3CLY 
_atom_sites.fract_transf_matrix[1][1]    0.018038 
_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]    0.014607 
_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]    0.011667 
_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 MG A 1 1801 301 MG MG . 
C 2 MG A 1 1802 302 MG MG . 
D 3 ACP A 1 1803 300 ACP PCP . 
E 4 HOH A 1 1901 1 HOH HOH . 
E 4 HOH A 2 1902 2 HOH HOH . 
E 4 HOH A 3 1903 3 HOH HOH . 
E 4 HOH A 4 1904 4 HOH HOH . 
E 4 HOH A 5 1905 5 HOH HOH . 
E 4 HOH A 6 1906 6 HOH HOH . 
E 4 HOH A 7 1907 7 HOH HOH . 
E 4 HOH A 8 1908 8 HOH HOH . 
E 4 HOH A 9 1909 9 HOH HOH . 
E 4 HOH A 10 1910 10 HOH HOH . 
E 4 HOH A 11 1911 11 HOH HOH . 
E 4 HOH A 12 1912 12 HOH HOH . 
E 4 HOH A 13 1913 13 HOH HOH . 
E 4 HOH A 14 1914 14 HOH HOH . 
E 4 HOH A 15 1915 15 HOH HOH . 
E 4 HOH A 16 1916 16 HOH HOH . 
E 4 HOH A 17 1917 17 HOH HOH . 
E 4 HOH A 18 1918 18 HOH HOH . 
E 4 HOH A 19 1919 19 HOH HOH . 
E 4 HOH A 20 1920 20 HOH HOH . 
E 4 HOH A 21 1921 21 HOH HOH . 
E 4 HOH A 22 1922 22 HOH HOH . 
E 4 HOH A 23 1923 23 HOH HOH . 
E 4 HOH A 24 1924 24 HOH HOH . 
E 4 HOH A 25 1925 25 HOH HOH . 
E 4 HOH A 26 1926 26 HOH HOH . 
E 4 HOH A 27 1927 27 HOH HOH . 
E 4 HOH A 28 1928 28 HOH HOH . 
E 4 HOH A 29 1929 29 HOH HOH . 
E 4 HOH A 30 1930 30 HOH HOH . 
E 4 HOH A 31 1931 31 HOH HOH . 
E 4 HOH A 32 1932 32 HOH HOH . 
E 4 HOH A 33 1933 33 HOH HOH . 
E 4 HOH A 34 1934 34 HOH HOH . 
E 4 HOH A 35 1935 35 HOH HOH . 
E 4 HOH A 36 1936 36 HOH HOH . 
E 4 HOH A 37 1937 37 HOH HOH . 
E 4 HOH A 38 1938 38 HOH HOH . 
E 4 HOH A 39 1939 39 HOH HOH . 
E 4 HOH A 40 1940 40 HOH HOH . 
E 4 HOH A 41 1941 41 HOH HOH . 
E 4 HOH A 42 1942 42 HOH HOH . 
E 4 HOH A 43 1943 43 HOH HOH . 
E 4 HOH A 44 1944 44 HOH HOH . 
E 4 HOH A 45 1945 45 HOH HOH . 
E 4 HOH A 46 1946 46 HOH HOH . 
E 4 HOH A 47 1947 47 HOH HOH . 
E 4 HOH A 48 1948 48 HOH HOH . 
E 4 HOH A 49 1949 49 HOH HOH . 
E 4 HOH A 50 1950 50 HOH HOH . 
E 4 HOH A 51 1951 51 HOH HOH . 
E 4 HOH A 52 1952 52 HOH HOH . 
E 4 HOH A 53 1953 53 HOH HOH . 
E 4 HOH A 54 1954 54 HOH HOH . 
E 4 HOH A 55 1955 55 HOH HOH . 
E 4 HOH A 56 1956 56 HOH HOH . 
E 4 HOH A 57 1957 57 HOH HOH . 
E 4 HOH A 58 1958 58 HOH HOH . 
E 4 HOH A 59 1959 59 HOH HOH . 
E 4 HOH A 60 1960 60 HOH HOH . 
E 4 HOH A 61 1961 61 HOH HOH . 
E 4 HOH A 62 1962 62 HOH HOH . 
E 4 HOH A 63 1963 63 HOH HOH . 
E 4 HOH A 64 1964 64 HOH HOH . 
E 4 HOH A 65 1965 65 HOH HOH . 
E 4 HOH A 66 1966 66 HOH HOH . 
E 4 HOH A 67 1967 67 HOH HOH . 
E 4 HOH A 68 1968 68 HOH HOH . 
E 4 HOH A 69 1969 69 HOH HOH . 
E 4 HOH A 70 1970 70 HOH HOH . 
E 4 HOH A 71 1971 71 HOH HOH . 
E 4 HOH A 72 1972 72 HOH HOH . 
E 4 HOH A 73 1973 73 HOH HOH . 
E 4 HOH A 74 1974 74 HOH HOH . 
E 4 HOH A 75 1975 75 HOH HOH . 
E 4 HOH A 76 1976 76 HOH HOH . 
E 4 HOH A 77 1977 77 HOH HOH . 
E 4 HOH A 78 1978 78 HOH HOH . 
E 4 HOH A 79 1979 79 HOH HOH . 
E 4 HOH A 80 1980 80 HOH HOH . 
E 4 HOH A 81 1981 81 HOH HOH . 
E 4 HOH A 82 1982 82 HOH HOH . 
E 4 HOH A 83 1983 83 HOH HOH . 
E 4 HOH A 84 1984 84 HOH HOH . 
E 4 HOH A 85 1985 85 HOH HOH . 
E 4 HOH A 86 1986 86 HOH HOH . 
E 4 HOH A 87 1987 87 HOH HOH . 
E 4 HOH A 88 1988 88 HOH HOH . 
E 4 HOH A 89 1989 89 HOH HOH . 
E 4 HOH A 90 1990 90 HOH HOH . 
E 4 HOH A 91 1991 91 HOH HOH . 
E 4 HOH A 92 1992 92 HOH HOH . 
E 4 HOH A 93 1993 93 HOH HOH . 
E 4 HOH A 94 1994 94 HOH HOH . 
E 4 HOH A 95 1995 95 HOH HOH . 
E 4 HOH A 96 1996 96 HOH HOH . 
E 4 HOH A 97 1997 97 HOH HOH . 
E 4 HOH A 98 1998 98 HOH HOH . 
E 4 HOH A 99 1999 99 HOH HOH . 
E 4 HOH A 100 2000 100 HOH HOH . 
E 4 HOH A 101 2001 101 HOH HOH . 
E 4 HOH A 102 2002 102 HOH HOH . 
E 4 HOH A 103 2003 103 HOH HOH . 
E 4 HOH A 104 2004 104 HOH HOH . 
E 4 HOH A 105 2005 105 HOH HOH . 
E 4 HOH A 106 2006 106 HOH HOH . 
E 4 HOH A 107 2007 107 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 . . . D 3 18.59 -1.613 28.696 1 34.57 ? PG ACP 1803 A 1 
HETATM 2 O O1G ACP . . . D 3 18.839 -0.762 27.521 1 32.96 ? O1G ACP 1803 A 1 
HETATM 3 O O2G ACP . . . D 3 18.085 -0.951 29.94 1 33.38 ? O2G ACP 1803 A 1 
HETATM 4 O O3G ACP . . . D 3 19.623 -2.638 28.908 1 32.93 ? O3G ACP 1803 A 1 
HETATM 5 P PB ACP . . . D 3 15.843 -1.634 27.581 1 31.87 ? PB ACP 1803 A 1 
HETATM 6 O O1B ACP . . . D 3 14.872 -2.713 27.287 1 32.45 ? O1B ACP 1803 A 1 
HETATM 7 O O2B ACP . . . D 3 15.491 -0.709 28.675 1 32.62 ? O2B ACP 1803 A 1 
HETATM 8 C C3B ACP . . . D 3 17.228 -2.388 28.11 1 32.96 ? C3B ACP 1803 A 1 
HETATM 9 P PA ACP . . . D 3 15.656 0.462 25.624 1 23.66 ? PA ACP 1803 A 1 
HETATM 10 O O1A ACP . . . D 3 14.239 0.77 25.932 1 24.99 ? O1A ACP 1803 A 1 
HETATM 11 O O2A ACP . . . D 3 16.598 1.557 25.804 1 24.13 ? O2A ACP 1803 A 1 
HETATM 12 O O3A ACP . . . D 3 16.097 -0.856 26.277 1 27.39 ? O3A ACP 1803 A 1 
HETATM 13 O O5' ACP . . . D 3 15.779 0.273 24.057 1 23.22 ? O5' ACP 1803 A 1 
HETATM 14 C C5' ACP . . . D 3 16.979 -0.253 23.439 1 21.42 ? C5' ACP 1803 A 1 
HETATM 15 C C4' ACP . . . D 3 17.179 0.359 22.071 1 21.42 ? C4' ACP 1803 A 1 
HETATM 16 O O4' ACP . . . D 3 16.023 0.062 21.236 1 21.3 ? O4' ACP 1803 A 1 
HETATM 17 C C3' ACP . . . D 3 17.28 1.877 22.046 1 20.92 ? C3' ACP 1803 A 1 
HETATM 18 O O3' ACP . . . D 3 18.605 2.316 22.322 1 20.33 ? O3' ACP 1803 A 1 
HETATM 19 C C2' ACP . . . D 3 16.857 2.195 20.617 1 20.9 ? C2' ACP 1803 A 1 
HETATM 20 O O2' ACP . . . D 3 17.891 1.98 19.676 1 20.75 ? O2' ACP 1803 A 1 
HETATM 21 C C1' ACP . . . D 3 15.727 1.178 20.411 1 20.91 ? C1' ACP 1803 A 1 
HETATM 22 N N9 ACP . . . D 3 14.416 1.707 20.802 1 21.03 ? N9 ACP 1803 A 1 
HETATM 23 C C8 ACP . . . D 3 13.813 1.639 22.039 1 20 ? C8 ACP 1803 A 1 
HETATM 24 N N7 ACP . . . D 3 12.653 2.242 22.095 1 20.8 ? N7 ACP 1803 A 1 
HETATM 25 C C5 ACP . . . D 3 12.47 2.734 20.81 1 21.94 ? C5 ACP 1803 A 1 
HETATM 26 C C6 ACP . . . D 3 11.429 3.47 20.222 1 22.58 ? C6 ACP 1803 A 1 
HETATM 27 N N6 ACP . . . D 3 10.339 3.861 20.884 1 22.82 ? N6 ACP 1803 A 1 
HETATM 28 N N1 ACP . . . D 3 11.549 3.802 18.919 1 22.5 ? N1 ACP 1803 A 1 
HETATM 29 C C2 ACP . . . D 3 12.648 3.41 18.259 1 22.97 ? C2 ACP 1803 A 1 
HETATM 30 N N3 ACP . . . D 3 13.695 2.714 18.701 1 22.46 ? N3 ACP 1803 A 1 
HETATM 31 C C4 ACP . . . D 3 13.542 2.403 20 1 21.11 ? C4 ACP 1803 A 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#