data_1AFL
#
_model_server_result.job_id            jF-IHszU2sTEdfcbqog_SQ 
_model_server_result.datetime_utc      '2024-11-28 09:27:47' 
_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          1afl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":125}' 
#
_entry.id    1AFL 
#
_exptl.entry_id    1AFL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE" 
_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          90.08 
_cell.angle_gamma         90 
_cell.entry_id            1AFL 
_cell.length_a            101.93 
_cell.length_b            33.44 
_cell.length_c            73.69 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1AFL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_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,D,G 1 1 
B,E,F,H 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 E N 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
disulf ? disulf1 A SG CYS 26 A CYS 26 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf2 A SG CYS 40 A CYS 40 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf3 A SG CYS 58 A CYS 58 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf4 A SG CYS 65 A CYS 65 1_555 A SG CYS 72 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf5 B SG CYS 26 B CYS 26 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf6 B SG CYS 40 B CYS 40 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf7 B SG CYS 58 B CYS 58 1_555 B SG CYS 110 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf8 B SG CYS 65 B CYS 65 1_555 B SG CYS 72 B CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE" 
_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
PB O1B ATR doub 70 n n 
PB O2B ATR sing 71 n n 
PB O3B ATR sing 72 n n 
PB O3A ATR sing 73 n n 
O2B HOB2 ATR sing 74 n n 
O3B HOB3 ATR sing 75 n n 
PA O1A ATR doub 76 n n 
PA O2A ATR sing 77 n n 
PA O3A ATR sing 78 n n 
PA O5' ATR sing 79 n n 
O2A HOA2 ATR sing 80 n n 
O5' C5' ATR sing 81 n n 
C5' C4' ATR sing 82 n n 
C5' "H5'1" ATR sing 83 n n 
C5' "H5'2" ATR sing 84 n n 
C4' O4' ATR sing 85 n n 
C4' C3' ATR sing 86 n n 
C4' H4' ATR sing 87 n n 
O4' C1' ATR sing 88 n n 
C3' O3' ATR sing 89 n n 
C3' C2' ATR sing 90 n n 
C3' H3' ATR sing 91 n n 
O3' HO3' ATR sing 92 n n 
C2' O2' ATR sing 93 n n 
C2' C1' ATR sing 94 n n 
C2' H2' ATR sing 95 n n 
O2' P2' ATR sing 96 n n 
P2' O1P ATR doub 97 n n 
P2' O2P ATR sing 98 n n 
P2' O3P ATR sing 99 n n 
O2P HOP2 ATR sing 100 n n 
O3P HOP3 ATR sing 101 n n 
C1' N9 ATR sing 102 n n 
C1' H1' ATR sing 103 n n 
N9 C8 ATR sing 104 n y 
N9 C4 ATR sing 105 n y 
C8 N7 ATR doub 106 n y 
C8 H8 ATR sing 107 n n 
N7 C5 ATR sing 108 n y 
C5 C6 ATR sing 109 n y 
C5 C4 ATR doub 110 n y 
C6 N6 ATR sing 111 n n 
C6 N1 ATR doub 112 n y 
N6 HN61 ATR sing 113 n n 
N6 HN62 ATR sing 114 n n 
N1 C2 ATR sing 115 n y 
C2 N3 ATR doub 116 n y 
C2 H2 ATR sing 117 n n 
N3 C4 ATR sing 118 n y 
#
_atom_sites.entry_id                     1AFL 
_atom_sites.fract_transf_matrix[1][1]    0.009811 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000014 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.029904 
_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]    0.01357 
_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 ATR A 1 125 125 ATR ATR . 
D 3 CIT A 1 999 999 CIT CIT . 
E 2 ATR B 1 125 125 ATR ATR . 
F 3 CIT B 1 998 998 CIT CIT . 
G 4 HOH A 1 1000 1 HOH HOH . 
G 4 HOH A 2 1001 2 HOH HOH . 
G 4 HOH A 3 1002 3 HOH HOH . 
G 4 HOH A 4 1003 4 HOH HOH . 
G 4 HOH A 5 1004 5 HOH HOH . 
G 4 HOH A 6 1005 6 HOH HOH . 
G 4 HOH A 7 1006 7 HOH HOH . 
G 4 HOH A 8 1007 8 HOH HOH . 
G 4 HOH A 9 1008 9 HOH HOH . 
G 4 HOH A 10 1009 10 HOH HOH . 
G 4 HOH A 11 1010 11 HOH HOH . 
G 4 HOH A 12 1011 13 HOH HOH . 
G 4 HOH A 13 1012 15 HOH HOH . 
G 4 HOH A 14 1013 16 HOH HOH . 
G 4 HOH A 15 1014 18 HOH HOH . 
G 4 HOH A 16 1015 19 HOH HOH . 
G 4 HOH A 17 1016 20 HOH HOH . 
G 4 HOH A 18 1017 21 HOH HOH . 
G 4 HOH A 19 1018 22 HOH HOH . 
G 4 HOH A 20 1019 23 HOH HOH . 
G 4 HOH A 21 1020 24 HOH HOH . 
G 4 HOH A 22 1021 37 HOH HOH . 
G 4 HOH A 23 1022 53 HOH HOH . 
G 4 HOH A 24 1023 56 HOH HOH . 
G 4 HOH A 25 1024 57 HOH HOH . 
G 4 HOH A 26 1025 58 HOH HOH . 
G 4 HOH A 27 1026 60 HOH HOH . 
G 4 HOH A 28 1027 63 HOH HOH . 
G 4 HOH A 29 1028 64 HOH HOH . 
G 4 HOH A 30 1029 65 HOH HOH . 
G 4 HOH A 31 1030 70 HOH HOH . 
G 4 HOH A 32 1031 71 HOH HOH . 
G 4 HOH A 33 1032 74 HOH HOH . 
G 4 HOH A 34 1033 75 HOH HOH . 
G 4 HOH A 35 1034 78 HOH HOH . 
G 4 HOH A 36 1035 80 HOH HOH . 
G 4 HOH A 37 1036 81 HOH HOH . 
G 4 HOH A 38 1037 83 HOH HOH . 
G 4 HOH A 39 1038 84 HOH HOH . 
G 4 HOH A 40 1039 85 HOH HOH . 
G 4 HOH A 41 1040 86 HOH HOH . 
G 4 HOH A 42 1041 87 HOH HOH . 
G 4 HOH A 43 1042 88 HOH HOH . 
G 4 HOH A 44 1043 90 HOH HOH . 
G 4 HOH A 45 1044 91 HOH HOH . 
G 4 HOH A 46 1045 92 HOH HOH . 
G 4 HOH A 47 1046 93 HOH HOH . 
G 4 HOH A 48 1047 94 HOH HOH . 
G 4 HOH A 49 1048 96 HOH HOH . 
G 4 HOH A 50 1049 97 HOH HOH . 
G 4 HOH A 51 1050 98 HOH HOH . 
G 4 HOH A 52 1051 99 HOH HOH . 
G 4 HOH A 53 1052 101 HOH HOH . 
G 4 HOH A 54 1053 102 HOH HOH . 
G 4 HOH A 55 1054 103 HOH HOH . 
G 4 HOH A 56 1055 104 HOH HOH . 
G 4 HOH A 57 1056 106 HOH HOH . 
G 4 HOH A 58 1057 107 HOH HOH . 
G 4 HOH A 59 1058 108 HOH HOH . 
G 4 HOH A 60 1059 109 HOH HOH . 
G 4 HOH A 61 1060 110 HOH HOH . 
G 4 HOH A 62 1061 111 HOH HOH . 
G 4 HOH A 63 1062 116 HOH HOH . 
G 4 HOH A 64 1063 118 HOH HOH . 
G 4 HOH A 65 1064 119 HOH HOH . 
G 4 HOH A 66 1065 120 HOH HOH . 
G 4 HOH A 67 1066 122 HOH HOH . 
H 4 HOH B 1 999 12 HOH HOH . 
H 4 HOH B 2 1000 14 HOH HOH . 
H 4 HOH B 3 1001 17 HOH HOH . 
H 4 HOH B 4 1002 25 HOH HOH . 
H 4 HOH B 5 1003 26 HOH HOH . 
H 4 HOH B 6 1004 27 HOH HOH . 
H 4 HOH B 7 1005 28 HOH HOH . 
H 4 HOH B 8 1006 29 HOH HOH . 
H 4 HOH B 9 1007 30 HOH HOH . 
H 4 HOH B 10 1008 31 HOH HOH . 
H 4 HOH B 11 1009 32 HOH HOH . 
H 4 HOH B 12 1010 33 HOH HOH . 
H 4 HOH B 13 1011 34 HOH HOH . 
H 4 HOH B 14 1012 35 HOH HOH . 
H 4 HOH B 15 1013 36 HOH HOH . 
H 4 HOH B 16 1014 38 HOH HOH . 
H 4 HOH B 17 1015 39 HOH HOH . 
H 4 HOH B 18 1016 40 HOH HOH . 
H 4 HOH B 19 1017 41 HOH HOH . 
H 4 HOH B 20 1018 42 HOH HOH . 
H 4 HOH B 21 1019 43 HOH HOH . 
H 4 HOH B 22 1020 44 HOH HOH . 
H 4 HOH B 23 1021 45 HOH HOH . 
H 4 HOH B 24 1022 46 HOH HOH . 
H 4 HOH B 25 1023 47 HOH HOH . 
H 4 HOH B 26 1024 48 HOH HOH . 
H 4 HOH B 27 1025 49 HOH HOH . 
H 4 HOH B 28 1026 50 HOH HOH . 
H 4 HOH B 29 1027 51 HOH HOH . 
H 4 HOH B 30 1028 52 HOH HOH . 
H 4 HOH B 31 1029 54 HOH HOH . 
H 4 HOH B 32 1030 55 HOH HOH . 
H 4 HOH B 33 1031 59 HOH HOH . 
H 4 HOH B 34 1032 61 HOH HOH . 
H 4 HOH B 35 1033 62 HOH HOH . 
H 4 HOH B 36 1034 66 HOH HOH . 
H 4 HOH B 37 1035 67 HOH HOH . 
H 4 HOH B 38 1036 68 HOH HOH . 
H 4 HOH B 39 1037 69 HOH HOH . 
H 4 HOH B 40 1038 72 HOH HOH . 
H 4 HOH B 41 1039 73 HOH HOH . 
H 4 HOH B 42 1040 76 HOH HOH . 
H 4 HOH B 43 1041 77 HOH HOH . 
H 4 HOH B 44 1042 79 HOH HOH . 
H 4 HOH B 45 1043 82 HOH HOH . 
H 4 HOH B 46 1044 89 HOH HOH . 
H 4 HOH B 47 1045 95 HOH HOH . 
H 4 HOH B 48 1046 100 HOH HOH . 
H 4 HOH B 49 1047 105 HOH HOH . 
H 4 HOH B 50 1048 112 HOH HOH . 
H 4 HOH B 51 1049 113 HOH HOH . 
H 4 HOH B 52 1050 114 HOH HOH . 
H 4 HOH B 53 1051 115 HOH HOH . 
H 4 HOH B 54 1052 117 HOH HOH . 
H 4 HOH B 55 1053 121 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 PB ATR . . . E 2 9.209 7.097 2.633 1 30.79 ? PB ATR 125 B 1 
HETATM 2 O O1B ATR . . . E 2 8.783 7.302 4.022 1 33.13 ? O1B ATR 125 B 1 
HETATM 3 O O2B ATR . . . E 2 10.027 5.875 2.468 1 28.9 ? O2B ATR 125 B 1 
HETATM 4 O O3B ATR . . . E 2 8.084 7.266 1.68 1 33.06 ? O3B ATR 125 B 1 
HETATM 5 P PA ATR . . . E 2 10.591 9.841 2.298 1 45.75 ? PA ATR 125 B 1 
HETATM 6 O O1A ATR . . . E 2 12.076 10.063 2.321 1 45.11 ? O1A ATR 125 B 1 
HETATM 7 O O2A ATR . . . E 2 9.764 10.523 3.361 1 44.25 ? O2A ATR 125 B 1 
HETATM 8 O O3A ATR . . . E 2 10.265 8.188 2.075 1 35.92 ? O3A ATR 125 B 1 
HETATM 9 O O5' ATR . . . E 2 10.047 10.373 0.789 1 44.15 ? O5' ATR 125 B 1 
HETATM 10 C C5' ATR . . . E 2 10.741 9.732 -0.232 1 41.31 ? C5' ATR 125 B 1 
HETATM 11 C C4' ATR . . . E 2 11.808 10.475 -0.781 1 41.03 ? C4' ATR 125 B 1 
HETATM 12 O O4' ATR . . . E 2 12.092 9.601 -1.852 1 42.34 ? O4' ATR 125 B 1 
HETATM 13 C C3' ATR . . . E 2 11.437 11.823 -1.499 1 44.23 ? C3' ATR 125 B 1 
HETATM 14 O O3' ATR . . . E 2 11.368 13.033 -0.65 1 43.8 ? O3' ATR 125 B 1 
HETATM 15 C C2' ATR . . . E 2 12.582 11.954 -2.56 1 44.78 ? C2' ATR 125 B 1 
HETATM 16 O O2' ATR . . . E 2 13.981 12.121 -2.135 1 49.43 ? O2' ATR 125 B 1 
HETATM 17 P P2' ATR . . . E 2 15.194 12.393 -3.346 1 54.17 ? P2' ATR 125 B 1 
HETATM 18 O O1P ATR . . . E 2 15.792 11.054 -3.772 1 51.24 ? O1P ATR 125 B 1 
HETATM 19 O O2P ATR . . . E 2 14.4 13.137 -4.438 1 52.71 ? O2P ATR 125 B 1 
HETATM 20 O O3P ATR . . . E 2 16.076 13.234 -2.44 1 52.49 ? O3P ATR 125 B 1 
HETATM 21 C C1' ATR . . . E 2 12.59 10.463 -2.923 1 42.77 ? C1' ATR 125 B 1 
HETATM 22 N N9 ATR . . . E 2 11.833 10.231 -4.171 1 38.62 ? N9 ATR 125 B 1 
HETATM 23 C C8 ATR . . . E 2 12.415 10.092 -5.415 1 36.75 ? C8 ATR 125 B 1 
HETATM 24 N N7 ATR . . . E 2 11.582 9.664 -6.303 1 35.85 ? N7 ATR 125 B 1 
HETATM 25 C C5 ATR . . . E 2 10.351 9.51 -5.612 1 37.03 ? C5 ATR 125 B 1 
HETATM 26 C C6 ATR . . . E 2 9.068 9.036 -6.005 1 36.12 ? C6 ATR 125 B 1 
HETATM 27 N N6 ATR . . . E 2 8.86 8.633 -7.262 1 36.57 ? N6 ATR 125 B 1 
HETATM 28 N N1 ATR . . . E 2 8.077 9 -5.051 1 35.12 ? N1 ATR 125 B 1 
HETATM 29 C C2 ATR . . . E 2 8.334 9.413 -3.808 1 34.69 ? C2 ATR 125 B 1 
HETATM 30 N N3 ATR . . . E 2 9.474 9.87 -3.314 1 35.53 ? N3 ATR 125 B 1 
HETATM 31 C C4 ATR . . . E 2 10.473 9.883 -4.286 1 37.91 ? C4 ATR 125 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#