data_3DGE
#
_model_server_result.job_id            9SIpDHmrq6OEqNEcDMeA3Q 
_model_server_result.datetime_utc      '2024-11-26 01:30:44' 
_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          3dge 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":500}' 
#
_entry.id    3DGE 
#
_exptl.entry_id    3DGE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-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          108.42 
_cell.angle_gamma         90 
_cell.entry_id            3DGE 
_cell.length_a            183.958 
_cell.length_b            90.668 
_cell.length_c            68.985 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DGE 
_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
PISA tetrameric 4 author_and_software_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
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,F,G,H,J,K,L,M 1 1 
C,D,G,H,L,M 2 1 
A,B,E,F,J,K 3 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
? 3 E N N 
? 3 G 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 99 A CYS 330 1_555 A SG CYS 128 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf2 C SG CYS 99 B CYS 330 1_555 C SG CYS 128 B CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-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 ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     3DGE 
_atom_sites.fract_transf_matrix[1][1]    0.005436 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00181 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011029 
_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]    0.015279 
_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
E 3 ADP A 1 500 500 ADP ADP . 
F 4 SO4 C 1 150 150 SO4 SO4 . 
G 3 ADP B 1 600 600 ADP ADP . 
H 4 SO4 D 1 160 160 SO4 SO4 . 
I 5 CIT N 1 3 3 CIT CIT . 
J 6 HOH A 1 1 1 HOH HOH . 
J 6 HOH A 2 11 11 HOH HOH . 
J 6 HOH A 3 14 14 HOH HOH . 
J 6 HOH A 4 17 17 HOH HOH . 
J 6 HOH A 5 18 18 HOH HOH . 
J 6 HOH A 6 21 21 HOH HOH . 
J 6 HOH A 7 22 22 HOH HOH . 
J 6 HOH A 8 23 23 HOH HOH . 
J 6 HOH A 9 32 32 HOH HOH . 
J 6 HOH A 10 38 38 HOH HOH . 
J 6 HOH A 11 42 42 HOH HOH . 
J 6 HOH A 12 47 47 HOH HOH . 
J 6 HOH A 13 52 52 HOH HOH . 
J 6 HOH A 14 54 54 HOH HOH . 
J 6 HOH A 15 59 59 HOH HOH . 
J 6 HOH A 16 60 60 HOH HOH . 
J 6 HOH A 17 69 69 HOH HOH . 
J 6 HOH A 18 78 78 HOH HOH . 
J 6 HOH A 19 108 108 HOH HOH . 
J 6 HOH A 20 109 109 HOH HOH . 
J 6 HOH A 21 110 110 HOH HOH . 
J 6 HOH A 22 111 111 HOH HOH . 
J 6 HOH A 23 115 115 HOH HOH . 
J 6 HOH A 24 116 116 HOH HOH . 
J 6 HOH A 25 125 125 HOH HOH . 
J 6 HOH A 26 126 126 HOH HOH . 
J 6 HOH A 27 127 127 HOH HOH . 
J 6 HOH A 28 128 128 HOH HOH . 
J 6 HOH A 29 136 136 HOH HOH . 
J 6 HOH A 30 137 137 HOH HOH . 
J 6 HOH A 31 141 141 HOH HOH . 
J 6 HOH A 32 142 142 HOH HOH . 
J 6 HOH A 33 149 149 HOH HOH . 
J 6 HOH A 34 151 151 HOH HOH . 
J 6 HOH A 35 152 152 HOH HOH . 
J 6 HOH A 36 154 154 HOH HOH . 
J 6 HOH A 37 160 160 HOH HOH . 
K 6 HOH C 1 151 4 HOH HOH . 
K 6 HOH C 2 152 6 HOH HOH . 
K 6 HOH C 3 153 13 HOH HOH . 
K 6 HOH C 4 154 25 HOH HOH . 
K 6 HOH C 5 155 31 HOH HOH . 
K 6 HOH C 6 156 33 HOH HOH . 
K 6 HOH C 7 157 36 HOH HOH . 
K 6 HOH C 8 158 39 HOH HOH . 
K 6 HOH C 9 159 41 HOH HOH . 
K 6 HOH C 10 160 48 HOH HOH . 
K 6 HOH C 11 161 49 HOH HOH . 
K 6 HOH C 12 162 50 HOH HOH . 
K 6 HOH C 13 163 61 HOH HOH . 
K 6 HOH C 14 164 62 HOH HOH . 
K 6 HOH C 15 165 68 HOH HOH . 
K 6 HOH C 16 166 77 HOH HOH . 
K 6 HOH C 17 167 93 HOH HOH . 
K 6 HOH C 18 168 99 HOH HOH . 
K 6 HOH C 19 169 100 HOH HOH . 
K 6 HOH C 20 170 101 HOH HOH . 
K 6 HOH C 21 171 106 HOH HOH . 
K 6 HOH C 22 172 112 HOH HOH . 
K 6 HOH C 23 173 114 HOH HOH . 
K 6 HOH C 24 174 134 HOH HOH . 
K 6 HOH C 25 175 140 HOH HOH . 
K 6 HOH C 26 176 148 HOH HOH . 
K 6 HOH C 27 177 161 HOH HOH . 
L 6 HOH B 1 2 2 HOH HOH . 
L 6 HOH B 2 5 5 HOH HOH . 
L 6 HOH B 3 8 8 HOH HOH . 
L 6 HOH B 4 9 9 HOH HOH . 
L 6 HOH B 5 10 10 HOH HOH . 
L 6 HOH B 6 12 12 HOH HOH . 
L 6 HOH B 7 19 19 HOH HOH . 
L 6 HOH B 8 20 20 HOH HOH . 
L 6 HOH B 9 24 24 HOH HOH . 
L 6 HOH B 10 27 27 HOH HOH . 
L 6 HOH B 11 28 28 HOH HOH . 
L 6 HOH B 12 29 29 HOH HOH . 
L 6 HOH B 13 30 30 HOH HOH . 
L 6 HOH B 14 34 34 HOH HOH . 
L 6 HOH B 15 35 35 HOH HOH . 
L 6 HOH B 16 40 40 HOH HOH . 
L 6 HOH B 17 43 43 HOH HOH . 
L 6 HOH B 18 45 45 HOH HOH . 
L 6 HOH B 19 46 46 HOH HOH . 
L 6 HOH B 20 51 51 HOH HOH . 
L 6 HOH B 21 53 53 HOH HOH . 
L 6 HOH B 22 57 57 HOH HOH . 
L 6 HOH B 23 70 70 HOH HOH . 
L 6 HOH B 24 72 72 HOH HOH . 
L 6 HOH B 25 73 73 HOH HOH . 
L 6 HOH B 26 74 74 HOH HOH . 
L 6 HOH B 27 76 76 HOH HOH . 
L 6 HOH B 28 81 81 HOH HOH . 
L 6 HOH B 29 82 82 HOH HOH . 
L 6 HOH B 30 83 83 HOH HOH . 
L 6 HOH B 31 84 84 HOH HOH . 
L 6 HOH B 32 85 85 HOH HOH . 
L 6 HOH B 33 86 86 HOH HOH . 
L 6 HOH B 34 87 87 HOH HOH . 
L 6 HOH B 35 88 88 HOH HOH . 
L 6 HOH B 36 94 94 HOH HOH . 
L 6 HOH B 37 95 95 HOH HOH . 
L 6 HOH B 38 96 96 HOH HOH . 
L 6 HOH B 39 97 97 HOH HOH . 
L 6 HOH B 40 98 98 HOH HOH . 
L 6 HOH B 41 113 113 HOH HOH . 
L 6 HOH B 42 117 117 HOH HOH . 
L 6 HOH B 43 119 119 HOH HOH . 
L 6 HOH B 44 121 121 HOH HOH . 
L 6 HOH B 45 122 122 HOH HOH . 
L 6 HOH B 46 123 123 HOH HOH . 
L 6 HOH B 47 124 124 HOH HOH . 
L 6 HOH B 48 133 133 HOH HOH . 
L 6 HOH B 49 138 138 HOH HOH . 
L 6 HOH B 50 143 143 HOH HOH . 
L 6 HOH B 51 144 144 HOH HOH . 
L 6 HOH B 52 145 145 HOH HOH . 
L 6 HOH B 53 146 146 HOH HOH . 
L 6 HOH B 54 147 147 HOH HOH . 
L 6 HOH B 55 153 153 HOH HOH . 
L 6 HOH B 56 155 155 HOH HOH . 
L 6 HOH B 57 156 156 HOH HOH . 
L 6 HOH B 58 157 157 HOH HOH . 
L 6 HOH B 59 158 158 HOH HOH . 
L 6 HOH B 60 159 159 HOH HOH . 
M 6 HOH D 1 161 3 HOH HOH . 
M 6 HOH D 2 162 7 HOH HOH . 
M 6 HOH D 3 163 16 HOH HOH . 
M 6 HOH D 4 164 26 HOH HOH . 
M 6 HOH D 5 165 37 HOH HOH . 
M 6 HOH D 6 166 44 HOH HOH . 
M 6 HOH D 7 167 55 HOH HOH . 
M 6 HOH D 8 168 56 HOH HOH . 
M 6 HOH D 9 169 58 HOH HOH . 
M 6 HOH D 10 170 63 HOH HOH . 
M 6 HOH D 11 171 64 HOH HOH . 
M 6 HOH D 12 172 65 HOH HOH . 
M 6 HOH D 13 173 66 HOH HOH . 
M 6 HOH D 14 174 67 HOH HOH . 
M 6 HOH D 15 175 71 HOH HOH . 
M 6 HOH D 16 176 75 HOH HOH . 
M 6 HOH D 17 177 79 HOH HOH . 
M 6 HOH D 18 178 89 HOH HOH . 
M 6 HOH D 19 179 90 HOH HOH . 
M 6 HOH D 20 180 91 HOH HOH . 
M 6 HOH D 21 181 92 HOH HOH . 
M 6 HOH D 22 182 102 HOH HOH . 
M 6 HOH D 23 183 103 HOH HOH . 
M 6 HOH D 24 184 104 HOH HOH . 
M 6 HOH D 25 185 105 HOH HOH . 
M 6 HOH D 26 186 107 HOH HOH . 
M 6 HOH D 27 187 118 HOH HOH . 
M 6 HOH D 28 188 120 HOH HOH . 
M 6 HOH D 29 189 129 HOH HOH . 
M 6 HOH D 30 190 130 HOH HOH . 
M 6 HOH D 31 191 131 HOH HOH . 
M 6 HOH D 32 192 132 HOH HOH . 
M 6 HOH D 33 193 135 HOH HOH . 
M 6 HOH D 34 194 139 HOH HOH . 
M 6 HOH D 35 195 150 HOH HOH . 
M 6 HOH D 36 196 162 HOH HOH . 
N 6 HOH N 1 15 15 HOH HOH . 
N 6 HOH N 2 80 80 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 ADP . . . E 3 41.355 56.029 29.607 1 72.38 ? PB ADP 500 A 1 
HETATM 2 O O1B ADP . . . E 3 41.57 55.828 28.123 1 73.81 ? O1B ADP 500 A 1 
HETATM 3 O O2B ADP . . . E 3 40.722 57.37 29.91 1 65.21 ? O2B ADP 500 A 1 
HETATM 4 O O3B ADP . . . E 3 42.539 55.625 30.485 1 71.52 ? O3B ADP 500 A 1 
HETATM 5 P PA ADP . . . E 3 39.421 53.826 29.239 1 70.38 ? PA ADP 500 A 1 
HETATM 6 O O1A ADP . . . E 3 39.922 52.451 29.622 1 71.01 ? O1A ADP 500 A 1 
HETATM 7 O O2A ADP . . . E 3 39.236 54.076 27.764 1 69.27 ? O2A ADP 500 A 1 
HETATM 8 O O3A ADP . . . E 3 40.331 54.876 30.076 1 71.4 ? O3A ADP 500 A 1 
HETATM 9 O O5' ADP . . . E 3 37.991 54.235 29.913 1 71.2 ? O5' ADP 500 A 1 
HETATM 10 C C5' ADP . . . E 3 37.636 55.635 29.983 1 68.87 ? C5' ADP 500 A 1 
HETATM 11 C C4' ADP . . . E 3 36.826 56.034 31.217 1 67.26 ? C4' ADP 500 A 1 
HETATM 12 O O4' ADP . . . E 3 36.454 54.855 31.928 1 65.91 ? O4' ADP 500 A 1 
HETATM 13 C C3' ADP . . . E 3 37.601 56.883 32.222 1 68.03 ? C3' ADP 500 A 1 
HETATM 14 O O3' ADP . . . E 3 37.409 58.301 32.097 1 70.36 ? O3' ADP 500 A 1 
HETATM 15 C C2' ADP . . . E 3 37.188 56.378 33.607 1 67.05 ? C2' ADP 500 A 1 
HETATM 16 O O2' ADP . . . E 3 36.241 57.194 34.325 1 66.98 ? O2' ADP 500 A 1 
HETATM 17 C C1' ADP . . . E 3 36.53 55.045 33.343 1 63.33 ? C1' ADP 500 A 1 
HETATM 18 N N9 ADP . . . E 3 37.248 53.922 33.99 1 57.18 ? N9 ADP 500 A 1 
HETATM 19 C C8 ADP . . . E 3 37.893 52.923 33.356 1 56.43 ? C8 ADP 500 A 1 
HETATM 20 N N7 ADP . . . E 3 38.415 52.026 34.247 1 55.01 ? N7 ADP 500 A 1 
HETATM 21 C C5 ADP . . . E 3 38.098 52.457 35.48 1 52.11 ? C5 ADP 500 A 1 
HETATM 22 C C6 ADP . . . E 3 38.34 51.968 36.862 1 50.92 ? C6 ADP 500 A 1 
HETATM 23 N N6 ADP . . . E 3 39.042 50.815 37.087 1 48.81 ? N6 ADP 500 A 1 
HETATM 24 N N1 ADP . . . E 3 37.838 52.724 37.873 1 51.18 ? N1 ADP 500 A 1 
HETATM 25 C C2 ADP . . . E 3 37.134 53.866 37.643 1 52.24 ? C2 ADP 500 A 1 
HETATM 26 N N3 ADP . . . E 3 36.866 54.374 36.416 1 52.16 ? N3 ADP 500 A 1 
HETATM 27 C C4 ADP . . . E 3 37.324 53.713 35.309 1 53.93 ? C4 ADP 500 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#