data_6DUQ
#
_model_server_result.job_id            1hyG7LmdLnfUXsMURpug_g 
_model_server_result.datetime_utc      '2024-11-12 21:27:31' 
_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          6duq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"JA","auth_seq_id":1000}' 
#
_entry.id    6DUQ 
#
_exptl.entry_id    6DUQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         89.94 
_cell.angle_beta          89.9 
_cell.angle_gamma         60.01 
_cell.entry_id            6DUQ 
_cell.length_a            126.35 
_cell.length_b            126.32 
_cell.length_c            166.82 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DUQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 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
? tridecameric 13 author_defined_assembly 1 
? tridecameric 13 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,E,G,I,K,P,Q,R,V,W,X,Z,AA,BA,CA,GA,HA,IA,MA,NA,OA,SA,TA,UA,YA,ZA,AB,EB,FB,GB 1 1 
B,D,F,H,J,L,M,N,O,S,T,U,Y,DA,EA,FA,JA,KA,LA,PA,QA,RA,VA,WA,XA,BB,CB,DB,HB,IB,JB 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
? 4 AA N N 
? 4 DA N N 
? 4 GA N N 
? 4 JA N N 
? 4 MA N N 
? 4 PA N N 
? 4 SA N N 
? 4 VA N N 
? 4 YA N N 
? 4 BB N N 
? 4 EB N N 
? 4 HB 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
metalc ? metalc1 A OG1 THR 188 L THR 185 1_555 BA MG MG . L MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc2 AA O1B ADP . L ADP 1000 1_555 BA MG MG . L MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc3 AA O2B ADP . L ADP 1000 1_555 CA BE BEF . L BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.737 ? 
metalc ? metalc4 B OG1 THR 188 A THR 185 1_555 EA MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc5 DA O1B ADP . A ADP 1000 1_555 EA MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc6 DA O2B ADP . A ADP 1000 1_555 FA BE BEF . A BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? 
metalc ? metalc7 C OG1 THR 188 G THR 185 1_555 HA MG MG . G MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
metalc ? metalc8 GA O1B ADP . G ADP 1000 1_555 HA MG MG . G MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc9 GA O2B ADP . G ADP 1000 1_555 IA BE BEF . G BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? 
metalc ? metalc10 D OG1 THR 188 B THR 185 1_555 KA MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
metalc ? metalc11 JA O1B ADP . B ADP 1000 1_555 KA MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc12 JA O2B ADP . B ADP 1000 1_555 LA BE BEF . B BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.715 ? 
metalc ? metalc13 E OG1 THR 188 H THR 185 1_555 NA MG MG . H MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc14 MA O1B ADP . H ADP 1000 1_555 NA MG MG . H MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? 
metalc ? metalc15 MA O2B ADP . H ADP 1000 1_555 OA BE BEF . H BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? 
metalc ? metalc16 F OG1 THR 188 C THR 185 1_555 QA MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc17 PA O1B ADP . C ADP 1000 1_555 QA MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc18 PA O2B ADP . C ADP 1000 1_555 RA BE BEF . C BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.749 ? 
metalc ? metalc19 G OG1 THR 188 I THR 185 1_555 TA MG MG . I MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc20 SA O1B ADP . I ADP 1000 1_555 TA MG MG . I MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc21 SA O2B ADP . I ADP 1000 1_555 UA BE BEF . I BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.762 ? 
metalc ? metalc22 H OG1 THR 188 D THR 185 1_555 WA MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc23 VA O1B ADP . D ADP 1000 1_555 WA MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc24 VA O2B ADP . D ADP 1000 1_555 XA BE BEF . D BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.734 ? 
metalc ? metalc25 I OG1 THR 188 K THR 185 1_555 ZA MG MG . K MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
metalc ? metalc26 YA O1B ADP . K ADP 1000 1_555 ZA MG MG . K MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc27 YA O2B ADP . K ADP 1000 1_555 AB BE BEF . K BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.749 ? 
metalc ? metalc28 J OG1 THR 188 F THR 185 1_555 CB MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc29 BB O1B ADP . F ADP 1000 1_555 CB MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc30 BB O2B ADP . F ADP 1000 1_555 DB BE BEF . F BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? 
metalc ? metalc31 K OG1 THR 188 J THR 185 1_555 FB MG MG . J MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc32 EB O1B ADP . J ADP 1000 1_555 FB MG MG . J MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc33 EB O2B ADP . J ADP 1000 1_555 GB BE BEF . J BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.741 ? 
metalc ? metalc34 L OG1 THR 188 E THR 185 1_555 IB MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
metalc ? metalc35 HB O1B ADP . E ADP 1000 1_555 IB MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? 
metalc ? metalc36 HB O2B ADP . E ADP 1000 1_555 JB BE BEF . E BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? 
#
_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                     6DUQ 
_atom_sites.fract_transf_matrix[1][1]    0.007915 
_atom_sites.fract_transf_matrix[1][2]    -0.004567 
_atom_sites.fract_transf_matrix[1][3]    -0.000013 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00914 
_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]    0.005994 
_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
AA 4 ADP L 1 1000 1000 ADP ADP . 
BA 5 MG L 1 1001 1001 MG MG . 
CA 6 BEF L 1 1002 1002 BEF BEF . 
DA 4 ADP A 1 1000 1000 ADP ADP . 
EA 5 MG A 1 1001 1001 MG MG . 
FA 6 BEF A 1 1002 1002 BEF BEF . 
GA 4 ADP G 1 1000 1000 ADP ADP . 
HA 5 MG G 1 1001 1001 MG MG . 
IA 6 BEF G 1 1002 1002 BEF BEF . 
JA 4 ADP B 1 1000 1000 ADP ADP . 
KA 5 MG B 1 1001 1001 MG MG . 
LA 6 BEF B 1 1002 1002 BEF BEF . 
MA 4 ADP H 1 1000 1000 ADP ADP . 
NA 5 MG H 1 1001 1001 MG MG . 
OA 6 BEF H 1 1002 1002 BEF BEF . 
PA 4 ADP C 1 1000 1000 ADP ADP . 
QA 5 MG C 1 1001 1001 MG MG . 
RA 6 BEF C 1 1002 1002 BEF BEF . 
SA 4 ADP I 1 1000 1000 ADP ADP . 
TA 5 MG I 1 1001 1001 MG MG . 
UA 6 BEF I 1 1002 1002 BEF BEF . 
VA 4 ADP D 1 1000 1000 ADP ADP . 
WA 5 MG D 1 1001 1001 MG MG . 
XA 6 BEF D 1 1002 1002 BEF BEF . 
YA 4 ADP K 1 1000 1000 ADP ADP . 
ZA 5 MG K 1 1001 1001 MG MG . 
AB 6 BEF K 1 1002 1002 BEF BEF . 
BB 4 ADP F 1 1000 1000 ADP ADP . 
CB 5 MG F 1 1001 1001 MG MG . 
DB 6 BEF F 1 1002 1002 BEF BEF . 
EB 4 ADP J 1 1000 1000 ADP ADP . 
FB 5 MG J 1 1001 1001 MG MG . 
GB 6 BEF J 1 1002 1002 BEF BEF . 
HB 4 ADP E 1 1000 1000 ADP ADP . 
IB 5 MG E 1 1001 1001 MG MG . 
JB 6 BEF E 1 1002 1002 BEF BEF . 
#
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 . . . JA 4 -88.035 23.798 70.217 1 133.54 ? PB ADP 1000 B 1 
HETATM 2 O O1B ADP . . . JA 4 -88.349 25.035 69.421 1 143.69 ? O1B ADP 1000 B 1 
HETATM 3 O O2B ADP . . . JA 4 -88.534 22.519 69.588 1 133.54 ? O2B ADP 1000 B 1 
HETATM 4 O O3B ADP . . . JA 4 -86.633 23.76 70.767 1 133.54 ? O3B ADP 1000 B 1 
HETATM 5 P PA ADP . . . JA 4 -90.313 24.771 71.53 1 153.08 ? PA ADP 1000 B 1 
HETATM 6 O O1A ADP . . . JA 4 -91.116 24.228 70.372 1 133.54 ? O1A ADP 1000 B 1 
HETATM 7 O O2A ADP . . . JA 4 -90.016 26.243 71.69 1 133.54 ? O2A ADP 1000 B 1 
HETATM 8 O O3A ADP . . . JA 4 -88.914 23.981 71.548 1 142.96 ? O3A ADP 1000 B 1 
HETATM 9 O O5' ADP . . . JA 4 -91.008 24.25 72.887 1 177.89 ? O5' ADP 1000 B 1 
HETATM 10 C C5' ADP . . . JA 4 -91.73 23.02 72.885 1 145.57 ? C5' ADP 1000 B 1 
HETATM 11 C C4' ADP . . . JA 4 -92.65 22.975 74.092 1 133.54 ? C4' ADP 1000 B 1 
HETATM 12 O O4' ADP . . . JA 4 -91.967 23.381 75.276 1 135.09 ? O4' ADP 1000 B 1 
HETATM 13 C C3' ADP . . . JA 4 -93.782 23.966 73.935 1 135.46 ? C3' ADP 1000 B 1 
HETATM 14 O O3' ADP . . . JA 4 -94.902 23.332 73.32 1 161.72 ? O3' ADP 1000 B 1 
HETATM 15 C C2' ADP . . . JA 4 -94.106 24.405 75.345 1 133.54 ? C2' ADP 1000 B 1 
HETATM 16 O O2' ADP . . . JA 4 -95.171 23.611 75.876 1 154.42 ? O2' ADP 1000 B 1 
HETATM 17 C C1' ADP . . . JA 4 -92.844 24.119 76.127 1 133.54 ? C1' ADP 1000 B 1 
HETATM 18 N N9 ADP . . . JA 4 -92.242 25.428 76.414 1 133.54 ? N9 ADP 1000 B 1 
HETATM 19 C C8 ADP . . . JA 4 -91.196 25.973 75.777 1 133.54 ? C8 ADP 1000 B 1 
HETATM 20 N N7 ADP . . . JA 4 -90.909 27.192 76.293 1 133.54 ? N7 ADP 1000 B 1 
HETATM 21 C C5 ADP . . . JA 4 -91.792 27.441 77.279 1 133.54 ? C5 ADP 1000 B 1 
HETATM 22 C C6 ADP . . . JA 4 -92.061 28.544 78.235 1 133.54 ? C6 ADP 1000 B 1 
HETATM 23 N N6 ADP . . . JA 4 -91.308 29.67 78.254 1 133.54 ? N6 ADP 1000 B 1 
HETATM 24 N N1 ADP . . . JA 4 -93.09 28.386 79.096 1 134.47 ? N1 ADP 1000 B 1 
HETATM 25 C C2 ADP . . . JA 4 -93.852 27.277 79.098 1 134.27 ? C2 ADP 1000 B 1 
HETATM 26 N N3 ADP . . . JA 4 -93.666 26.243 78.26 1 133.54 ? N3 ADP 1000 B 1 
HETATM 27 C C4 ADP . . . JA 4 -92.67 26.268 77.348 1 133.54 ? C4 ADP 1000 B 1 
#
_model_server_stats.io_time_ms              81 
_model_server_stats.parse_time_ms           30 
_model_server_stats.create_model_time_ms    45 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#