data_4PJ1
#
_model_server_result.job_id            vjnx2his42QTkdKpjpECsg 
_model_server_result.datetime_utc      '2024-11-21 13:14:02' 
_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          4pj1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"QA","auth_seq_id":601}' 
#
_entry.id    4PJ1 
#
_exptl.entry_id    4PJ1 
_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    14 
_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            4PJ1 
_cell.length_a            199.1 
_cell.length_b            199.1 
_cell.length_c            627.39 
_cell.Z_PDB               112 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PJ1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41 21 2' 
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_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    28-meric 
_pdbx_struct_assembly.oligomeric_count      28 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 CA N N 
? 3 EA N N 
? 3 GA N N 
? 3 IA N N 
? 3 KA N N 
? 3 MA N N 
? 3 OA N N 
? 3 QA N N 
? 3 SA N N 
? 3 UA N N 
? 3 WA N N 
? 3 YA N N 
? 3 AB N N 
? 3 CB N N 
#
_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                     4PJ1 
_atom_sites.fract_transf_matrix[1][1]    0.005023 
_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]    0.005023 
_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]    0.001594 
_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
CA 3 ADP A 1 601 1 ADP ADP . 
DA 4 MG A 1 602 1 MG MG . 
EA 3 ADP B 1 601 2 ADP ADP . 
FA 4 MG B 1 602 2 MG MG . 
GA 3 ADP C 1 601 3 ADP ADP . 
HA 4 MG C 1 602 3 MG MG . 
IA 3 ADP D 1 601 4 ADP ADP . 
JA 4 MG D 1 602 4 MG MG . 
KA 3 ADP E 1 601 5 ADP ADP . 
LA 4 MG E 1 602 5 MG MG . 
MA 3 ADP F 1 601 6 ADP ADP . 
NA 4 MG F 1 602 6 MG MG . 
OA 3 ADP G 1 601 7 ADP ADP . 
PA 4 MG G 1 602 7 MG MG . 
QA 3 ADP H 1 601 14 ADP ADP . 
RA 4 MG H 1 602 14 MG MG . 
SA 3 ADP I 1 601 8 ADP ADP . 
TA 4 MG I 1 602 8 MG MG . 
UA 3 ADP J 1 601 9 ADP ADP . 
VA 4 MG J 1 602 9 MG MG . 
WA 3 ADP K 1 601 10 ADP ADP . 
XA 4 MG K 1 602 10 MG MG . 
YA 3 ADP L 1 601 11 ADP ADP . 
ZA 4 MG L 1 602 11 MG MG . 
AB 3 ADP M 1 601 12 ADP ADP . 
BB 4 MG M 1 602 12 MG MG . 
CB 3 ADP N 1 601 13 ADP ADP . 
DB 4 MG N 1 602 13 MG MG . 
#
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 . . . QA 3 95.042 -42.032 20.753 1 86.63 ? PB ADP 601 H 1 
HETATM 2 O O1B ADP . . . QA 3 93.757 -41.446 21.29 1 77.19 ? O1B ADP 601 H 1 
HETATM 3 O O2B ADP . . . QA 3 96.248 -41.807 21.633 1 80.82 ? O2B ADP 601 H 1 
HETATM 4 O O3B ADP . . . QA 3 94.925 -43.445 20.235 1 75.59 ? O3B ADP 601 H 1 
HETATM 5 P PA ADP . . . QA 3 95.763 -39.633 19.441 1 81.84 ? PA ADP 601 H 1 
HETATM 6 O O1A ADP . . . QA 3 94.842 -38.85 18.536 1 88.57 ? O1A ADP 601 H 1 
HETATM 7 O O2A ADP . . . QA 3 95.99 -39.212 20.873 1 89.88 ? O2A ADP 601 H 1 
HETATM 8 O O3A ADP . . . QA 3 95.342 -41.188 19.414 1 79.61 ? O3A ADP 601 H 1 
HETATM 9 O O5' ADP . . . QA 3 97.201 -39.768 18.741 1 80.75 ? O5' ADP 601 H 1 
HETATM 10 C C5' ADP . . . QA 3 98.301 -40.206 19.532 1 87.66 ? C5' ADP 601 H 1 
HETATM 11 C C4' ADP . . . QA 3 99.477 -40.538 18.629 1 91.18 ? C4' ADP 601 H 1 
HETATM 12 O O4' ADP . . . QA 3 99.847 -39.376 17.887 1 93.55 ? O4' ADP 601 H 1 
HETATM 13 C C3' ADP . . . QA 3 100.689 -40.965 19.442 1 88.37 ? C3' ADP 601 H 1 
HETATM 14 O O3' ADP . . . QA 3 101.146 -42.237 18.975 1 76.57 ? O3' ADP 601 H 1 
HETATM 15 C C2' ADP . . . QA 3 101.747 -39.914 19.175 1 87.27 ? C2' ADP 601 H 1 
HETATM 16 O O2' ADP . . . QA 3 103.028 -40.517 18.976 1 92.85 ? O2' ADP 601 H 1 
HETATM 17 C C1' ADP . . . QA 3 101.267 -39.235 17.905 1 91.18 ? C1' ADP 601 H 1 
HETATM 18 N N9 ADP . . . QA 3 101.663 -37.808 17.86 1 95.85 ? N9 ADP 601 H 1 
HETATM 19 C C8 ADP . . . QA 3 101.131 -36.796 18.571 1 97.9 ? C8 ADP 601 H 1 
HETATM 20 N N7 ADP . . . QA 3 101.743 -35.621 18.269 1 98.52 ? N7 ADP 601 H 1 
HETATM 21 C C5 ADP . . . QA 3 102.688 -35.881 17.345 1 89.88 ? C5 ADP 601 H 1 
HETATM 22 C C6 ADP . . . QA 3 103.698 -35.102 16.591 1 86.38 ? C6 ADP 601 H 1 
HETATM 23 N N6 ADP . . . QA 3 103.826 -33.765 16.768 1 84.98 ? N6 ADP 601 H 1 
HETATM 24 N N1 ADP . . . QA 3 104.487 -35.77 15.719 1 86.27 ? N1 ADP 601 H 1 
HETATM 25 C C2 ADP . . . QA 3 104.373 -37.098 15.53 1 83.39 ? C2 ADP 601 H 1 
HETATM 26 N N3 ADP . . . QA 3 103.481 -37.866 16.179 1 87.32 ? N3 ADP 601 H 1 
HETATM 27 C C4 ADP . . . QA 3 102.629 -37.325 17.081 1 95.17 ? C4 ADP 601 H 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    152 
_model_server_stats.query_time_ms           234 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#