data_4PL5
#
_model_server_result.job_id            05RqYHdbNUvSKk7vF1CD3g 
_model_server_result.datetime_utc      '2024-11-16 14:29:50' 
_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          4pl5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1001}' 
#
_entry.id    4PL5 
#
_exptl.entry_id    4PL5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          99.49 
_cell.angle_gamma         90 
_cell.entry_id            4PL5 
_cell.length_a            319.22 
_cell.length_b            63.03 
_cell.length_c            140.78 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PL5 
_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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 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,B,E,F,G,H,I,J 1 1 
C,D,K,L,M,N 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 E N N 
? 2 H N N 
? 2 K N N 
? 2 M 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
covale ? covale1 B NZ LYS 365 A LYS 907 1_555 G C01 31L . A 31L 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.243 ? 
metalc ? metalc1 A OD1 ASN 151 B ASN 693 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? 
metalc ? metalc2 A OD2 ASP 169 B ASP 711 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? 
metalc ? metalc3 E O2A ADP . B ADP 1001 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? 
metalc ? metalc4 E O3A ADP . B ADP 1001 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc5 B OD1 ASN 151 A ASN 693 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? 
metalc ? metalc6 B OD2 ASP 169 A ASP 711 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc7 H O2B ADP . A ADP 1002 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc8 H O2A ADP . A ADP 1002 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc9 C OD1 ASN 151 C ASN 693 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc10 K O3A ADP . C ADP 1001 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? 
metalc ? metalc11 D OD1 ASN 151 D ASN 693 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? 
metalc ? metalc12 M O1B ADP . D ADP 1001 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc13 M O1A ADP . D ADP 1001 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? 
metalc ? metalc14 M O3A ADP . D ADP 1001 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? 
#
_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 46 n n 
PB O2B ADP sing 47 n n 
PB O3B ADP sing 48 n n 
PB O3A ADP sing 49 n n 
O2B HOB2 ADP sing 50 n n 
O3B HOB3 ADP sing 51 n n 
PA O1A ADP doub 52 n n 
PA O2A ADP sing 53 n n 
PA O3A ADP sing 54 n n 
PA O5' ADP sing 55 n n 
O2A HOA2 ADP sing 56 n n 
O5' C5' ADP sing 57 n n 
C5' C4' ADP sing 58 n n 
C5' "H5'1" ADP sing 59 n n 
C5' "H5'2" ADP sing 60 n n 
C4' O4' ADP sing 61 n n 
C4' C3' ADP sing 62 n n 
C4' H4' ADP sing 63 n n 
O4' C1' ADP sing 64 n n 
C3' O3' ADP sing 65 n n 
C3' C2' ADP sing 66 n n 
C3' H3' ADP sing 67 n n 
O3' HO3' ADP sing 68 n n 
C2' O2' ADP sing 69 n n 
C2' C1' ADP sing 70 n n 
C2' H2' ADP sing 71 n n 
O2' HO2' ADP sing 72 n n 
C1' N9 ADP sing 73 n n 
C1' H1' ADP sing 74 n n 
N9 C8 ADP sing 75 n y 
N9 C4 ADP sing 76 n y 
C8 N7 ADP doub 77 n y 
C8 H8 ADP sing 78 n n 
N7 C5 ADP sing 79 n y 
C5 C6 ADP sing 80 n y 
C5 C4 ADP doub 81 n y 
C6 N6 ADP sing 82 n n 
C6 N1 ADP doub 83 n y 
N6 HN61 ADP sing 84 n n 
N6 HN62 ADP sing 85 n n 
N1 C2 ADP sing 86 n y 
C2 N3 ADP doub 87 n y 
C2 H2 ADP sing 88 n n 
N3 C4 ADP sing 89 n y 
#
_atom_sites.entry_id                     4PL5 
_atom_sites.fract_transf_matrix[1][1]    0.003133 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000524 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015865 
_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]    0.007202 
_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 2 ADP B 1 1001 1 ADP ADP . 
F 3 MG B 1 1002 1 MG MG . 
G 4 31L A 1 1001 401 31L 573 . 
H 2 ADP A 1 1002 1 ADP ADP . 
I 3 MG A 1 1003 1 MG MG . 
J 5 PEU A 1 1004 1 PEU PEU . 
K 2 ADP C 1 1001 1 ADP ADP . 
L 3 MG C 1 1002 1 MG MG . 
M 2 ADP D 1 1001 1 ADP ADP . 
N 3 MG D 1 1002 1 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 . . . K 2 15.575 22.757 75.531 1 72.1 ? PB ADP 1001 C 1 
HETATM 2 O O1B ADP . . . K 2 16.512 22.402 74.395 1 66.97 ? O1B ADP 1001 C 1 
HETATM 3 O O2B ADP . . . K 2 15.966 24.001 76.3 1 60.8 ? O2B ADP 1001 C 1 
HETATM 4 O O3B ADP . . . K 2 15.235 21.58 76.402 1 82.59 ? O3B ADP 1001 C 1 
HETATM 5 P PA ADP . . . K 2 13.843 23.563 73.376 1 73.18 ? PA ADP 1001 C 1 
HETATM 6 O O1A ADP . . . K 2 15.103 23.597 72.538 1 72.14 ? O1A ADP 1001 C 1 
HETATM 7 O O2A ADP . . . K 2 12.666 22.785 72.851 1 73.08 ? O2A ADP 1001 C 1 
HETATM 8 O O3A ADP . . . K 2 14.128 23.098 74.898 1 58.45 ? O3A ADP 1001 C 1 
HETATM 9 O O5' ADP . . . K 2 13.327 25.05 73.694 1 56.01 ? O5' ADP 1001 C 1 
HETATM 10 C C5' ADP . . . K 2 13.842 25.712 74.843 1 59.47 ? C5' ADP 1001 C 1 
HETATM 11 C C4' ADP . . . K 2 12.735 26.45 75.575 1 68.61 ? C4' ADP 1001 C 1 
HETATM 12 O O4' ADP . . . K 2 11.458 26.177 75.004 1 66.52 ? O4' ADP 1001 C 1 
HETATM 13 C C3' ADP . . . K 2 12.64 26.014 77.024 1 81.01 ? C3' ADP 1001 C 1 
HETATM 14 O O3' ADP . . . K 2 13.34 26.943 77.859 1 91.5 ? O3' ADP 1001 C 1 
HETATM 15 C C2' ADP . . . K 2 11.158 26.022 77.347 1 75 ? C2' ADP 1001 C 1 
HETATM 16 O O2' ADP . . . K 2 10.865 27.184 78.122 1 75.04 ? O2' ADP 1001 C 1 
HETATM 17 C C1' ADP . . . K 2 10.446 26.17 76.017 1 68.66 ? C1' ADP 1001 C 1 
HETATM 18 N N9 ADP . . . K 2 9.474 25.072 75.752 1 67.88 ? N9 ADP 1001 C 1 
HETATM 19 C C8 ADP . . . K 2 9.763 23.906 75.137 1 70.79 ? C8 ADP 1001 C 1 
HETATM 20 N N7 ADP . . . K 2 8.67 23.107 75.018 1 64.27 ? N7 ADP 1001 C 1 
HETATM 21 C C5 ADP . . . K 2 7.644 23.779 75.569 1 63.65 ? C5 ADP 1001 C 1 
HETATM 22 C C6 ADP . . . K 2 6.207 23.507 75.783 1 64.31 ? C6 ADP 1001 C 1 
HETATM 23 N N6 ADP . . . K 2 5.665 22.334 75.367 1 62.65 ? N6 ADP 1001 C 1 
HETATM 24 N N1 ADP . . . K 2 5.472 24.462 76.403 1 62.74 ? N1 ADP 1001 C 1 
HETATM 25 C C2 ADP . . . K 2 6.02 25.623 76.812 1 61.52 ? C2 ADP 1001 C 1 
HETATM 26 N N3 ADP . . . K 2 7.319 25.934 76.649 1 61.49 ? N3 ADP 1001 C 1 
HETATM 27 C C4 ADP . . . K 2 8.171 25.07 76.047 1 63.03 ? C4 ADP 1001 C 1 
#
_model_server_stats.io_time_ms              42 
_model_server_stats.parse_time_ms           41 
_model_server_stats.create_model_time_ms    113 
_model_server_stats.query_time_ms           506 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           27 
#