data_5LU4
#
_model_server_result.job_id            wiN7KDakoq67I351WbRslQ 
_model_server_result.datetime_utc      '2025-03-11 05:03:11' 
_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          5lu4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":901}' 
#
_entry.id    5LU4 
#
_exptl.entry_id    5LU4 
_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    2 
_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            5LU4 
_cell.length_a            74.159 
_cell.length_b            126.515 
_cell.length_c            218.998 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LU4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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,C,D,E,F,J 1 1 
B,G,H,I,K 1 2 
B,G,H,I,K 2 1 
A,C,D,E,F,J 2 3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_995 -x+9/2,-y+4,z+1/2 -1 0 0 0 -1 0 0 0 1 333.7155 506.06 109.499 
3 'crystal symmetry operation' 2_994 -x+9/2,-y+4,z-1/2 -1 0 0 0 -1 0 0 0 1 333.7155 506.06 -109.499 
#
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 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
metalc ? metalc1 A OE1 GLU 324 A GLU 324 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc2 A OE2 GLU 324 A GLU 324 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? 
metalc ? metalc3 A OE1 GLN 336 A GLN 336 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc4 A OD2 ASP 622 A ASP 622 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? 
metalc ? metalc5 A OE2 GLU 748 A GLU 748 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
metalc ? metalc6 A OD2 ASP 772 A ASP 772 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc7 C O2B ADP . A ADP 901 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc8 C O3A ADP . A ADP 901 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc9 C O5' ADP . A ADP 901 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? 
metalc ? metalc10 E OXT PYR . A PYR 903 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? 
metalc ? metalc11 B OE1 GLU 324 B GLU 324 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
metalc ? metalc12 B OE2 GLU 324 B GLU 324 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? 
metalc ? metalc13 B OE1 GLN 336 B GLN 336 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc14 B OD2 ASP 622 B ASP 622 1_555 I MG MG . B MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc15 B OE2 GLU 748 B GLU 748 1_555 I MG MG . B MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc16 B OD2 ASP 772 B ASP 772 1_555 I MG MG . B MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? 
metalc ? metalc17 G O1B ADP . B ADP 901 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
metalc ? metalc18 G O2B ADP . B ADP 901 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? 
metalc ? metalc19 G O3A ADP . B ADP 901 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? 
#
_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                     5LU4 
_atom_sites.fract_transf_matrix[1][1]    0.013485 
_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]    0.007904 
_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]    0.004566 
_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 ADP A 1 901 873 ADP ADP . 
D 3 MG A 1 902 874 MG MG . 
E 4 PYR A 1 903 875 PYR PYR . 
F 3 MG A 1 904 876 MG MG . 
G 2 ADP B 1 901 873 ADP ADP . 
H 3 MG B 1 902 874 MG MG . 
I 3 MG B 1 903 875 MG MG . 
J 5 HOH A 1 1001 878 HOH HOH . 
K 5 HOH B 1 1001 876 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 . . . G 2 150.376 241.308 202.936 1 121.15 ? PB ADP 901 B 1 
HETATM 2 O O1B ADP . . . G 2 150.718 240.023 202.142 1 76.41 ? O1B ADP 901 B 1 
HETATM 3 O O2B ADP . . . G 2 151.575 242.219 203.228 1 102.22 ? O2B ADP 901 B 1 
HETATM 4 O O3B ADP . . . G 2 149.207 242.025 202.243 1 90.53 ? O3B ADP 901 B 1 
HETATM 5 P PA ADP . . . G 2 148.5 241.29 205.182 1 70.57 ? PA ADP 901 B 1 
HETATM 6 O O1A ADP . . . G 2 148.221 242.738 204.771 1 65.73 ? O1A ADP 901 B 1 
HETATM 7 O O2A ADP . . . G 2 147.707 240.073 204.829 1 63 ? O2A ADP 901 B 1 
HETATM 8 O O3A ADP . . . G 2 149.948 240.925 204.507 1 97.45 ? O3A ADP 901 B 1 
HETATM 9 O O5' ADP . . . G 2 148.529 241.29 206.772 1 66.54 ? O5' ADP 901 B 1 
HETATM 10 C C5' ADP . . . G 2 148.88 242.451 207.534 1 63.13 ? C5' ADP 901 B 1 
HETATM 11 C C4' ADP . . . G 2 149.788 242.081 208.718 1 67.32 ? C4' ADP 901 B 1 
HETATM 12 O O4' ADP . . . G 2 149.025 241.765 209.879 1 68.43 ? O4' ADP 901 B 1 
HETATM 13 C C3' ADP . . . G 2 150.652 240.837 208.548 1 68.51 ? C3' ADP 901 B 1 
HETATM 14 O O3' ADP . . . G 2 151.763 240.968 209.455 1 73.35 ? O3' ADP 901 B 1 
HETATM 15 C C2' ADP . . . G 2 149.753 239.695 208.949 1 63.24 ? C2' ADP 901 B 1 
HETATM 16 O O2' ADP . . . G 2 150.419 238.496 209.325 1 57.78 ? O2' ADP 901 B 1 
HETATM 17 C C1' ADP . . . G 2 148.998 240.354 210.11 1 70.38 ? C1' ADP 901 B 1 
HETATM 18 N N9 ADP . . . G 2 147.586 239.853 210.21 1 80.33 ? N9 ADP 901 B 1 
HETATM 19 C C8 ADP . . . G 2 146.643 239.781 209.231 1 80.6 ? C8 ADP 901 B 1 
HETATM 20 N N7 ADP . . . G 2 145.51 239.228 209.709 1 80.79 ? N7 ADP 901 B 1 
HETATM 21 C C5 ADP . . . G 2 145.712 238.962 211.002 1 76.87 ? C5 ADP 901 B 1 
HETATM 22 C C6 ADP . . . G 2 144.925 238.385 212.099 1 80.12 ? C6 ADP 901 B 1 
HETATM 23 N N6 ADP . . . G 2 143.661 238.009 211.842 1 85.68 ? N6 ADP 901 B 1 
HETATM 24 N N1 ADP . . . G 2 145.498 238.263 213.326 1 79.37 ? N1 ADP 901 B 1 
HETATM 25 C C2 ADP . . . G 2 146.769 238.658 213.532 1 79.31 ? C2 ADP 901 B 1 
HETATM 26 N N3 ADP . . . G 2 147.541 239.192 212.569 1 78.9 ? N3 ADP 901 B 1 
HETATM 27 C C4 ADP . . . G 2 147.068 239.379 211.325 1 74.45 ? C4 ADP 901 B 1 
#
_model_server_stats.io_time_ms              129 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#