data_1LKX
#
_model_server_result.job_id            clRILo4k3GhPA-n0P6a72g 
_model_server_result.datetime_utc      '2024-12-27 13:23:31' 
_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          1lkx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":891}' 
#
_entry.id    1LKX 
#
_exptl.entry_id    1LKX 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.86 
_cell.angle_gamma         90 
_cell.entry_id            1LKX 
_cell.length_a            51.818 
_cell.length_b            143.667 
_cell.length_c            236.05 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1LKX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,Q 1 1 
B,H,I,J,R 2 1 
C,K,L,M,S 3 1 
D,N,O,P,T 4 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 G N N 
? 4 J N N 
? 4 M N N 
? 4 P 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 108 A THR 108 1_555 E MG MG . A MG 790 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc2 A OG SER 158 A SER 158 1_555 E MG MG . A MG 790 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc3 E MG MG . A MG 790 1_555 G O2A ADP . A ADP 791 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.118 ? 
metalc ? metalc4 E MG MG . A MG 790 1_555 G O1B ADP . A ADP 791 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
metalc ? metalc5 E MG MG . A MG 790 1_555 F O2 VO4 . A VO4 792 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
metalc ? metalc6 E MG MG . A MG 790 1_555 Q O HOH . A HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? 
metalc ? metalc7 E MG MG . A MG 790 1_555 Q O HOH . A HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.069 ? 
metalc ? metalc8 G O2B ADP . A ADP 791 1_555 F V VO4 . A VO4 792 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc9 B OG1 THR 108 B THR 108 1_555 H MG MG . B MG 793 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc10 B OG SER 158 B SER 158 1_555 H MG MG . B MG 793 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc11 H MG MG . B MG 793 1_555 J O1B ADP . B ADP 794 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? 
metalc ? metalc12 H MG MG . B MG 793 1_555 J O2A ADP . B ADP 794 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? 
metalc ? metalc13 H MG MG . B MG 793 1_555 I O3 VO4 . B VO4 795 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
metalc ? metalc14 H MG MG . B MG 793 1_555 R O HOH . B HOH 796 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? 
metalc ? metalc15 H MG MG . B MG 793 1_555 R O HOH . B HOH 797 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? 
metalc ? metalc16 J O2B ADP . B ADP 794 1_555 I V VO4 . B VO4 795 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? 
metalc ? metalc17 C OG1 THR 108 C THR 108 1_555 K MG MG . C MG 890 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc18 C OG SER 158 C SER 158 1_555 K MG MG . C MG 890 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
metalc ? metalc19 K MG MG . C MG 890 1_555 M O2B ADP . C ADP 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
metalc ? metalc20 K MG MG . C MG 890 1_555 M O1B ADP . C ADP 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? 
metalc ? metalc21 K MG MG . C MG 890 1_555 L O2 VO4 . C VO4 892 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? 
metalc ? metalc22 K MG MG . C MG 890 1_555 S O HOH . C HOH 897 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? 
metalc ? metalc23 K MG MG . C MG 890 1_555 S O HOH . C HOH 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? 
metalc ? metalc24 M O2B ADP . C ADP 891 1_555 L V VO4 . C VO4 892 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.794 ? 
metalc ? metalc25 D OG1 THR 108 D THR 108 1_555 N MG MG . D MG 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc26 D OG SER 158 D SER 158 1_555 N MG MG . D MG 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc27 N MG MG . D MG 893 1_555 P O3B ADP . D ADP 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? 
metalc ? metalc28 N MG MG . D MG 893 1_555 P O2B ADP . D ADP 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? 
metalc ? metalc29 N MG MG . D MG 893 1_555 O O3 VO4 . D VO4 895 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc30 N MG MG . D MG 893 1_555 T O HOH . D HOH 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc31 P O3B ADP . D ADP 894 1_555 O V VO4 . D VO4 895 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.691 ? 
#
_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                     1LKX 
_atom_sites.fract_transf_matrix[1][1]    0.019298 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001641 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006961 
_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]    0.004252 
_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 MG A 1 790 790 MG MG . 
F 3 VO4 A 1 792 792 VO4 VO4 . 
G 4 ADP A 1 791 791 ADP ADP . 
H 2 MG B 1 793 790 MG MG . 
I 3 VO4 B 1 795 792 VO4 VO4 . 
J 4 ADP B 1 794 791 ADP ADP . 
K 2 MG C 1 890 790 MG MG . 
L 3 VO4 C 1 892 792 VO4 VO4 . 
M 4 ADP C 1 891 791 ADP ADP . 
N 2 MG D 1 893 790 MG MG . 
O 3 VO4 D 1 895 792 VO4 VO4 . 
P 4 ADP D 1 894 791 ADP ADP . 
Q 5 HOH A 1 793 6 HOH WAT . 
Q 5 HOH A 2 794 7 HOH WAT . 
Q 5 HOH A 3 795 11 HOH WAT . 
Q 5 HOH A 4 796 12 HOH WAT . 
Q 5 HOH A 5 797 16 HOH WAT . 
Q 5 HOH A 6 798 18 HOH WAT . 
Q 5 HOH A 7 799 19 HOH WAT . 
Q 5 HOH A 8 800 21 HOH WAT . 
Q 5 HOH A 9 801 22 HOH WAT . 
Q 5 HOH A 10 802 23 HOH WAT . 
Q 5 HOH A 11 803 36 HOH WAT . 
Q 5 HOH A 12 804 38 HOH WAT . 
Q 5 HOH A 13 805 39 HOH WAT . 
Q 5 HOH A 14 806 44 HOH WAT . 
Q 5 HOH A 15 807 55 HOH WAT . 
Q 5 HOH A 16 808 57 HOH WAT . 
Q 5 HOH A 17 809 60 HOH WAT . 
Q 5 HOH A 18 810 61 HOH WAT . 
R 5 HOH B 1 796 2 HOH WAT . 
R 5 HOH B 2 797 3 HOH WAT . 
R 5 HOH B 3 798 8 HOH WAT . 
R 5 HOH B 4 799 17 HOH WAT . 
R 5 HOH B 5 800 24 HOH WAT . 
R 5 HOH B 6 801 26 HOH WAT . 
R 5 HOH B 7 802 31 HOH WAT . 
R 5 HOH B 8 803 34 HOH WAT . 
R 5 HOH B 9 804 35 HOH WAT . 
R 5 HOH B 10 805 40 HOH WAT . 
R 5 HOH B 11 806 41 HOH WAT . 
R 5 HOH B 12 807 42 HOH WAT . 
R 5 HOH B 13 808 46 HOH WAT . 
R 5 HOH B 14 809 54 HOH WAT . 
R 5 HOH B 15 810 62 HOH WAT . 
R 5 HOH B 16 811 63 HOH WAT . 
S 5 HOH C 1 893 1 HOH WAT . 
S 5 HOH C 2 894 4 HOH WAT . 
S 5 HOH C 3 895 5 HOH WAT . 
S 5 HOH C 4 896 9 HOH WAT . 
S 5 HOH C 5 897 10 HOH WAT . 
S 5 HOH C 6 898 13 HOH WAT . 
S 5 HOH C 7 899 14 HOH WAT . 
S 5 HOH C 8 900 20 HOH WAT . 
S 5 HOH C 9 901 27 HOH WAT . 
S 5 HOH C 10 902 32 HOH WAT . 
S 5 HOH C 11 903 37 HOH WAT . 
S 5 HOH C 12 904 43 HOH WAT . 
S 5 HOH C 13 905 47 HOH WAT . 
S 5 HOH C 14 906 48 HOH WAT . 
S 5 HOH C 15 907 49 HOH WAT . 
S 5 HOH C 16 908 51 HOH WAT . 
S 5 HOH C 17 909 52 HOH WAT . 
S 5 HOH C 18 910 53 HOH WAT . 
S 5 HOH C 19 911 56 HOH WAT . 
T 5 HOH D 1 896 15 HOH WAT . 
T 5 HOH D 2 897 25 HOH WAT . 
T 5 HOH D 3 898 28 HOH WAT . 
T 5 HOH D 4 899 29 HOH WAT . 
T 5 HOH D 5 900 30 HOH WAT . 
T 5 HOH D 6 901 33 HOH WAT . 
T 5 HOH D 7 902 45 HOH WAT . 
T 5 HOH D 8 903 50 HOH WAT . 
T 5 HOH D 9 904 58 HOH WAT . 
T 5 HOH D 10 905 59 HOH WAT . 
T 5 HOH D 11 906 64 HOH WAT . 
#
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 . . . M 4 114.758 122.76 37.097 1 15.02 ? PB ADP 891 C 1 
HETATM 2 O O1B ADP . . . M 4 115.186 121.445 37.623 1 18.98 ? O1B ADP 891 C 1 
HETATM 3 O O2B ADP . . . M 4 114.608 123.819 38.076 1 15.83 ? O2B ADP 891 C 1 
HETATM 4 O O3B ADP . . . M 4 115.788 123.075 36.013 1 14.25 ? O3B ADP 891 C 1 
HETATM 5 P PA ADP . . . M 4 112.4 121.385 36.196 1 20.21 ? PA ADP 891 C 1 
HETATM 6 O O1A ADP . . . M 4 113.187 120.162 35.96 1 22.08 ? O1A ADP 891 C 1 
HETATM 7 O O2A ADP . . . M 4 111.493 121.377 37.363 1 19.25 ? O2A ADP 891 C 1 
HETATM 8 O O3A ADP . . . M 4 113.35 122.673 36.382 1 19.23 ? O3A ADP 891 C 1 
HETATM 9 O O5' ADP . . . M 4 111.631 121.653 34.835 1 22.24 ? O5' ADP 891 C 1 
HETATM 10 C C5' ADP . . . M 4 110.63 122.712 34.809 1 25.95 ? C5' ADP 891 C 1 
HETATM 11 C C4' ADP . . . M 4 109.457 122.167 34.032 1 30.08 ? C4' ADP 891 C 1 
HETATM 12 O O4' ADP . . . M 4 109.97 121.87 32.741 1 31.76 ? O4' ADP 891 C 1 
HETATM 13 C C3' ADP . . . M 4 108.967 120.816 34.473 1 31.33 ? C3' ADP 891 C 1 
HETATM 14 O O3' ADP . . . M 4 108.36 120.702 35.761 1 27.88 ? O3' ADP 891 C 1 
HETATM 15 C C2' ADP . . . M 4 108.202 120.403 33.242 1 30.99 ? C2' ADP 891 C 1 
HETATM 16 O O2' ADP . . . M 4 106.949 121.004 33.116 1 31.28 ? O2' ADP 891 C 1 
HETATM 17 C C1' ADP . . . M 4 109.214 120.771 32.2 1 32.5 ? C1' ADP 891 C 1 
HETATM 18 N N9 ADP . . . M 4 110.139 119.68 31.866 1 34.4 ? N9 ADP 891 C 1 
HETATM 19 C C8 ADP . . . M 4 111.472 119.617 32.053 1 35.29 ? C8 ADP 891 C 1 
HETATM 20 N N7 ADP . . . M 4 112.029 118.585 31.51 1 36.91 ? N7 ADP 891 C 1 
HETATM 21 C C5 ADP . . . M 4 111.003 117.915 30.926 1 37.75 ? C5 ADP 891 C 1 
HETATM 22 C C6 ADP . . . M 4 110.982 116.718 30.181 1 39.52 ? C6 ADP 891 C 1 
HETATM 23 N N6 ADP . . . M 4 112.091 116.05 29.925 1 38.66 ? N6 ADP 891 C 1 
HETATM 24 N N1 ADP . . . M 4 109.729 116.264 29.696 1 40.66 ? N1 ADP 891 C 1 
HETATM 25 C C2 ADP . . . M 4 108.585 117.026 29.981 1 39.88 ? C2 ADP 891 C 1 
HETATM 26 N N3 ADP . . . M 4 108.54 118.176 30.684 1 40.12 ? N3 ADP 891 C 1 
HETATM 27 C C4 ADP . . . M 4 109.807 118.568 31.134 1 37.65 ? C4 ADP 891 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          20 
_model_server_stats.element_count           27 
#