data_3WDL
#
_model_server_result.job_id            0lcIw-coflVonNFGWCSsXw 
_model_server_result.datetime_utc      '2024-11-04 23:28:06' 
_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          3wdl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":901}' 
#
_entry.id    3WDL 
#
_exptl.entry_id    3WDL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_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          110.43 
_cell.angle_gamma         90 
_cell.entry_id            3WDL 
_cell.length_a            79.655 
_cell.length_b            80.071 
_cell.length_c            83.998 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3WDL 
_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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_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,K,L 1 1 
C,D,H,I,J,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 F N N 
? 2 H N N 
? 2 I 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 B OD1 ASP 163 B ASP 163 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc2 F O1B ATP . B ATP 901 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc3 F O2A ATP . B ATP 901 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? 
metalc ? metalc4 F O2G ATP . B ATP 901 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? 
metalc ? metalc5 G MG MG . B MG 902 1_555 L O HOH . B HOH 1025 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc6 G MG MG . B MG 902 1_555 L O HOH . B HOH 1032 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc7 D OD1 ASP 163 D ASP 163 1_555 J MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc8 I O1B ATP . D ATP 301 1_555 J MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? 
metalc ? metalc9 I O2G ATP . D ATP 301 1_555 J MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc10 I O1A ATP . D ATP 301 1_555 J MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? 
metalc ? metalc11 J MG MG . D MG 302 1_555 N O HOH . D HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc12 J MG MG . D MG 302 1_555 N O HOH . D HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "ADENOSINE-5'-TRIPHOSPHATE" 
_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
PG O1G ATP doub 70 n n 
PG O2G ATP sing 71 n n 
PG O3G ATP sing 72 n n 
PG O3B ATP sing 73 n n 
O2G HOG2 ATP sing 74 n n 
O3G HOG3 ATP sing 75 n n 
PB O1B ATP doub 76 n n 
PB O2B ATP sing 77 n n 
PB O3B ATP sing 78 n n 
PB O3A ATP sing 79 n n 
O2B HOB2 ATP sing 80 n n 
PA O1A ATP doub 81 n n 
PA O2A ATP sing 82 n n 
PA O3A ATP sing 83 n n 
PA O5' ATP sing 84 n n 
O2A HOA2 ATP sing 85 n n 
O5' C5' ATP sing 86 n n 
C5' C4' ATP sing 87 n n 
C5' "H5'1" ATP sing 88 n n 
C5' "H5'2" ATP sing 89 n n 
C4' O4' ATP sing 90 n n 
C4' C3' ATP sing 91 n n 
C4' H4' ATP sing 92 n n 
O4' C1' ATP sing 93 n n 
C3' O3' ATP sing 94 n n 
C3' C2' ATP sing 95 n n 
C3' H3' ATP sing 96 n n 
O3' HO3' ATP sing 97 n n 
C2' O2' ATP sing 98 n n 
C2' C1' ATP sing 99 n n 
C2' H2' ATP sing 100 n n 
O2' HO2' ATP sing 101 n n 
C1' N9 ATP sing 102 n n 
C1' H1' ATP sing 103 n n 
N9 C8 ATP sing 104 n y 
N9 C4 ATP sing 105 n y 
C8 N7 ATP doub 106 n y 
C8 H8 ATP sing 107 n n 
N7 C5 ATP sing 108 n y 
C5 C6 ATP sing 109 n y 
C5 C4 ATP doub 110 n y 
C6 N6 ATP sing 111 n n 
C6 N1 ATP doub 112 n y 
N6 HN61 ATP sing 113 n n 
N6 HN62 ATP sing 114 n n 
N1 C2 ATP sing 115 n y 
C2 N3 ATP doub 116 n y 
C2 H2 ATP sing 117 n n 
N3 C4 ATP sing 118 n y 
#
_atom_sites.entry_id                     3WDL 
_atom_sites.fract_transf_matrix[1][1]    0.012554 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004676 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012489 
_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]    0.012704 
_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 ATP A 1 900 900 ATP ATP . 
F 2 ATP B 1 901 901 ATP ATP . 
G 3 MG B 1 902 1 MG MG2 . 
H 2 ATP C 1 301 902 ATP ATP . 
I 2 ATP D 1 301 903 ATP ATP . 
J 3 MG D 1 302 2 MG MG2 . 
K 4 HOH A 1 1001 2 HOH TIP . 
K 4 HOH A 2 1002 3 HOH TIP . 
K 4 HOH A 3 1003 5 HOH TIP . 
K 4 HOH A 4 1004 13 HOH TIP . 
K 4 HOH A 5 1005 17 HOH TIP . 
K 4 HOH A 6 1006 22 HOH TIP . 
K 4 HOH A 7 1007 24 HOH TIP . 
K 4 HOH A 8 1008 31 HOH TIP . 
K 4 HOH A 9 1009 33 HOH TIP . 
K 4 HOH A 10 1010 40 HOH TIP . 
K 4 HOH A 11 1011 44 HOH TIP . 
K 4 HOH A 12 1012 48 HOH TIP . 
K 4 HOH A 13 1013 56 HOH TIP . 
K 4 HOH A 14 1014 61 HOH TIP . 
K 4 HOH A 15 1015 75 HOH TIP . 
K 4 HOH A 16 1016 76 HOH TIP . 
L 4 HOH B 1 1001 1 HOH TIP . 
L 4 HOH B 2 1002 7 HOH TIP . 
L 4 HOH B 3 1003 10 HOH TIP . 
L 4 HOH B 4 1004 11 HOH TIP . 
L 4 HOH B 5 1005 12 HOH TIP . 
L 4 HOH B 6 1006 14 HOH TIP . 
L 4 HOH B 7 1007 15 HOH TIP . 
L 4 HOH B 8 1008 19 HOH TIP . 
L 4 HOH B 9 1009 21 HOH TIP . 
L 4 HOH B 10 1010 23 HOH TIP . 
L 4 HOH B 11 1011 25 HOH TIP . 
L 4 HOH B 12 1012 27 HOH TIP . 
L 4 HOH B 13 1013 28 HOH TIP . 
L 4 HOH B 14 1014 34 HOH TIP . 
L 4 HOH B 15 1015 36 HOH TIP . 
L 4 HOH B 16 1016 37 HOH TIP . 
L 4 HOH B 17 1017 42 HOH TIP . 
L 4 HOH B 18 1018 45 HOH TIP . 
L 4 HOH B 19 1019 46 HOH TIP . 
L 4 HOH B 20 1020 50 HOH TIP . 
L 4 HOH B 21 1021 52 HOH TIP . 
L 4 HOH B 22 1022 53 HOH TIP . 
L 4 HOH B 23 1023 54 HOH TIP . 
L 4 HOH B 24 1024 57 HOH TIP . 
L 4 HOH B 25 1025 58 HOH TIP . 
L 4 HOH B 26 1026 59 HOH TIP . 
L 4 HOH B 27 1027 60 HOH TIP . 
L 4 HOH B 28 1028 65 HOH TIP . 
L 4 HOH B 29 1029 66 HOH TIP . 
L 4 HOH B 30 1030 70 HOH TIP . 
L 4 HOH B 31 1031 71 HOH TIP . 
L 4 HOH B 32 1032 72 HOH TIP . 
L 4 HOH B 33 1033 77 HOH TIP . 
L 4 HOH B 34 1034 78 HOH TIP . 
L 4 HOH B 35 1035 79 HOH TIP . 
L 4 HOH B 36 1036 80 HOH TIP . 
M 4 HOH C 1 401 4 HOH TIP . 
M 4 HOH C 2 402 6 HOH TIP . 
M 4 HOH C 3 403 8 HOH TIP . 
M 4 HOH C 4 404 9 HOH TIP . 
M 4 HOH C 5 405 16 HOH TIP . 
M 4 HOH C 6 406 20 HOH TIP . 
M 4 HOH C 7 407 26 HOH TIP . 
M 4 HOH C 8 408 29 HOH TIP . 
M 4 HOH C 9 409 30 HOH TIP . 
M 4 HOH C 10 410 38 HOH TIP . 
M 4 HOH C 11 411 41 HOH TIP . 
M 4 HOH C 12 412 43 HOH TIP . 
M 4 HOH C 13 413 49 HOH TIP . 
M 4 HOH C 14 414 55 HOH TIP . 
M 4 HOH C 15 415 62 HOH TIP . 
M 4 HOH C 16 416 63 HOH TIP . 
M 4 HOH C 17 417 64 HOH TIP . 
M 4 HOH C 18 418 67 HOH TIP . 
M 4 HOH C 19 419 68 HOH TIP . 
M 4 HOH C 20 420 69 HOH TIP . 
M 4 HOH C 21 421 81 HOH TIP . 
M 4 HOH C 22 422 82 HOH TIP . 
M 4 HOH C 23 423 83 HOH TIP . 
M 4 HOH C 24 424 84 HOH TIP . 
N 4 HOH D 1 401 18 HOH TIP . 
N 4 HOH D 2 402 32 HOH TIP . 
N 4 HOH D 3 403 35 HOH TIP . 
N 4 HOH D 4 404 39 HOH TIP . 
N 4 HOH D 5 405 47 HOH TIP . 
N 4 HOH D 6 406 51 HOH TIP . 
N 4 HOH D 7 407 73 HOH TIP . 
N 4 HOH D 8 408 74 HOH TIP . 
#
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 PG ATP . . . F 2 32.172 -36.483 35.249 1 28.69 ? PG ATP 901 B 1 
HETATM 2 O O1G ATP . . . F 2 33.391 -36.765 36.095 1 35.44 ? O1G ATP 901 B 1 
HETATM 3 O O2G ATP . . . F 2 31.539 -35.135 35.5 1 28.94 ? O2G ATP 901 B 1 
HETATM 4 O O3G ATP . . . F 2 31.191 -37.628 35.168 1 33.38 ? O3G ATP 901 B 1 
HETATM 5 P PB ATP . . . F 2 33.746 -35.159 33.355 1 29.68 ? PB ATP 901 B 1 
HETATM 6 O O1B ATP . . . F 2 33.754 -34.162 34.489 1 27.16 ? O1B ATP 901 B 1 
HETATM 7 O O2B ATP . . . F 2 35.044 -35.755 32.866 1 32.66 ? O2B ATP 901 B 1 
HETATM 8 O O3B ATP . . . F 2 32.756 -36.366 33.754 1 36.2 ? O3B ATP 901 B 1 
HETATM 9 P PA ATP . . . F 2 32.294 -33.045 32.242 1 53.2 ? PA ATP 901 B 1 
HETATM 10 O O1A ATP . . . F 2 33.367 -31.988 32.137 1 51.57 ? O1A ATP 901 B 1 
HETATM 11 O O2A ATP . . . F 2 31.384 -33.079 33.446 1 45.6 ? O2A ATP 901 B 1 
HETATM 12 O O3A ATP . . . F 2 32.994 -34.488 32.099 1 40.15 ? O3A ATP 901 B 1 
HETATM 13 O O5' ATP . . . F 2 31.378 -32.966 30.92 1 49.73 ? O5' ATP 901 B 1 
HETATM 14 C C5' ATP . . . F 2 31.883 -33.407 29.661 1 47.3 ? C5' ATP 901 B 1 
HETATM 15 C C4' ATP . . . F 2 31.496 -34.864 29.441 1 43.77 ? C4' ATP 901 B 1 
HETATM 16 O O4' ATP . . . F 2 30.473 -34.947 28.445 1 40.31 ? O4' ATP 901 B 1 
HETATM 17 C C3' ATP . . . F 2 32.683 -35.683 28.959 1 43.37 ? C3' ATP 901 B 1 
HETATM 18 O O3' ATP . . . F 2 32.965 -36.732 29.89 1 42.95 ? O3' ATP 901 B 1 
HETATM 19 C C2' ATP . . . F 2 32.279 -36.27 27.622 1 43.04 ? C2' ATP 901 B 1 
HETATM 20 O O2' ATP . . . F 2 32.293 -37.699 27.689 1 48.91 ? O2' ATP 901 B 1 
HETATM 21 C C1' ATP . . . F 2 30.868 -35.775 27.347 1 40.3 ? C1' ATP 901 B 1 
HETATM 22 N N9 ATP . . . F 2 30.851 -34.983 26.092 1 35.38 ? N9 ATP 901 B 1 
HETATM 23 C C8 ATP . . . F 2 31.468 -33.803 25.897 1 37 ? C8 ATP 901 B 1 
HETATM 24 N N7 ATP . . . F 2 31.256 -33.341 24.638 1 30.44 ? N7 ATP 901 B 1 
HETATM 25 C C5 ATP . . . F 2 30.485 -34.241 24.002 1 29.81 ? C5 ATP 901 B 1 
HETATM 26 C C6 ATP . . . F 2 29.89 -34.374 22.651 1 31.18 ? C6 ATP 901 B 1 
HETATM 27 N N6 ATP . . . F 2 30.084 -33.424 21.704 1 34.34 ? N6 ATP 901 B 1 
HETATM 28 N N1 ATP . . . F 2 29.148 -35.474 22.396 1 28.76 ? N1 ATP 901 B 1 
HETATM 29 C C2 ATP . . . F 2 28.948 -36.424 23.327 1 27.11 ? C2 ATP 901 B 1 
HETATM 30 N N3 ATP . . . F 2 29.456 -36.369 24.571 1 28.92 ? N3 ATP 901 B 1 
HETATM 31 C C4 ATP . . . F 2 30.22 -35.322 24.964 1 32.15 ? C4 ATP 901 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#