data_4WYB
#
_model_server_result.job_id            wIBvspSaMP0i_IfySdlfSA 
_model_server_result.datetime_utc      '2024-10-19 08:28:30' 
_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          4wyb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"EA","auth_seq_id":401}' 
#
_entry.id    4WYB 
#
_exptl.entry_id    4WYB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    12 
_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         120 
_cell.entry_id            4WYB 
_cell.length_a            138.753 
_cell.length_b            138.753 
_cell.length_c            356.651 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4WYB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32' 
#
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 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
PISA dimeric 2 author_and_software_defined_assembly 5 
PISA dimeric 2 author_and_software_defined_assembly 6 
PISA dimeric 2 author_and_software_defined_assembly 7 
PISA dimeric 2 author_and_software_defined_assembly 8 
PISA dimeric 2 author_and_software_defined_assembly 9 
PISA dimeric 2 author_and_software_defined_assembly 10 
PISA dimeric 2 author_and_software_defined_assembly 11 
PISA dimeric 2 author_and_software_defined_assembly 12 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,Y,Z 1 1 
C,D,AA,BA 2 1 
E,F,CA,DA 3 1 
G,H,EA,FA 4 1 
I,J,GA,HA 5 1 
K,L,IA,JA 6 1 
M,N,KA,LA 7 1 
O,P,MA,NA 8 1 
Q,R,OA,PA 9 1 
S,T,QA,RA 10 1 
U,V,SA,TA 11 1 
W,X,UA,VA 12 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 Y N N 
? 3 AA N N 
? 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 
#
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 GLN 139 A GLN 137 1_555 Z CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc2 Y O3G ATP . A ATP 401 1_555 Z CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? 
metalc ? metalc3 Y O1B ATP . A ATP 401 1_555 Z CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
metalc ? metalc4 C OE1 GLN 139 C GLN 137 1_555 BA CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc5 AA O1G ATP . C ATP 401 1_555 BA CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? 
metalc ? metalc6 AA O1B ATP . C ATP 401 1_555 BA CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? 
metalc ? metalc7 E OE1 GLN 139 E GLN 137 1_555 DA CA CA . E CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? 
metalc ? metalc8 CA O2G ATP . E ATP 401 1_555 DA CA CA . E CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? 
metalc ? metalc9 CA O1B ATP . E ATP 401 1_555 DA CA CA . E CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc10 G OE1 GLN 139 G GLN 137 1_555 FA CA CA . G CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
metalc ? metalc11 EA O1G ATP . G ATP 401 1_555 FA CA CA . G CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc12 EA O2B ATP . G ATP 401 1_555 FA CA CA . G CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc13 GA O3G ATP . I ATP 401 1_555 HA CA CA . I CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.145 ? 
metalc ? metalc14 GA O2B ATP . I ATP 401 1_555 HA CA CA . I CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc15 K OE1 GLN 139 K GLN 137 1_555 JA CA CA . K CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? 
metalc ? metalc16 IA O1G ATP . K ATP 401 1_555 JA CA CA . K CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.01 ? 
metalc ? metalc17 IA O1B ATP . K ATP 401 1_555 JA CA CA . K CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc18 KA O1B ATP . M ATP 401 1_555 LA CA CA . M CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc19 O OE1 GLN 139 O GLN 137 1_555 NA CA CA . O CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
metalc ? metalc20 MA O2G ATP . O ATP 401 1_555 NA CA CA . O CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? 
metalc ? metalc21 MA O2B ATP . O ATP 401 1_555 NA CA CA . O CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 
metalc ? metalc22 Q OE1 GLN 139 Q GLN 137 1_555 PA CA CA . Q CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? 
metalc ? metalc23 OA O2G ATP . Q ATP 401 1_555 PA CA CA . Q CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? 
metalc ? metalc24 OA O2B ATP . Q ATP 401 1_555 PA CA CA . Q CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? 
metalc ? metalc25 S OE1 GLN 139 S GLN 137 1_555 RA CA CA . S CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? 
metalc ? metalc26 QA O2G ATP . S ATP 401 1_555 RA CA CA . S CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? 
metalc ? metalc27 QA O2B ATP . S ATP 401 1_555 RA CA CA . S CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? 
metalc ? metalc28 U OE1 GLN 139 U GLN 137 1_555 TA CA CA . U CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? 
metalc ? metalc29 SA O2G ATP . U ATP 401 1_555 TA CA CA . U CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? 
metalc ? metalc30 SA O1B ATP . U ATP 401 1_555 TA CA CA . U CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
metalc ? metalc31 W OE1 GLN 139 X GLN 137 1_555 VA CA CA . X CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? 
metalc ? metalc32 UA O1G ATP . X ATP 401 1_555 VA CA CA . X CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc33 UA O2B ATP . X ATP 401 1_555 VA CA CA . X CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
#
_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                     4WYB 
_atom_sites.fract_transf_matrix[1][1]    0.007207 
_atom_sites.fract_transf_matrix[1][2]    0.004161 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008322 
_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]    0.002804 
_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
Y 3 ATP A 1 401 1 ATP ATP . 
Z 4 CA A 1 402 2 CA CA . 
AA 3 ATP C 1 401 1 ATP ATP . 
BA 4 CA C 1 402 2 CA CA . 
CA 3 ATP E 1 401 1 ATP ATP . 
DA 4 CA E 1 402 2 CA CA . 
EA 3 ATP G 1 401 1 ATP ATP . 
FA 4 CA G 1 402 2 CA CA . 
GA 3 ATP I 1 401 1 ATP ATP . 
HA 4 CA I 1 402 2 CA CA . 
IA 3 ATP K 1 401 1 ATP ATP . 
JA 4 CA K 1 402 2 CA CA . 
KA 3 ATP M 1 401 1 ATP ATP . 
LA 4 CA M 1 402 2 CA CA . 
MA 3 ATP O 1 401 1 ATP ATP . 
NA 4 CA O 1 402 2 CA CA . 
OA 3 ATP Q 1 401 1 ATP ATP . 
PA 4 CA Q 1 402 2 CA CA . 
QA 3 ATP S 1 401 1 ATP ATP . 
RA 4 CA S 1 402 2 CA CA . 
SA 3 ATP U 1 401 1 ATP ATP . 
TA 4 CA U 1 402 2 CA CA . 
UA 3 ATP X 1 401 1 ATP ATP . 
VA 4 CA X 1 402 2 CA CA . 
#
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 . . . EA 3 255.136 -23.857 29.043 1 83.18 ? PG ATP 401 G 1 
HETATM 2 O O1G ATP . . . EA 3 256.128 -22.673 28.846 1 88.69 ? O1G ATP 401 G 1 
HETATM 3 O O2G ATP . . . EA 3 255.702 -24.814 30.027 1 79.19 ? O2G ATP 401 G 1 
HETATM 4 O O3G ATP . . . EA 3 253.773 -23.311 29.569 1 75.62 ? O3G ATP 401 G 1 
HETATM 5 P PB ATP . . . EA 3 256.087 -24.852 26.41 1 89.67 ? PB ATP 401 G 1 
HETATM 6 O O1B ATP . . . EA 3 256.151 -26.293 26.021 1 86.31 ? O1B ATP 401 G 1 
HETATM 7 O O2B ATP . . . EA 3 257.425 -24.431 26.971 1 82.84 ? O2B ATP 401 G 1 
HETATM 8 O O3B ATP . . . EA 3 254.889 -24.633 27.568 1 80.57 ? O3B ATP 401 G 1 
HETATM 9 P PA ATP . . . EA 3 256.833 -23.443 24.018 1 100.58 ? PA ATP 401 G 1 
HETATM 10 O O1A ATP . . . EA 3 257.77 -24.548 23.715 1 88.28 ? O1A ATP 401 G 1 
HETATM 11 O O2A ATP . . . EA 3 257.622 -22.241 24.588 1 89.01 ? O2A ATP 401 G 1 
HETATM 12 O O3A ATP . . . EA 3 255.733 -23.953 25.094 1 90.83 ? O3A ATP 401 G 1 
HETATM 13 O O5' ATP . . . EA 3 256.024 -22.99 22.604 1 89.02 ? O5' ATP 401 G 1 
HETATM 14 C C5' ATP . . . EA 3 254.971 -23.823 22.135 1 88.25 ? C5' ATP 401 G 1 
HETATM 15 C C4' ATP . . . EA 3 253.656 -22.98 21.985 1 93.44 ? C4' ATP 401 G 1 
HETATM 16 O O4' ATP . . . EA 3 253.977 -21.621 21.288 1 91.69 ? O4' ATP 401 G 1 
HETATM 17 C C3' ATP . . . EA 3 252.831 -23.576 21.211 1 100.79 ? C3' ATP 401 G 1 
HETATM 18 O O3' ATP . . . EA 3 251.434 -23.269 21.606 1 100.59 ? O3' ATP 401 G 1 
HETATM 19 C C2' ATP . . . EA 3 253.128 -22.997 19.699 1 102.71 ? C2' ATP 401 G 1 
HETATM 20 O O2' ATP . . . EA 3 251.944 -23.127 18.882 1 97.05 ? O2' ATP 401 G 1 
HETATM 21 C C1' ATP . . . EA 3 253.421 -21.751 19.851 1 97.66 ? C1' ATP 401 G 1 
HETATM 22 N N9 ATP . . . EA 3 254.465 -21.335 18.86 1 96.82 ? N9 ATP 401 G 1 
HETATM 23 C C8 ATP . . . EA 3 255.63 -21.811 18.399 1 91.86 ? C8 ATP 401 G 1 
HETATM 24 N N7 ATP . . . EA 3 256.081 -20.947 17.501 1 88.69 ? N7 ATP 401 G 1 
HETATM 25 C C5 ATP . . . EA 3 255.212 -19.952 17.408 1 92.06 ? C5 ATP 401 G 1 
HETATM 26 C C6 ATP . . . EA 3 255.192 -18.816 16.643 1 93.11 ? C6 ATP 401 G 1 
HETATM 27 N N6 ATP . . . EA 3 256.101 -18.22 15.62 1 98.03 ? N6 ATP 401 G 1 
HETATM 28 N N1 ATP . . . EA 3 254.19 -17.974 16.743 1 93.5 ? N1 ATP 401 G 1 
HETATM 29 C C2 ATP . . . EA 3 253.162 -18.227 17.613 1 91.17 ? C2 ATP 401 G 1 
HETATM 30 N N3 ATP . . . EA 3 253.176 -19.336 18.362 1 92.82 ? N3 ATP 401 G 1 
HETATM 31 C C4 ATP . . . EA 3 254.2 -20.198 18.258 1 95.13 ? C4 ATP 401 G 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    47 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#