data_5YWB
#
_model_server_result.job_id            fAYDBfjrOiMM2Em0JMSyeg 
_model_server_result.datetime_utc      '2024-11-30 10:03:01' 
_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          5ywb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":2502}' 
#
_entry.id    5YWB 
#
_exptl.entry_id    5YWB 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_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         90 
_cell.entry_id            5YWB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YWB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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 I N N 
? 3 J N N 
? 3 K N N 
? 3 N N N 
? 3 O N N 
? 3 P N N 
? 3 S N N 
? 3 T N N 
? 3 U N N 
? 3 X N N 
? 3 Y N N 
? 3 Z 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
disulf ? disulf1 A SG CYS 110 A CYS 110 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 C SG CYS 110 C CYS 110 1_555 C SG CYS 142 C CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 E SG CYS 110 E CYS 110 1_555 E SG CYS 142 E CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf4 G SG CYS 110 G CYS 110 1_555 G SG CYS 142 G CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc1 B OG SER 720 B SER 720 1_555 L MG MG . B MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc2 B OE1 GLN 775 B GLN 775 1_555 L MG MG . B MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc3 J O2B ADP . B ADP 2501 1_555 L MG MG . B MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc4 J O3B ADP . B ADP 2501 1_555 L MG MG . B MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc5 K O2B ADP . B ADP 2502 1_555 M MG MG . B MG 2504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc6 D OG SER 720 D SER 720 1_555 Q MG MG . D MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc7 D OE1 GLN 775 D GLN 775 1_555 Q MG MG . D MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc8 O O2B ADP . D ADP 2501 1_555 Q MG MG . D MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc9 O O3B ADP . D ADP 2501 1_555 Q MG MG . D MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc10 P O2B ADP . D ADP 2502 1_555 R MG MG . D MG 2504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc11 F OG SER 720 F SER 720 1_555 V MG MG . F MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc12 F OE1 GLN 775 F GLN 775 1_555 V MG MG . F MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc13 T O2B ADP . F ADP 2501 1_555 V MG MG . F MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc14 T O3B ADP . F ADP 2501 1_555 V MG MG . F MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc15 U O2B ADP . F ADP 2502 1_555 W MG MG . F MG 2504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc16 H OG SER 720 H SER 720 1_555 AA MG MG . H MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc17 H OE1 GLN 775 H GLN 775 1_555 AA MG MG . H MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc18 Y O2B ADP . H ADP 2501 1_555 AA MG MG . H MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc19 Y O3B ADP . H ADP 2501 1_555 AA MG MG . H MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc20 Z O2B ADP . H ADP 2502 1_555 BA MG MG . H MG 2504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
#
_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                     5YWB 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
I 3 ADP A 1 401 401 ADP ADP . 
J 3 ADP B 1 2501 2501 ADP ADP . 
K 3 ADP B 1 2502 2502 ADP ADP . 
L 4 MG B 1 2503 2503 MG MG . 
M 4 MG B 1 2504 2504 MG MG . 
N 3 ADP C 1 401 401 ADP ADP . 
O 3 ADP D 1 2501 2501 ADP ADP . 
P 3 ADP D 1 2502 2502 ADP ADP . 
Q 4 MG D 1 2503 2503 MG MG . 
R 4 MG D 1 2504 2504 MG MG . 
S 3 ADP E 1 401 401 ADP ADP . 
T 3 ADP F 1 2501 2501 ADP ADP . 
U 3 ADP F 1 2502 2502 ADP ADP . 
V 4 MG F 1 2503 2503 MG MG . 
W 4 MG F 1 2504 2504 MG MG . 
X 3 ADP G 1 401 401 ADP ADP . 
Y 3 ADP H 1 2501 2501 ADP ADP . 
Z 3 ADP H 1 2502 2502 ADP ADP . 
AA 4 MG H 1 2503 2503 MG MG . 
BA 4 MG H 1 2504 2504 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 . . . P 3 215.525 107.042 125.749 1 348.67 ? PB ADP 2502 D 1 
HETATM 2 O O1B ADP . . . P 3 215.455 107.044 124.241 1 345.21 ? O1B ADP 2502 D 1 
HETATM 3 O O2B ADP . . . P 3 216.796 106.371 126.213 1 346.57 ? O2B ADP 2502 D 1 
HETATM 4 O O3B ADP . . . P 3 215.469 108.458 126.273 1 348.32 ? O3B ADP 2502 D 1 
HETATM 5 P PA ADP . . . P 3 214.056 105.977 127.89 1 367.88 ? PA ADP 2502 D 1 
HETATM 6 O O1A ADP . . . P 3 214.998 104.884 128.337 1 363.09 ? O1A ADP 2502 D 1 
HETATM 7 O O2A ADP . . . P 3 214.341 107.256 128.645 1 365.3 ? O2A ADP 2502 D 1 
HETATM 8 O O3A ADP . . . P 3 214.256 106.225 126.312 1 354.79 ? O3A ADP 2502 D 1 
HETATM 9 O O5' ADP . . . P 3 212.538 105.515 128.166 1 364.28 ? O5' ADP 2502 D 1 
HETATM 10 C C5' ADP . . . P 3 211.464 106.067 127.408 1 360.98 ? C5' ADP 2502 D 1 
HETATM 11 C C4' ADP . . . P 3 210.264 106.312 128.314 1 360.72 ? C4' ADP 2502 D 1 
HETATM 12 O O4' ADP . . . P 3 210.525 105.779 129.615 1 364.23 ? O4' ADP 2502 D 1 
HETATM 13 C C3' ADP . . . P 3 209.988 107.798 128.479 1 364.61 ? C3' ADP 2502 D 1 
HETATM 14 O O3' ADP . . . P 3 208.636 108.071 128.103 1 371.91 ? O3' ADP 2502 D 1 
HETATM 15 C C2' ADP . . . P 3 210.198 108.092 129.95 1 368.04 ? C2' ADP 2502 D 1 
HETATM 16 O O2' ADP . . . P 3 209.129 108.896 130.456 1 369.32 ? O2' ADP 2502 D 1 
HETATM 17 C C1' ADP . . . P 3 210.195 106.732 130.626 1 375.46 ? C1' ADP 2502 D 1 
HETATM 18 N N9 ADP . . . P 3 211.209 106.682 131.708 1 395.25 ? N9 ADP 2502 D 1 
HETATM 19 C C8 ADP . . . P 3 212.542 106.615 131.531 1 399.09 ? C8 ADP 2502 D 1 
HETATM 20 N N7 ADP . . . P 3 213.192 106.578 132.72 1 401.66 ? N7 ADP 2502 D 1 
HETATM 21 C C5 ADP . . . P 3 212.261 106.614 133.688 1 396.96 ? C5 ADP 2502 D 1 
HETATM 22 C C6 ADP . . . P 3 212.263 106.606 135.166 1 400.19 ? C6 ADP 2502 D 1 
HETATM 23 N N6 ADP . . . P 3 213.429 106.542 135.849 1 403.39 ? N6 ADP 2502 D 1 
HETATM 24 N N1 ADP . . . P 3 211.073 106.658 135.801 1 413.89 ? N1 ADP 2502 D 1 
HETATM 25 C C2 ADP . . . P 3 209.913 106.718 135.12 1 412.32 ? C2 ADP 2502 D 1 
HETATM 26 N N3 ADP . . . P 3 209.836 106.731 133.778 1 411.08 ? N3 ADP 2502 D 1 
HETATM 27 C C4 ADP . . . P 3 210.955 106.682 133.018 1 398.62 ? C4 ADP 2502 D 1 
#
_model_server_stats.io_time_ms              137 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    60 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          24 
_model_server_stats.element_count           27 
#