data_4AP0
#
_model_server_result.job_id            6YFLZdVO0i748dQZwV_bOw 
_model_server_result.datetime_utc      '2024-10-22 03:29:09' 
_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          4ap0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1003}' 
#
_entry.id    4AP0 
#
_exptl.entry_id    4AP0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.02 
_cell.angle_gamma         90 
_cell.entry_id            4AP0 
_cell.length_a            64.723 
_cell.length_b            112.607 
_cell.length_c            106.913 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4AP0 
_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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_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,H,I,W 1 1 
B,J,K,L,M,N,O,X 2 1 
C,P,Q,R,Y 3 1 
D,S,T,U,V,Z 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
? 3 F N N 
? 3 K N N 
? 3 Q N N 
? 3 T 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 114 A THR 112 1_555 E MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc2 E MG MG . A MG 1001 1_555 F O3B ADP . A ADP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc3 E MG MG . A MG 1001 1_555 W O HOH . A HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc4 E MG MG . A MG 1001 1_555 W O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc5 E MG MG . A MG 1001 1_555 W O HOH . A HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc6 B OG1 THR 114 B THR 112 1_555 J MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc7 J MG MG . B MG 1001 1_555 K O3B ADP . B ADP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc8 J MG MG . B MG 1001 1_555 X O HOH . B HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc9 J MG MG . B MG 1001 1_555 X O HOH . B HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc10 J MG MG . B MG 1001 1_555 X O HOH . B HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc11 C OG1 THR 114 C THR 112 1_555 P MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc12 P MG MG . C MG 1001 1_555 Q O3B ADP . C ADP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc13 P MG MG . C MG 1001 1_555 Y O HOH . C HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc14 P MG MG . C MG 1001 1_555 Y O HOH . C HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc15 P MG MG . C MG 1001 1_555 Y O HOH . C HOH 2010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc16 D OG1 THR 114 D THR 112 1_555 S MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc17 S MG MG . D MG 1001 1_555 T O3B ADP . D ADP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc18 S MG MG . D MG 1001 1_555 Z O HOH . D HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc19 S MG MG . D MG 1001 1_555 Z O HOH . D HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc20 S MG MG . D MG 1001 1_555 Z O HOH . D HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
#
_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                     4AP0 
_atom_sites.fract_transf_matrix[1][1]    0.01545 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000005 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00888 
_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]    0.009353 
_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 1001 1001 MG MG . 
F 3 ADP A 1 1003 1003 ADP ADP . 
G 4 CL A 1 1367 1367 CL CL . 
H 4 CL A 1 1368 1368 CL CL . 
I 5 G7X A 1 2001 2001 G7X G7X . 
J 2 MG B 1 1001 1001 MG MG . 
K 3 ADP B 1 1003 1003 ADP ADP . 
L 4 CL B 1 1360 1360 CL CL . 
M 4 CL B 1 1361 1361 CL CL . 
N 4 CL B 1 1362 1362 CL CL . 
O 5 G7X B 1 2001 2001 G7X G7X . 
P 2 MG C 1 1001 1001 MG MG . 
Q 3 ADP C 1 1003 1003 ADP ADP . 
R 5 G7X C 1 2001 2001 G7X G7X . 
S 2 MG D 1 1001 1001 MG MG . 
T 3 ADP D 1 1003 1003 ADP ADP . 
U 4 CL D 1 1365 1365 CL CL . 
V 5 G7X D 1 2001 2001 G7X G7X . 
W 6 HOH A 1 2000 2000 HOH HOH . 
W 6 HOH A 2 2002 2002 HOH HOH . 
W 6 HOH A 3 2003 2003 HOH HOH . 
W 6 HOH A 4 2004 2004 HOH HOH . 
W 6 HOH A 5 2005 2005 HOH HOH . 
W 6 HOH A 6 2006 2006 HOH HOH . 
W 6 HOH A 7 2007 2007 HOH HOH . 
W 6 HOH A 8 2008 2008 HOH HOH . 
W 6 HOH A 9 2009 2009 HOH HOH . 
X 6 HOH B 1 2000 2000 HOH HOH . 
X 6 HOH B 2 2002 2002 HOH HOH . 
X 6 HOH B 3 2003 2003 HOH HOH . 
X 6 HOH B 4 2004 2004 HOH HOH . 
X 6 HOH B 5 2005 2005 HOH HOH . 
X 6 HOH B 6 2006 2006 HOH HOH . 
Y 6 HOH C 1 2000 2000 HOH HOH . 
Y 6 HOH C 2 2002 2002 HOH HOH . 
Y 6 HOH C 3 2003 2003 HOH HOH . 
Y 6 HOH C 4 2004 2004 HOH HOH . 
Y 6 HOH C 5 2005 2005 HOH HOH . 
Y 6 HOH C 6 2006 2006 HOH HOH . 
Y 6 HOH C 7 2007 2007 HOH HOH . 
Y 6 HOH C 8 2008 2008 HOH HOH . 
Y 6 HOH C 9 2009 2009 HOH HOH . 
Y 6 HOH C 10 2010 2010 HOH HOH . 
Z 6 HOH D 1 2000 2000 HOH HOH . 
Z 6 HOH D 2 2002 2002 HOH HOH . 
Z 6 HOH D 3 2003 2003 HOH HOH . 
Z 6 HOH D 4 2004 2004 HOH HOH . 
Z 6 HOH D 5 2005 2005 HOH HOH . 
Z 6 HOH D 6 2006 2006 HOH HOH . 
Z 6 HOH D 7 2007 2007 HOH HOH . 
Z 6 HOH D 8 2008 2008 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 . . . K 3 47.202 8.597 2.586 1 30.25 ? PB ADP 1003 B 1 
HETATM 2 O O1B ADP . . . K 3 46.309 8.727 1.371 1 54.06 ? O1B ADP 1003 B 1 
HETATM 3 O O2B ADP . . . K 3 48.172 9.729 2.793 1 42.53 ? O2B ADP 1003 B 1 
HETATM 4 O O3B ADP . . . K 3 46.489 8.228 3.867 1 45.51 ? O3B ADP 1003 B 1 
HETATM 5 P PA ADP . . . K 3 47.405 5.792 2.11 1 27.47 ? PA ADP 1003 B 1 
HETATM 6 O O1A ADP . . . K 3 47.53 4.916 3.333 1 44.05 ? O1A ADP 1003 B 1 
HETATM 7 O O2A ADP . . . K 3 46.044 6.041 1.47 1 44 ? O2A ADP 1003 B 1 
HETATM 8 O O3A ADP . . . K 3 48.086 7.256 2.353 1 18.3 ? O3A ADP 1003 B 1 
HETATM 9 O O5' ADP . . . K 3 48.483 5.156 1.064 1 41.55 ? O5' ADP 1003 B 1 
HETATM 10 C C5' ADP . . . K 3 48.356 5.186 -0.362 1 24.45 ? C5' ADP 1003 B 1 
HETATM 11 C C4' ADP . . . K 3 48.774 3.814 -0.858 1 38.51 ? C4' ADP 1003 B 1 
HETATM 12 O O4' ADP . . . K 3 50.195 3.635 -0.66 1 44.95 ? O4' ADP 1003 B 1 
HETATM 13 C C3' ADP . . . K 3 48.044 2.799 -0.015 1 26.45 ? C3' ADP 1003 B 1 
HETATM 14 O O3' ADP . . . K 3 47.632 1.711 -0.842 1 43.46 ? O3' ADP 1003 B 1 
HETATM 15 C C2' ADP . . . K 3 49.106 2.312 0.937 1 39.76 ? C2' ADP 1003 B 1 
HETATM 16 O O2' ADP . . . K 3 48.85 0.952 1.303 1 36.1 ? O2' ADP 1003 B 1 
HETATM 17 C C1' ADP . . . K 3 50.419 2.508 0.186 1 21.62 ? C1' ADP 1003 B 1 
HETATM 18 N N9 ADP . . . K 3 51.487 2.737 1.191 1 33.18 ? N9 ADP 1003 B 1 
HETATM 19 C C8 ADP . . . K 3 51.518 3.724 2.108 1 44.59 ? C8 ADP 1003 B 1 
HETATM 20 N N7 ADP . . . K 3 52.636 3.647 2.883 1 44.24 ? N7 ADP 1003 B 1 
HETATM 21 C C5 ADP . . . K 3 53.347 2.578 2.46 1 35.28 ? C5 ADP 1003 B 1 
HETATM 22 C C6 ADP . . . K 3 54.621 1.913 2.833 1 37.46 ? C6 ADP 1003 B 1 
HETATM 23 N N6 ADP . . . K 3 55.4 2.378 3.847 1 45.16 ? N6 ADP 1003 B 1 
HETATM 24 N N1 ADP . . . K 3 54.988 0.817 2.126 1 29.65 ? N1 ADP 1003 B 1 
HETATM 25 C C2 ADP . . . K 3 54.247 0.341 1.114 1 34.07 ? C2 ADP 1003 B 1 
HETATM 26 N N3 ADP . . . K 3 53.09 0.894 0.718 1 28.72 ? N3 ADP 1003 B 1 
HETATM 27 C C4 ADP . . . K 3 52.593 1.993 1.34 1 30.92 ? C4 ADP 1003 B 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#