data_5SUP
#
_model_server_result.job_id            RXM1eG-fQaEhkoLrUao0dg 
_model_server_result.datetime_utc      '2025-04-25 09:15:48' 
_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          5sup 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":2000}' 
#
_entry.id    5SUP 
#
_exptl.entry_id    5SUP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            5SUP 
_cell.length_a            99.346 
_cell.length_b            99.346 
_cell.length_c            247.469 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5SUP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
PISA trimeric 3 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,G,J,K,L,S 1 1 
B,D,I,M,N,O,T 2 1 
C,F,H,P,Q,R,U 3 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 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
covale ? covale1 A NZ LYS 357 A LYS 413 1_555 A OE2 GLU 358 A GLU 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? 
metalc ? metalc1 J O2B ADP . A ADP 1000 1_555 K BE BEF . A BEF 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.625 ? 
metalc ? metalc2 J O1B ADP . A ADP 1000 1_555 L MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc3 L MG MG . A MG 1002 1_555 S O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc4 L MG MG . A MG 1002 1_555 S O HOH . A HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc5 L MG MG . A MG 1002 1_555 S O HOH . A HOH 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
metalc ? metalc6 L MG MG . A MG 1002 1_555 S O HOH . A HOH 1111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? 
metalc ? metalc7 M O3B ADP . B ADP 2000 1_555 N BE BEF . B BEF 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.569 ? 
metalc ? metalc8 M O2B ADP . B ADP 2000 1_555 O MG MG . B MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc9 O MG MG . B MG 2002 1_555 T O HOH . B HOH 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc10 O MG MG . B MG 2002 1_555 T O HOH . B HOH 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc11 O MG MG . B MG 2002 1_555 T O HOH . B HOH 2106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc12 O MG MG . B MG 2002 1_555 T O HOH . B HOH 2108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? 
metalc ? metalc13 P O2B ADP . C ADP 3000 1_555 Q BE BEF . C BEF 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? 
metalc ? metalc14 P O1B ADP . C ADP 3000 1_555 R MG MG . C MG 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc15 R MG MG . C MG 3002 1_555 U O HOH . C HOH 3101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc16 R MG MG . C MG 3002 1_555 U O HOH . C HOH 3102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc17 R MG MG . C MG 3002 1_555 U O HOH . C HOH 3104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc18 R MG MG . C MG 3002 1_555 U O HOH . C HOH 3105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
#
_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                     5SUP 
_atom_sites.fract_transf_matrix[1][1]    0.010066 
_atom_sites.fract_transf_matrix[1][2]    0.005812 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011623 
_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]    0.004041 
_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
J 4 ADP A 1 1000 1000 ADP ADP . 
K 5 BEF A 1 1001 1001 BEF BEF . 
L 6 MG A 1 1002 1002 MG MG . 
M 4 ADP B 1 2000 2000 ADP ADP . 
N 5 BEF B 1 2001 2001 BEF BEF . 
O 6 MG B 1 2002 2002 MG MG . 
P 4 ADP C 1 3000 3000 ADP ADP . 
Q 5 BEF C 1 3001 3001 BEF BEF . 
R 6 MG C 1 3002 3002 MG MG . 
S 7 HOH A 1 1101 20 HOH HOH . 
S 7 HOH A 2 1102 5 HOH HOH . 
S 7 HOH A 3 1103 21 HOH HOH . 
S 7 HOH A 4 1104 6 HOH HOH . 
S 7 HOH A 5 1105 19 HOH HOH . 
S 7 HOH A 6 1106 16 HOH HOH . 
S 7 HOH A 7 1107 7 HOH HOH . 
S 7 HOH A 8 1108 22 HOH HOH . 
S 7 HOH A 9 1109 10 HOH HOH . 
S 7 HOH A 10 1110 18 HOH HOH . 
S 7 HOH A 11 1111 8 HOH HOH . 
S 7 HOH A 12 1112 9 HOH HOH . 
S 7 HOH A 13 1113 23 HOH HOH . 
T 7 HOH B 1 2101 3 HOH HOH . 
T 7 HOH B 2 2102 17 HOH HOH . 
T 7 HOH B 3 2103 2 HOH HOH . 
T 7 HOH B 4 2104 26 HOH HOH . 
T 7 HOH B 5 2105 25 HOH HOH . 
T 7 HOH B 6 2106 1 HOH HOH . 
T 7 HOH B 7 2107 24 HOH HOH . 
T 7 HOH B 8 2108 4 HOH HOH . 
T 7 HOH B 9 2109 27 HOH HOH . 
U 7 HOH C 1 3101 12 HOH HOH . 
U 7 HOH C 2 3102 11 HOH HOH . 
U 7 HOH C 3 3103 15 HOH HOH . 
U 7 HOH C 4 3104 13 HOH HOH . 
U 7 HOH C 5 3105 14 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 . . . M 4 29.022 48.808 68.834 1 36.49 ? PB ADP 2000 B 1 
HETATM 2 O O1B ADP . . . M 4 29.357 47.595 68.004 1 37 ? O1B ADP 2000 B 1 
HETATM 3 O O2B ADP . . . M 4 30.072 49.894 68.813 1 41.03 ? O2B ADP 2000 B 1 
HETATM 4 O O3B ADP . . . M 4 27.602 49.294 68.661 1 46.15 ? O3B ADP 2000 B 1 
HETATM 5 P PA ADP . . . M 4 29.645 49.046 71.581 1 42.17 ? PA ADP 2000 B 1 
HETATM 6 O O1A ADP . . . M 4 31.126 49.234 71.37 1 38.43 ? O1A ADP 2000 B 1 
HETATM 7 O O2A ADP . . . M 4 28.73 50.224 71.82 1 39.99 ? O2A ADP 2000 B 1 
HETATM 8 O O3A ADP . . . M 4 29.05 48.223 70.332 1 46.87 ? O3A ADP 2000 B 1 
HETATM 9 O O5' ADP . . . M 4 29.436 47.971 72.757 1 44.81 ? O5' ADP 2000 B 1 
HETATM 10 C C5' ADP . . . M 4 28.114 47.633 73.162 1 48.28 ? C5' ADP 2000 B 1 
HETATM 11 C C4' ADP . . . M 4 28.1 47.248 74.634 1 53.64 ? C4' ADP 2000 B 1 
HETATM 12 O O4' ADP . . . M 4 28.701 45.971 74.831 1 54.21 ? O4' ADP 2000 B 1 
HETATM 13 C C3' ADP . . . M 4 28.881 48.256 75.463 1 52.65 ? C3' ADP 2000 B 1 
HETATM 14 O O3' ADP . . . M 4 28.012 48.828 76.443 1 46.72 ? O3' ADP 2000 B 1 
HETATM 15 C C2' ADP . . . M 4 29.978 47.48 76.153 1 50.39 ? C2' ADP 2000 B 1 
HETATM 16 O O2' ADP . . . M 4 29.995 47.809 77.544 1 53.2 ? O2' ADP 2000 B 1 
HETATM 17 C C1' ADP . . . M 4 29.589 46.026 75.946 1 53.57 ? C1' ADP 2000 B 1 
HETATM 18 N N9 ADP . . . M 4 30.772 45.191 75.656 1 45.34 ? N9 ADP 2000 B 1 
HETATM 19 C C8 ADP . . . M 4 31.648 45.365 74.65 1 47.29 ? C8 ADP 2000 B 1 
HETATM 20 N N7 ADP . . . M 4 32.61 44.408 74.68 1 46.34 ? N7 ADP 2000 B 1 
HETATM 21 C C5 ADP . . . M 4 32.344 43.603 75.726 1 46.43 ? C5 ADP 2000 B 1 
HETATM 22 C C6 ADP . . . M 4 32.953 42.4 76.335 1 50.68 ? C6 ADP 2000 B 1 
HETATM 23 N N6 ADP . . . M 4 34.075 41.849 75.814 1 49.64 ? N6 ADP 2000 B 1 
HETATM 24 N N1 ADP . . . M 4 32.351 41.872 77.426 1 51.8 ? N1 ADP 2000 B 1 
HETATM 25 C C2 ADP . . . M 4 31.236 42.409 77.954 1 49.43 ? C2 ADP 2000 B 1 
HETATM 26 N N3 ADP . . . M 4 30.631 43.499 77.455 1 55.29 ? N3 ADP 2000 B 1 
HETATM 27 C C4 ADP . . . M 4 31.13 44.126 76.364 1 43.75 ? C4 ADP 2000 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           27 
#