data_5I0I
#
_model_server_result.job_id            zcSwQhR_xs8GAiu3lH4OfQ 
_model_server_result.datetime_utc      '2025-02-05 08:58:41' 
_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          5i0i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":903}' 
#
_entry.id    5I0I 
#
_exptl.entry_id    5I0I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          9 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            5I0I 
_cell.length_a            113.95 
_cell.length_b            173.41 
_cell.length_c            178.75 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5I0I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 software_defined_assembly 1 
PISA trimeric 3 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,C,E,G,H,I,J,K,L,M,N,O,U,W 1 1 
B,D,F,P,Q,R,S,T,V,X 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
? 9 J N N 
? 9 R 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 162 A THR 164 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc2 A OG SER 217 A SER 219 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc3 H MG MG . A MG 902 1_555 I O1 VO4 . A VO4 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc4 H MG MG . A MG 902 1_555 J O1B ADP . A ADP 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc5 H MG MG . A MG 902 1_555 W O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc6 H MG MG . A MG 902 1_555 W O HOH . A HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? 
metalc ? metalc7 I V VO4 . A VO4 903 1_555 J O3B ADP . A ADP 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc8 B OG1 THR 162 B THR 164 1_555 Q MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc9 B OG SER 217 B SER 219 1_555 Q MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc10 Q MG MG . B MG 902 1_555 R O2B ADP . B ADP 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc11 Q MG MG . B MG 902 1_555 S O1 VO4 . B VO4 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc12 Q MG MG . B MG 902 1_555 X O HOH . B HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
metalc ? metalc13 Q MG MG . B MG 902 1_555 X O HOH . B HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc14 R O3B ADP . B ADP 903 1_555 S V VO4 . B VO4 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? 
#
_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                     5I0I 
_atom_sites.fract_transf_matrix[1][1]    0.008776 
_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]    0.005767 
_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]    0.005594 
_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
G 6 MPO A 1 901 1 MPO MPO . 
H 7 MG A 1 902 1 MG MG . 
I 8 VO4 A 1 903 998 VO4 VO4 . 
J 9 ADP A 1 904 999 ADP ADP . 
K 10 SO4 A 1 905 2 SO4 SO4 . 
L 10 SO4 A 1 906 5 SO4 SO4 . 
M 10 SO4 A 1 907 6 SO4 SO4 . 
N 10 SO4 A 1 908 7 SO4 SO4 . 
O 10 SO4 A 1 909 8 SO4 SO4 . 
P 6 MPO B 1 901 2 MPO MPO . 
Q 7 MG B 1 902 2 MG MG . 
R 9 ADP B 1 903 999 ADP ADP . 
S 8 VO4 B 1 904 998 VO4 VO4 . 
T 10 SO4 B 1 905 3 SO4 SO4 . 
U 10 SO4 C 1 201 1 SO4 SO4 . 
V 10 SO4 E 1 201 4 SO4 SO4 . 
W 11 HOH A 1 1001 2 HOH HOH . 
W 11 HOH A 2 1002 11 HOH HOH . 
W 11 HOH A 3 1003 27 HOH HOH . 
W 11 HOH A 4 1004 24 HOH HOH . 
W 11 HOH A 5 1005 14 HOH HOH . 
W 11 HOH A 6 1006 1 HOH HOH . 
W 11 HOH A 7 1007 32 HOH HOH . 
W 11 HOH A 8 1008 12 HOH HOH . 
W 11 HOH A 9 1009 23 HOH HOH . 
W 11 HOH A 10 1010 33 HOH HOH . 
W 11 HOH A 11 1011 30 HOH HOH . 
X 11 HOH B 1 1001 31 HOH HOH . 
X 11 HOH B 2 1002 6 HOH HOH . 
X 11 HOH B 3 1003 3 HOH HOH . 
X 11 HOH B 4 1004 26 HOH HOH . 
X 11 HOH B 5 1005 29 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 . . . R 9 8.348 -10.472 -33.737 1 106.02 ? PB ADP 903 B 1 
HETATM 2 O O1B ADP . . . R 9 8.034 -11.772 -34.472 1 103.83 ? O1B ADP 903 B 1 
HETATM 3 O O2B ADP . . . R 9 7.358 -10.094 -32.671 1 103.84 ? O2B ADP 903 B 1 
HETATM 4 O O3B ADP . . . R 9 9.718 -10.529 -33.254 1 103.72 ? O3B ADP 903 B 1 
HETATM 5 P PA ADP . . . R 9 7.855 -7.903 -34.992 1 116.66 ? PA ADP 903 B 1 
HETATM 6 O O1A ADP . . . R 9 6.381 -8.054 -34.898 1 116.47 ? O1A ADP 903 B 1 
HETATM 7 O O2A ADP . . . R 9 8.373 -6.943 -33.898 1 118.61 ? O2A ADP 903 B 1 
HETATM 8 O O3A ADP . . . R 9 8.504 -9.348 -34.853 1 112.11 ? O3A ADP 903 B 1 
HETATM 9 O O5' ADP . . . R 9 8.442 -7.377 -36.36 1 117.48 ? O5' ADP 903 B 1 
HETATM 10 C C5' ADP . . . R 9 9.789 -6.876 -36.464 1 119.05 ? C5' ADP 903 B 1 
HETATM 11 C C4' ADP . . . R 9 9.834 -5.781 -37.497 1 119.28 ? C4' ADP 903 B 1 
HETATM 12 O O4' ADP . . . R 9 9.337 -6.294 -38.747 1 119.2 ? O4' ADP 903 B 1 
HETATM 13 C C3' ADP . . . R 9 8.983 -4.557 -37.186 1 118.26 ? C3' ADP 903 B 1 
HETATM 14 O O3' ADP . . . R 9 9.776 -3.639 -36.447 1 117.72 ? O3' ADP 903 B 1 
HETATM 15 C C2' ADP . . . R 9 8.618 -4.034 -38.579 1 122.57 ? C2' ADP 903 B 1 
HETATM 16 O O2' ADP . . . R 9 9.594 -3.184 -39.176 1 129.06 ? O2' ADP 903 B 1 
HETATM 17 C C1' ADP . . . R 9 8.553 -5.318 -39.403 1 121.22 ? C1' ADP 903 B 1 
HETATM 18 N N9 ADP . . . R 9 7.212 -5.848 -39.63 1 120.48 ? N9 ADP 903 B 1 
HETATM 19 C C8 ADP . . . R 9 6.633 -6.945 -39.044 1 120.3 ? C8 ADP 903 B 1 
HETATM 20 N N7 ADP . . . R 9 5.432 -7.22 -39.493 1 119.56 ? N7 ADP 903 B 1 
HETATM 21 C C5 ADP . . . R 9 5.203 -6.234 -40.441 1 121.7 ? C5 ADP 903 B 1 
HETATM 22 C C6 ADP . . . R 9 4.119 -5.982 -41.301 1 123.77 ? C6 ADP 903 B 1 
HETATM 23 N N6 ADP . . . R 9 2.974 -6.666 -41.262 1 123.18 ? N6 ADP 903 B 1 
HETATM 24 N N1 ADP . . . R 9 4.239 -4.958 -42.18 1 126.86 ? N1 ADP 903 B 1 
HETATM 25 C C2 ADP . . . R 9 5.361 -4.227 -42.173 1 127.44 ? C2 ADP 903 B 1 
HETATM 26 N N3 ADP . . . R 9 6.437 -4.355 -41.391 1 125.48 ? N3 ADP 903 B 1 
HETATM 27 C C4 ADP . . . R 9 6.296 -5.385 -40.541 1 122.09 ? C4 ADP 903 B 1 
#
_model_server_stats.io_time_ms              35 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#