data_4UBF
#
_model_server_result.job_id            wx1k1NeGpxnzbFucNlfmEQ 
_model_server_result.datetime_utc      '2024-11-22 22:08:02' 
_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          4ubf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":602}' 
#
_entry.id    4UBF 
#
_exptl.entry_id    4UBF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_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          95.84 
_cell.angle_gamma         90 
_cell.entry_id            4UBF 
_cell.length_a            46.306 
_cell.length_b            245.644 
_cell.length_c            79.399 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4UBF 
_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 trimeric 3 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_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,B,E,F,G,H,I,J,K,Q,R,U 1 1 
C,D,L,M,N,O,P,S,T 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
? 4 G N N 
? 4 I 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
metalc ? metalc1 A OG1 THR 149 A THR 355 1_555 F MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? 
metalc ? metalc2 F MG MG . A MG 601 1_555 G O1B ADP . A ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc3 F MG MG . A MG 601 1_555 Q O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc4 H MG MG . A MG 603 1_555 Q O HOH . A HOH 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? 
metalc ? metalc5 H MG MG . A MG 603 1_555 Q O HOH . A HOH 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc6 B OG1 THR 149 B THR 355 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? 
metalc ? metalc7 I O1B ADP . B ADP 601 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc8 I O2B ADP . B ADP 601 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc9 I O3A ADP . B ADP 601 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? 
metalc ? metalc10 J MG MG . B MG 602 1_555 R O HOH . B HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc11 K MG MG . B MG 603 1_555 R O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
metalc ? metalc12 K MG MG . B MG 603 1_555 R O HOH . B HOH 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? 
metalc ? metalc13 L MG MG . C MG 601 1_555 S O HOH . C HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc14 O MG MG . D MG 601 1_555 P O1B ADP . D ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc15 O MG MG . D MG 601 1_555 P O2B ADP . D ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? 
metalc ? metalc16 O MG MG . D MG 601 1_555 T O HOH . D HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc17 O MG MG . D MG 601 1_555 T O HOH . D HOH 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc18 O MG MG . D MG 601 1_555 T O HOH . D HOH 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? 
#
_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                     4UBF 
_atom_sites.fract_transf_matrix[1][1]    0.021595 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002207 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004071 
_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]    0.01266 
_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
F 3 MG A 1 601 602 MG MG . 
G 4 ADP A 1 602 601 ADP ADP . 
H 3 MG A 1 603 2 MG MG . 
I 4 ADP B 1 601 601 ADP ADP . 
J 3 MG B 1 602 1 MG MG . 
K 3 MG B 1 603 4 MG MG . 
L 3 MG C 1 601 602 MG MG . 
M 4 ADP C 1 602 601 ADP ADP . 
N 3 MG C 1 603 3 MG MG . 
O 3 MG D 1 601 602 MG MG . 
P 4 ADP D 1 602 601 ADP ADP . 
Q 5 HOH A 1 701 6 HOH HOH . 
Q 5 HOH A 2 702 49 HOH HOH . 
Q 5 HOH A 3 703 104 HOH HOH . 
Q 5 HOH A 4 704 84 HOH HOH . 
Q 5 HOH A 5 705 109 HOH HOH . 
Q 5 HOH A 6 706 71 HOH HOH . 
Q 5 HOH A 7 707 66 HOH HOH . 
Q 5 HOH A 8 708 15 HOH HOH . 
Q 5 HOH A 9 709 79 HOH HOH . 
Q 5 HOH A 10 710 77 HOH HOH . 
Q 5 HOH A 11 711 42 HOH HOH . 
Q 5 HOH A 12 712 80 HOH HOH . 
Q 5 HOH A 13 713 82 HOH HOH . 
Q 5 HOH A 14 714 16 HOH HOH . 
R 5 HOH B 1 701 92 HOH HOH . 
R 5 HOH B 2 702 89 HOH HOH . 
R 5 HOH B 3 703 54 HOH HOH . 
R 5 HOH B 4 704 10 HOH HOH . 
R 5 HOH B 5 705 105 HOH HOH . 
R 5 HOH B 6 706 26 HOH HOH . 
R 5 HOH B 7 707 29 HOH HOH . 
R 5 HOH B 8 708 5 HOH HOH . 
R 5 HOH B 9 709 81 HOH HOH . 
R 5 HOH B 10 710 60 HOH HOH . 
R 5 HOH B 11 711 12 HOH HOH . 
R 5 HOH B 12 712 23 HOH HOH . 
R 5 HOH B 13 713 88 HOH HOH . 
R 5 HOH B 14 714 87 HOH HOH . 
R 5 HOH B 15 715 106 HOH HOH . 
R 5 HOH B 16 716 86 HOH HOH . 
R 5 HOH B 17 717 3 HOH HOH . 
R 5 HOH B 18 718 85 HOH HOH . 
R 5 HOH B 19 719 111 HOH HOH . 
R 5 HOH B 20 720 9 HOH HOH . 
S 5 HOH C 1 701 21 HOH HOH . 
S 5 HOH C 2 702 40 HOH HOH . 
S 5 HOH C 3 703 28 HOH HOH . 
S 5 HOH C 4 704 41 HOH HOH . 
S 5 HOH C 5 705 38 HOH HOH . 
S 5 HOH C 6 706 39 HOH HOH . 
S 5 HOH C 7 707 75 HOH HOH . 
S 5 HOH C 8 708 73 HOH HOH . 
S 5 HOH C 9 709 95 HOH HOH . 
S 5 HOH C 10 710 97 HOH HOH . 
S 5 HOH C 11 711 27 HOH HOH . 
S 5 HOH C 12 712 61 HOH HOH . 
S 5 HOH C 13 713 93 HOH HOH . 
S 5 HOH C 14 714 94 HOH HOH . 
S 5 HOH C 15 715 51 HOH HOH . 
S 5 HOH C 16 716 48 HOH HOH . 
S 5 HOH C 17 717 112 HOH HOH . 
T 5 HOH D 1 701 13 HOH HOH . 
T 5 HOH D 2 702 44 HOH HOH . 
T 5 HOH D 3 703 102 HOH HOH . 
T 5 HOH D 4 704 22 HOH HOH . 
T 5 HOH D 5 705 101 HOH HOH . 
T 5 HOH D 6 706 45 HOH HOH . 
T 5 HOH D 7 707 62 HOH HOH . 
T 5 HOH D 8 708 53 HOH HOH . 
T 5 HOH D 9 709 69 HOH HOH . 
T 5 HOH D 10 710 14 HOH HOH . 
T 5 HOH D 11 711 100 HOH HOH . 
T 5 HOH D 12 712 8 HOH HOH . 
T 5 HOH D 13 713 68 HOH HOH . 
T 5 HOH D 14 714 59 HOH HOH . 
T 5 HOH D 15 715 17 HOH HOH . 
T 5 HOH D 16 716 43 HOH HOH . 
U 5 HOH P 1 801 110 HOH HOH . 
U 5 HOH P 2 802 103 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 -12.825 -51.993 44.256 1 69.1 ? PB ADP 602 C 1 
HETATM 2 O O1B ADP . . . M 4 -13.093 -52.298 42.803 1 63 ? O1B ADP 602 C 1 
HETATM 3 O O2B ADP . . . M 4 -13.233 -53.109 45.186 1 66.93 ? O2B ADP 602 C 1 
HETATM 4 O O3B ADP . . . M 4 -13.292 -50.627 44.696 1 59.6 ? O3B ADP 602 C 1 
HETATM 5 P PA ADP . . . M 4 -10.466 -51.789 45.776 1 69.98 ? PA ADP 602 C 1 
HETATM 6 O O1A ADP . . . M 4 -9.532 -52.966 45.934 1 75.04 ? O1A ADP 602 C 1 
HETATM 7 O O2A ADP . . . M 4 -11.541 -51.567 46.813 1 62.19 ? O2A ADP 602 C 1 
HETATM 8 O O3A ADP . . . M 4 -11.213 -51.941 44.355 1 66.13 ? O3A ADP 602 C 1 
HETATM 9 O O5' ADP . . . M 4 -9.559 -50.468 45.664 1 71.77 ? O5' ADP 602 C 1 
HETATM 10 C C5' ADP . . . M 4 -9.111 -49.954 44.413 1 74.15 ? C5' ADP 602 C 1 
HETATM 11 C C4' ADP . . . M 4 -7.682 -49.464 44.62 1 78.31 ? C4' ADP 602 C 1 
HETATM 12 O O4' ADP . . . M 4 -7.682 -48.269 45.406 1 81.32 ? O4' ADP 602 C 1 
HETATM 13 C C3' ADP . . . M 4 -6.861 -50.495 45.378 1 58.56 ? C3' ADP 602 C 1 
HETATM 14 O O3' ADP . . . M 4 -5.574 -50.611 44.765 1 48.78 ? O3' ADP 602 C 1 
HETATM 15 C C2' ADP . . . M 4 -6.702 -49.925 46.773 1 64.8 ? C2' ADP 602 C 1 
HETATM 16 O O2' ADP . . . M 4 -5.428 -50.259 47.329 1 68.57 ? O2' ADP 602 C 1 
HETATM 17 C C1' ADP . . . M 4 -6.864 -48.426 46.57 1 70.98 ? C1' ADP 602 C 1 
HETATM 18 N N9 ADP . . . M 4 -7.522 -47.786 47.738 1 70.37 ? N9 ADP 602 C 1 
HETATM 19 C C8 ADP . . . M 4 -8.838 -47.818 48.017 1 63.02 ? C8 ADP 602 C 1 
HETATM 20 N N7 ADP . . . M 4 -9.119 -47.131 49.154 1 61.46 ? N7 ADP 602 C 1 
HETATM 21 C C5 ADP . . . M 4 -7.958 -46.64 49.626 1 65.3 ? C5 ADP 602 C 1 
HETATM 22 C C6 ADP . . . M 4 -7.534 -45.822 50.789 1 66.22 ? C6 ADP 602 C 1 
HETATM 23 N N6 ADP . . . M 4 -8.431 -45.379 51.704 1 67.03 ? N6 ADP 602 C 1 
HETATM 24 N N1 ADP . . . M 4 -6.22 -45.533 50.907 1 59.54 ? N1 ADP 602 C 1 
HETATM 25 C C2 ADP . . . M 4 -5.316 -45.966 50.008 1 58.45 ? C2 ADP 602 C 1 
HETATM 26 N N3 ADP . . . M 4 -5.629 -46.709 48.932 1 62.71 ? N3 ADP 602 C 1 
HETATM 27 C C4 ADP . . . M 4 -6.91 -47.074 48.688 1 67.82 ? C4 ADP 602 C 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#