data_3VKG
#
_model_server_result.job_id            VLtO9ye7VIh93UgUegWAPA 
_model_server_result.datetime_utc      '2025-03-06 23:31:00' 
_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          3vkg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":9003}' 
#
_entry.id    3VKG 
#
_exptl.entry_id    3VKG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_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            3VKG 
_cell.length_a            204.256 
_cell.length_b            221.806 
_cell.length_c            192.898 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VKG 
_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
? dimeric 2 author_defined_assembly 1 
PISA monomeric 1 software_defined_assembly 2 
PISA monomeric 1 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,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 1 1 
A,C,D,E,F,G,H,I,R 2 1 
B,J,K,L,M,N,O,P,Q,S 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
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M 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 I MG MG . A MG 1 1_555 A OG1 THR 920 A THR 2283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc2 I MG MG . A MG 1 1_555 A OE2 GLU 1033 A GLU 2396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc3 I MG MG . A MG 1 1_555 D O1B ADP . A ADP 9002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? 
metalc ? metalc4 I MG MG . A MG 1 1_555 D O3B ADP . A ADP 9002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? 
metalc ? metalc5 P MG MG . B MG 2 1_555 J O3B ADP . B ADP 9007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? 
metalc ? metalc6 P MG MG . B MG 2 1_555 J O2B ADP . B ADP 9007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? 
metalc ? metalc7 Q MG MG . B MG 3 1_555 B OG1 THR 920 B THR 2283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc8 Q MG MG . B MG 3 1_555 B OE2 GLU 1033 B GLU 2396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? 
metalc ? metalc9 Q MG MG . B MG 3 1_555 K O3B ADP . B ADP 9008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? 
#
_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                     3VKG 
_atom_sites.fract_transf_matrix[1][1]    0.004896 
_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]    0.004508 
_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]    0.005184 
_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
C 2 ADP A 1 9001 9001 ADP ADP . 
D 2 ADP A 1 9002 9002 ADP ADP . 
E 2 ADP A 1 9003 9003 ADP ADP . 
F 2 ADP A 1 9004 9004 ADP ADP . 
G 3 SPM A 1 9012 9012 SPM SPM . 
H 3 SPM A 1 9016 9016 SPM SPM . 
I 4 MG A 1 1 1 MG MG . 
J 2 ADP B 1 9007 9007 ADP ADP . 
K 2 ADP B 1 9008 9008 ADP ADP . 
L 2 ADP B 1 9009 9009 ADP ADP . 
M 2 ADP B 1 9010 9010 ADP ADP . 
N 3 SPM B 1 9018 9018 SPM SPM . 
O 3 SPM B 1 9022 9022 SPM SPM . 
P 4 MG B 1 2 2 MG MG . 
Q 4 MG B 1 3 3 MG MG . 
R 5 HOH A 1 13 13 HOH HOH . 
R 5 HOH A 2 14 14 HOH HOH . 
R 5 HOH A 3 15 15 HOH HOH . 
R 5 HOH A 4 16 16 HOH HOH . 
R 5 HOH A 5 17 17 HOH HOH . 
R 5 HOH A 6 18 18 HOH HOH . 
R 5 HOH A 7 19 19 HOH HOH . 
R 5 HOH A 8 20 20 HOH HOH . 
R 5 HOH A 9 21 21 HOH HOH . 
R 5 HOH A 10 22 22 HOH HOH . 
R 5 HOH A 11 23 23 HOH HOH . 
R 5 HOH A 12 25 25 HOH HOH . 
R 5 HOH A 13 27 27 HOH HOH . 
R 5 HOH A 14 28 28 HOH HOH . 
R 5 HOH A 15 30 30 HOH HOH . 
R 5 HOH A 16 32 32 HOH HOH . 
R 5 HOH A 17 33 33 HOH HOH . 
R 5 HOH A 18 35 35 HOH HOH . 
R 5 HOH A 19 36 36 HOH HOH . 
R 5 HOH A 20 37 37 HOH HOH . 
R 5 HOH A 21 38 38 HOH HOH . 
R 5 HOH A 22 41 41 HOH HOH . 
R 5 HOH A 23 42 42 HOH HOH . 
S 5 HOH B 1 1 1 HOH HOH . 
S 5 HOH B 2 4 4 HOH HOH . 
S 5 HOH B 3 5 5 HOH HOH . 
S 5 HOH B 4 6 6 HOH HOH . 
S 5 HOH B 5 7 7 HOH HOH . 
S 5 HOH B 6 8 8 HOH HOH . 
S 5 HOH B 7 9 9 HOH HOH . 
S 5 HOH B 8 10 10 HOH HOH . 
S 5 HOH B 9 11 11 HOH HOH . 
S 5 HOH B 10 12 12 HOH HOH . 
S 5 HOH B 11 24 24 HOH HOH . 
S 5 HOH B 12 26 26 HOH HOH . 
S 5 HOH B 13 29 29 HOH HOH . 
S 5 HOH B 14 31 31 HOH HOH . 
S 5 HOH B 15 34 34 HOH HOH . 
S 5 HOH B 16 39 39 HOH HOH . 
S 5 HOH B 17 40 40 HOH HOH . 
S 5 HOH B 18 4731 2 HOH HOH . 
S 5 HOH B 19 4732 3 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 . . . E 2 71.62 106.801 118.145 1 49.68 ? PB ADP 9003 A 1 
HETATM 2 O O1B ADP . . . E 2 72.021 106.383 116.746 1 50.03 ? O1B ADP 9003 A 1 
HETATM 3 O O2B ADP . . . E 2 72.728 107.422 118.942 1 48.17 ? O2B ADP 9003 A 1 
HETATM 4 O O3B ADP . . . E 2 70.337 107.56 118.214 1 50.2 ? O3B ADP 9003 A 1 
HETATM 5 P PA ADP . . . E 2 70.836 105.231 120.437 1 47.41 ? PA ADP 9003 A 1 
HETATM 6 O O1A ADP . . . E 2 69.544 104.514 120.479 1 52.87 ? O1A ADP 9003 A 1 
HETATM 7 O O2A ADP . . . E 2 70.894 106.56 121.098 1 52.81 ? O2A ADP 9003 A 1 
HETATM 8 O O3A ADP . . . E 2 71.248 105.383 118.874 1 49.63 ? O3A ADP 9003 A 1 
HETATM 9 O O5' ADP . . . E 2 71.893 104.178 121.105 1 49.03 ? O5' ADP 9003 A 1 
HETATM 10 C C5' ADP . . . E 2 72.894 104.467 122.128 1 48.34 ? C5' ADP 9003 A 1 
HETATM 11 C C4' ADP . . . E 2 73.073 103.215 123.052 1 47.12 ? C4' ADP 9003 A 1 
HETATM 12 O O4' ADP . . . E 2 74.105 103.389 124.077 1 47.98 ? O4' ADP 9003 A 1 
HETATM 13 C C3' ADP . . . E 2 71.793 102.942 123.797 1 46.32 ? C3' ADP 9003 A 1 
HETATM 14 O O3' ADP . . . E 2 71.257 101.674 123.39 1 44.96 ? O3' ADP 9003 A 1 
HETATM 15 C C2' ADP . . . E 2 72.111 102.977 125.302 1 45.42 ? C2' ADP 9003 A 1 
HETATM 16 O O2' ADP . . . E 2 71.761 101.781 125.952 1 48.36 ? O2' ADP 9003 A 1 
HETATM 17 C C1' ADP . . . E 2 73.602 103.231 125.409 1 45.68 ? C1' ADP 9003 A 1 
HETATM 18 N N9 ADP . . . E 2 73.985 104.366 126.335 1 45.08 ? N9 ADP 9003 A 1 
HETATM 19 C C8 ADP . . . E 2 74.811 105.398 126.038 1 44.49 ? C8 ADP 9003 A 1 
HETATM 20 N N7 ADP . . . E 2 74.944 106.241 127.101 1 43.88 ? N7 ADP 9003 A 1 
HETATM 21 C C5 ADP . . . E 2 74.202 105.755 128.104 1 44.21 ? C5 ADP 9003 A 1 
HETATM 22 C C6 ADP . . . E 2 73.887 106.146 129.507 1 44.06 ? C6 ADP 9003 A 1 
HETATM 23 N N6 ADP . . . E 2 74.422 107.266 130.044 1 44.97 ? N6 ADP 9003 A 1 
HETATM 24 N N1 ADP . . . E 2 73.043 105.341 130.236 1 43.1 ? N1 ADP 9003 A 1 
HETATM 25 C C2 ADP . . . E 2 72.491 104.215 129.731 1 41.93 ? C2 ADP 9003 A 1 
HETATM 26 N N3 ADP . . . E 2 72.741 103.806 128.458 1 43.08 ? N3 ADP 9003 A 1 
HETATM 27 C C4 ADP . . . E 2 73.567 104.515 127.608 1 44.32 ? C4 ADP 9003 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    67 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#