data_3VKH
#
_model_server_result.job_id            5isd2yf3Bmg_As3kehtVYg 
_model_server_result.datetime_utc      '2024-12-20 01:48:42' 
_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          3vkh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":9008}' 
#
_entry.id    3VKH 
#
_exptl.entry_id    3VKH 
_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            3VKH 
_cell.length_a            195.726 
_cell.length_b            228.955 
_cell.length_c            201.168 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VKH 
_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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_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,D,E,F 1 1 
B,G,H,I,J 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
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
#
_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                     3VKH 
_atom_sites.fract_transf_matrix[1][1]    0.005109 
_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]    0.004368 
_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]    0.004971 
_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 2 ADP B 1 9007 9007 ADP ADP . 
H 2 ADP B 1 9008 9008 ADP ADP . 
I 2 ADP B 1 9009 9009 ADP ADP . 
J 2 ADP B 1 9010 9010 ADP ADP . 
#
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 . . . H 2 135.897 119.045 150.18 1 129.3 ? PB ADP 9008 B 1 
HETATM 2 O O1B ADP . . . H 2 134.765 119.228 149.197 1 129.3 ? O1B ADP 9008 B 1 
HETATM 3 O O2B ADP . . . H 2 135.503 118.346 151.458 1 129.3 ? O2B ADP 9008 B 1 
HETATM 4 O O3B ADP . . . H 2 137.174 118.532 149.563 1 129.3 ? O3B ADP 9008 B 1 
HETATM 5 P PA ADP . . . H 2 135.234 121.47 151.479 1 129.3 ? PA ADP 9008 B 1 
HETATM 6 O O1A ADP . . . H 2 135.986 122.064 152.644 1 129.3 ? O1A ADP 9008 B 1 
HETATM 7 O O2A ADP . . . H 2 133.963 120.69 151.727 1 129.3 ? O2A ADP 9008 B 1 
HETATM 8 O O3A ADP . . . H 2 136.266 120.552 150.636 1 129.3 ? O3A ADP 9008 B 1 
HETATM 9 O O5' ADP . . . H 2 134.895 122.665 150.451 1 129.3 ? O5' ADP 9008 B 1 
HETATM 10 C C5' ADP . . . H 2 134.062 123.753 150.86 1 129.3 ? C5' ADP 9008 B 1 
HETATM 11 C C4' ADP . . . H 2 134.14 124.902 149.854 1 129.3 ? C4' ADP 9008 B 1 
HETATM 12 O O4' ADP . . . H 2 133.293 125.981 150.28 1 129.3 ? O4' ADP 9008 B 1 
HETATM 13 C C3' ADP . . . H 2 135.556 125.454 149.715 1 129.3 ? C3' ADP 9008 B 1 
HETATM 14 O O3' ADP . . . H 2 136.051 125.248 148.384 1 129.3 ? O3' ADP 9008 B 1 
HETATM 15 C C2' ADP . . . H 2 135.476 126.931 150.087 1 129.3 ? C2' ADP 9008 B 1 
HETATM 16 O O2' ADP . . . H 2 135.922 127.779 149.016 1 129.3 ? O2' ADP 9008 B 1 
HETATM 17 C C1' ADP . . . H 2 134.021 127.207 150.435 1 129.3 ? C1' ADP 9008 B 1 
HETATM 18 N N9 ADP . . . H 2 133.895 127.722 151.842 1 129.3 ? N9 ADP 9008 B 1 
HETATM 19 C C8 ADP . . . H 2 134.199 127.045 152.979 1 129.3 ? C8 ADP 9008 B 1 
HETATM 20 N N7 ADP . . . H 2 133.965 127.808 154.079 1 129.3 ? N7 ADP 9008 B 1 
HETATM 21 C C5 ADP . . . H 2 133.502 128.997 153.66 1 129.3 ? C5 ADP 9008 B 1 
HETATM 22 C C6 ADP . . . H 2 133.055 130.276 154.296 1 129.3 ? C6 ADP 9008 B 1 
HETATM 23 N N6 ADP . . . H 2 133.061 130.426 155.641 1 129.3 ? N6 ADP 9008 B 1 
HETATM 24 N N1 ADP . . . H 2 132.638 131.292 153.476 1 129.3 ? N1 ADP 9008 B 1 
HETATM 25 C C2 ADP . . . H 2 132.619 131.177 152.12 1 129.3 ? C2 ADP 9008 B 1 
HETATM 26 N N3 ADP . . . H 2 133.014 130.04 151.484 1 129.3 ? N3 ADP 9008 B 1 
HETATM 27 C C4 ADP . . . H 2 133.456 128.939 152.179 1 129.3 ? C4 ADP 9008 B 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    67 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#