data_4YC4
#
_model_server_result.job_id            Gllxs8MgFTIRGSArklSb5Q 
_model_server_result.datetime_utc      '2024-10-12 13:17:05' 
_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          4yc4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1202}' 
#
_entry.id    4YC4 
#
_exptl.entry_id    4YC4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            4YC4 
_cell.length_a            79.414 
_cell.length_b            103.77 
_cell.length_c            78.109 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YC4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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                     4YC4 
_atom_sites.fract_transf_matrix[1][1]    0.012592 
_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]    0.009637 
_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]    0.012803 
_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
B 2 M59 A 1 1201 1 M59 M59 . 
C 3 ADP A 1 1202 2 ADP ADP . 
D 4 HOH A 1 1301 5 HOH HOH . 
D 4 HOH A 2 1302 6 HOH HOH . 
D 4 HOH A 3 1303 4 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 . . . C 3 -11.02 226.18 71.948 0.8 109.11 ? PB ADP 1202 A 1 
HETATM 2 O O1B ADP . . . C 3 -11.525 224.851 71.417 0.8 105.84 ? O1B ADP 1202 A 1 
HETATM 3 O O2B ADP . . . C 3 -12.034 226.955 72.755 0.8 101.94 ? O2B ADP 1202 A 1 
HETATM 4 O O3B ADP . . . C 3 -9.626 226.13 72.542 0.8 95.29 ? O3B ADP 1202 A 1 
HETATM 5 P PA ADP . . . C 3 -10.213 226.398 69.326 0.8 98.93 ? PA ADP 1202 A 1 
HETATM 6 O O1A ADP . . . C 3 -11.34 225.841 68.467 0.8 93.7 ? O1A ADP 1202 A 1 
HETATM 7 O O2A ADP . . . C 3 -9.16 225.469 69.898 0.8 84.02 ? O2A ADP 1202 A 1 
HETATM 8 O O3A ADP . . . C 3 -10.847 227.088 70.631 0.8 96.27 ? O3A ADP 1202 A 1 
HETATM 9 O O5' ADP . . . C 3 -9.53 227.636 68.532 0.8 86.51 ? O5' ADP 1202 A 1 
HETATM 10 C C5' ADP . . . C 3 -9.448 227.645 67.108 0.8 73.24 ? C5' ADP 1202 A 1 
HETATM 11 C C4' ADP . . . C 3 -8.419 226.625 66.624 0.8 68.39 ? C4' ADP 1202 A 1 
HETATM 12 O O4' ADP . . . C 3 -7.361 227.302 65.955 0.8 73.23 ? O4' ADP 1202 A 1 
HETATM 13 C C3' ADP . . . C 3 -7.741 225.803 67.719 0.8 74.18 ? C3' ADP 1202 A 1 
HETATM 14 O O3' ADP . . . C 3 -8.169 224.442 67.685 0.8 75.88 ? O3' ADP 1202 A 1 
HETATM 15 C C2' ADP . . . C 3 -6.271 225.782 67.447 0.8 72.84 ? C2' ADP 1202 A 1 
HETATM 16 O O2' ADP . . . C 3 -5.86 224.409 67.333 0.8 71.5 ? O2' ADP 1202 A 1 
HETATM 17 C C1' ADP . . . C 3 -6.127 226.577 66.155 0.8 74.11 ? C1' ADP 1202 A 1 
HETATM 18 N N9 ADP . . . C 3 -4.955 227.499 66.198 0.8 68.38 ? N9 ADP 1202 A 1 
HETATM 19 C C8 ADP . . . C 3 -4.944 228.771 65.731 0.8 64.06 ? C8 ADP 1202 A 1 
HETATM 20 N N7 ADP . . . C 3 -3.721 229.326 65.91 0.8 63.33 ? N7 ADP 1202 A 1 
HETATM 21 C C5 ADP . . . C 3 -2.941 228.388 66.486 0.8 60.59 ? C5 ADP 1202 A 1 
HETATM 22 C C6 ADP . . . C 3 -1.554 228.316 66.943 0.8 56.91 ? C6 ADP 1202 A 1 
HETATM 23 N N6 ADP . . . C 3 -0.793 229.403 66.784 0.8 61.36 ? N6 ADP 1202 A 1 
HETATM 24 N N1 ADP . . . C 3 -1.071 227.18 67.498 0.8 56.29 ? N1 ADP 1202 A 1 
HETATM 25 C C2 ADP . . . C 3 -1.867 226.109 67.649 0.8 65.66 ? C2 ADP 1202 A 1 
HETATM 26 N N3 ADP . . . C 3 -3.166 226.106 67.251 0.8 67.43 ? N3 ADP 1202 A 1 
HETATM 27 C C4 ADP . . . C 3 -3.745 227.184 66.67 0.8 63.19 ? C4 ADP 1202 A 1 
HETATM 28 H "H5'1" ADP . . . C 3 -9.164 228.642 66.764 0.8 87.88 ? "H5'1" ADP 1202 A 1 
HETATM 29 H "H5'2" ADP . . . C 3 -10.426 227.407 66.684 0.8 87.88 ? "H5'2" ADP 1202 A 1 
HETATM 30 H H4' ADP . . . C 3 -8.914 225.935 65.926 0.8 82.07 ? H4' ADP 1202 A 1 
HETATM 31 H H3' ADP . . . C 3 -7.934 226.254 68.702 0.8 89.02 ? H3' ADP 1202 A 1 
HETATM 32 H HO3' ADP . . . C 3 -7.725 223.947 68.387 0.8 91.06 ? HO3' ADP 1202 A 1 
HETATM 33 H H2' ADP . . . C 3 -5.735 226.289 68.261 0.8 87.41 ? H2' ADP 1202 A 1 
HETATM 34 H HO2' ADP . . . C 3 -6.033 223.95 68.167 0.8 85.8 ? HO2' ADP 1202 A 1 
HETATM 35 H H1' ADP . . . C 3 -5.992 225.863 65.331 0.8 88.93 ? H1' ADP 1202 A 1 
HETATM 36 H H8 ADP . . . C 3 -5.793 229.275 65.286 0.8 76.87 ? H8 ADP 1202 A 1 
HETATM 37 H HN61 ADP . . . C 3 0.171 229.393 67.085 0.8 73.63 ? HN61 ADP 1202 A 1 
HETATM 38 H HN62 ADP . . . C 3 -1.182 230.234 66.362 0.8 73.63 ? HN62 ADP 1202 A 1 
HETATM 39 H H2 ADP . . . C 3 -1.457 225.213 68.097 0.8 78.79 ? H2 ADP 1202 A 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           39 
#