data_1V8Y
#
_model_server_result.job_id            5n46B93wljdya9YDMjzSzg 
_model_server_result.datetime_utc      '2024-10-18 23:32:52' 
_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          1v8y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":619}' 
#
_entry.id    1V8Y 
#
_exptl.entry_id    1V8Y 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ADENOSINE-5-DIPHOSPHORIBOSE 
_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         120 
_cell.entry_id            1V8Y 
_cell.length_a            49.655 
_cell.length_b            49.655 
_cell.length_c            118.473 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1V8Y 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 118.473 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OE1 GLU 44 A GLU 44 6_655 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
metalc ? metalc2 A OE2 GLU 70 A GLU 70 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc3 A OE1 GLU 82 A GLU 82 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc4 B ZN ZN . A ZN 300 1_555 E O HOH . A HOH 658 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc5 B ZN ZN . A ZN 300 1_555 E O HOH . A HOH 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
#
_chem_comp.formula           'C15 H23 N5 O14 P2' 
_chem_comp.formula_weight    559.316 
_chem_comp.id                APR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ADENOSINE-5-DIPHOSPHORIBOSE 
_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
N1 C2 APR sing 13 n y 
N1 C6 APR doub 14 n y 
C2 N3 APR doub 15 n y 
C2 H2 APR sing 16 n n 
N3 C4 APR sing 17 n y 
C4 C5 APR doub 18 n y 
C4 N9 APR sing 19 n y 
C5 C6 APR sing 20 n y 
C5 N7 APR sing 21 n y 
C6 N6 APR sing 22 n n 
N6 H61 APR sing 23 n n 
N6 H62 APR sing 24 n n 
N7 C8 APR doub 25 n y 
C8 N9 APR sing 26 n y 
C8 H8 APR sing 27 n n 
N9 C1' APR sing 28 n n 
C1' C2' APR sing 29 n n 
C1' O4' APR sing 30 n n 
C1' "H'1" APR sing 31 n n 
C2' O2' APR sing 32 n n 
C2' C3' APR sing 33 n n 
C2' "H'2" APR sing 34 n n 
O2' "HO'2" APR sing 35 n n 
C3' O3' APR sing 36 n n 
C3' C4' APR sing 37 n n 
C3' "H'3" APR sing 38 n n 
O3' "HO'3" APR sing 39 n n 
O4' C4' APR sing 40 n n 
C4' C5' APR sing 41 n n 
C4' "H'4" APR sing 42 n n 
C5' O5' APR sing 43 n n 
C5' "H5'1" APR sing 44 n n 
C5' "H5'2" APR sing 45 n n 
O5' PA APR sing 46 n n 
PA O1A APR doub 47 n n 
PA O2A APR sing 48 n n 
PA O3A APR sing 49 n n 
O2A HOA2 APR sing 50 n n 
O3A PB APR sing 51 n n 
PB O1B APR doub 52 n n 
PB O2B APR sing 53 n n 
PB O5D APR sing 54 n n 
O2B HOB2 APR sing 55 n n 
O5D C5D APR sing 56 n n 
C5D C4D APR sing 57 n n 
C5D H5R1 APR sing 58 n n 
C5D H5R2 APR sing 59 n n 
O4D C1D APR sing 60 n n 
O4D C4D APR sing 61 n n 
O1D C1D APR sing 62 n n 
O1D HOR1 APR sing 63 n n 
C1D C2D APR sing 64 n n 
C1D "HR'1" APR sing 65 n n 
O2D C2D APR sing 66 n n 
O2D HOR2 APR sing 67 n n 
C2D C3D APR sing 68 n n 
C2D "HR'2" APR sing 69 n n 
O3D C3D APR sing 70 n n 
O3D HOR3 APR sing 71 n n 
C3D C4D APR sing 72 n n 
C3D "HR'3" APR sing 73 n n 
C4D "HR'4" APR sing 74 n n 
#
_atom_sites.entry_id                     1V8Y 
_atom_sites.fract_transf_matrix[1][1]    0.020139 
_atom_sites.fract_transf_matrix[1][2]    0.011627 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023254 
_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]    0.008441 
_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 ZN A 1 300 300 ZN ZN2 . 
C 2 ZN A 1 301 301 ZN ZN2 . 
D 3 APR A 1 619 619 APR APR . 
E 4 HOH A 1 620 1 HOH TIP . 
E 4 HOH A 2 621 2 HOH TIP . 
E 4 HOH A 3 622 3 HOH TIP . 
E 4 HOH A 4 623 4 HOH TIP . 
E 4 HOH A 5 624 5 HOH TIP . 
E 4 HOH A 6 625 6 HOH TIP . 
E 4 HOH A 7 626 7 HOH TIP . 
E 4 HOH A 8 627 8 HOH TIP . 
E 4 HOH A 9 628 9 HOH TIP . 
E 4 HOH A 10 629 10 HOH TIP . 
E 4 HOH A 11 630 11 HOH TIP . 
E 4 HOH A 12 631 12 HOH TIP . 
E 4 HOH A 13 632 13 HOH TIP . 
E 4 HOH A 14 633 14 HOH TIP . 
E 4 HOH A 15 634 15 HOH TIP . 
E 4 HOH A 16 635 16 HOH TIP . 
E 4 HOH A 17 636 17 HOH TIP . 
E 4 HOH A 18 637 18 HOH TIP . 
E 4 HOH A 19 638 19 HOH TIP . 
E 4 HOH A 20 639 20 HOH TIP . 
E 4 HOH A 21 640 21 HOH TIP . 
E 4 HOH A 22 641 22 HOH TIP . 
E 4 HOH A 23 642 23 HOH TIP . 
E 4 HOH A 24 643 24 HOH TIP . 
E 4 HOH A 25 644 25 HOH TIP . 
E 4 HOH A 26 645 26 HOH TIP . 
E 4 HOH A 27 646 27 HOH TIP . 
E 4 HOH A 28 647 28 HOH TIP . 
E 4 HOH A 29 648 29 HOH TIP . 
E 4 HOH A 30 649 31 HOH TIP . 
E 4 HOH A 31 650 32 HOH TIP . 
E 4 HOH A 32 651 33 HOH TIP . 
E 4 HOH A 33 652 34 HOH TIP . 
E 4 HOH A 34 653 35 HOH TIP . 
E 4 HOH A 35 654 36 HOH TIP . 
E 4 HOH A 36 655 37 HOH TIP . 
E 4 HOH A 37 656 38 HOH TIP . 
E 4 HOH A 38 657 39 HOH TIP . 
E 4 HOH A 39 658 40 HOH TIP . 
E 4 HOH A 40 659 43 HOH TIP . 
E 4 HOH A 41 660 44 HOH TIP . 
E 4 HOH A 42 661 45 HOH TIP . 
E 4 HOH A 43 662 46 HOH TIP . 
E 4 HOH A 44 663 47 HOH TIP . 
E 4 HOH A 45 664 50 HOH TIP . 
E 4 HOH A 46 665 51 HOH TIP . 
E 4 HOH A 47 666 52 HOH TIP . 
E 4 HOH A 48 667 53 HOH TIP . 
E 4 HOH A 49 668 54 HOH TIP . 
E 4 HOH A 50 669 56 HOH TIP . 
E 4 HOH A 51 670 57 HOH TIP . 
E 4 HOH A 52 671 58 HOH TIP . 
E 4 HOH A 53 672 59 HOH TIP . 
E 4 HOH A 54 673 61 HOH TIP . 
E 4 HOH A 55 674 62 HOH TIP . 
E 4 HOH A 56 675 63 HOH TIP . 
E 4 HOH A 57 676 64 HOH TIP . 
E 4 HOH A 58 677 65 HOH TIP . 
#
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 N N1 APR . . . D 3 1.735 5.971 49.264 1 57.03 ? N1 APR 619 A 1 
HETATM 2 C C2 APR . . . D 3 2.04 5.139 48.154 1 57.83 ? C2 APR 619 A 1 
HETATM 3 N N3 APR . . . D 3 2.627 5.528 47.008 1 58.4 ? N3 APR 619 A 1 
HETATM 4 C C4 APR . . . D 3 2.949 6.929 46.966 1 59.26 ? C4 APR 619 A 1 
HETATM 5 C C5 APR . . . D 3 2.716 7.898 47.978 1 58.41 ? C5 APR 619 A 1 
HETATM 6 C C6 APR . . . D 3 2.062 7.369 49.212 1 57.52 ? C6 APR 619 A 1 
HETATM 7 N N6 APR . . . D 3 1.757 8.117 50.28 1 54.69 ? N6 APR 619 A 1 
HETATM 8 N N7 APR . . . D 3 3.169 9.144 47.563 1 59.09 ? N7 APR 619 A 1 
HETATM 9 C C8 APR . . . D 3 3.662 8.931 46.331 1 60.06 ? C8 APR 619 A 1 
HETATM 10 N N9 APR . . . D 3 3.552 7.62 45.93 1 60.22 ? N9 APR 619 A 1 
HETATM 11 C C1' APR . . . D 3 3.985 6.855 44.562 1 61.73 ? C1' APR 619 A 1 
HETATM 12 C C2' APR . . . D 3 3.24 7.457 43.345 1 62.48 ? C2' APR 619 A 1 
HETATM 13 O O2' APR . . . D 3 2.446 6.451 42.741 1 63.06 ? O2' APR 619 A 1 
HETATM 14 C C3' APR . . . D 3 4.344 8.001 42.359 1 62.86 ? C3' APR 619 A 1 
HETATM 15 O O3' APR . . . D 3 4.259 7.384 41.077 1 62.71 ? O3' APR 619 A 1 
HETATM 16 O O4' APR . . . D 3 5.33 7.048 44.291 1 62.41 ? O4' APR 619 A 1 
HETATM 17 C C4' APR . . . D 3 5.647 7.731 42.984 1 62.99 ? C4' APR 619 A 1 
HETATM 18 C C5' APR . . . D 3 6.332 9.016 43.229 1 63.44 ? C5' APR 619 A 1 
HETATM 19 O O5' APR . . . D 3 7.494 9.091 42.394 1 64.2 ? O5' APR 619 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           19 
#