data_5VDO
#
_model_server_result.job_id            J4NsgMBGshd-AQO47tb9qg 
_model_server_result.datetime_utc      '2024-10-15 12:24:31' 
_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          5vdo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":602}' 
#
_entry.id    5VDO 
#
_exptl.entry_id    5VDO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              674.411 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-amino-9-[(1R,3R,6R,8R,9R,11S,14R,16R,17R,18R)-16-(6-amino-9H-purin-9-yl)-3,11,17,18-tetrahydroxy-3,11-dioxido-2,4,7,10,12,15-hexaoxa-3,11-diphosphatricyclo[12.2.1.1~6,9~]octadec-8-yl]-1,9-dihydro-6H-purin-6-one 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          110.18 
_cell.angle_gamma         90 
_cell.entry_id            5VDO 
_cell.length_a            216.423 
_cell.length_b            47.67 
_cell.length_c            88.861 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VDO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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
? 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,G 1 1 
B,E,F,H 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
? 3 D N N 
? 3 F 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 NE2 HIS 231 A HIS 390 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc2 A SG CYS 237 A CYS 396 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? 
metalc ? metalc3 A SG CYS 238 A CYS 397 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc4 A SG CYS 245 A CYS 404 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc5 B NE2 HIS 231 B HIS 390 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc6 B SG CYS 237 B CYS 396 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? 
metalc ? metalc7 B SG CYS 238 B CYS 397 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc8 B SG CYS 245 B CYS 404 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
#
_chem_comp.formula           'C20 H24 N10 O13 P2' 
_chem_comp.formula_weight    674.411 
_chem_comp.id                1YC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-amino-9-[(1R,3R,6R,8R,9R,11S,14R,16R,17R,18R)-16-(6-amino-9H-purin-9-yl)-3,11,17,18-tetrahydroxy-3,11-dioxido-2,4,7,10,12,15-hexaoxa-3,11-diphosphatricyclo[12.2.1.1~6,9~]octadec-8-yl]-1,9-dihydro-6H-purin-6-one 
_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
OAI PBS 1YC doub 1 n n 
C5' C4' 1YC sing 2 n n 
C5' O5' 1YC sing 3 n n 
PBS OAH 1YC sing 4 n n 
PBS O5' 1YC sing 5 n n 
PBS OAZ 1YC sing 6 n n 
O4' C4' 1YC sing 7 n n 
O4' C1' 1YC sing 8 n n 
C4' C3' 1YC sing 9 n n 
C8 N7 1YC doub 10 n y 
C8 N9 1YC sing 11 n y 
OAZ CBM 1YC sing 12 n n 
N7 C5 1YC sing 13 n y 
N9 C1' 1YC sing 14 n n 
N9 C4 1YC sing 15 n y 
C1' C2' 1YC sing 16 n n 
C3' O3' 1YC sing 17 n n 
C3' C2' 1YC sing 18 n n 
C5 C4 1YC doub 19 n y 
C5 C6 1YC sing 20 n y 
C4 N3 1YC sing 21 n y 
N6 C6 1YC sing 22 n n 
C6 N1 1YC doub 23 n y 
NAA CBA 1YC sing 24 n n 
N3 C2 1YC doub 25 n y 
C2' O2' 1YC sing 26 n n 
OAE CBI 1YC sing 27 n n 
N1 C2 1YC sing 28 n y 
CBM CBI 1YC sing 29 n n 
CBM CBO 1YC sing 30 n n 
CBA NAS 1YC doub 31 n n 
CBA NAT 1YC sing 32 n n 
NAS CBG 1YC sing 33 n n 
CBI CBK 1YC sing 34 n n 
NAT CBC 1YC sing 35 n n 
CBG CBE 1YC doub 36 n y 
CBG NBQ 1YC sing 37 n y 
CBC CBE 1YC sing 38 n n 
CBC OAC 1YC doub 39 n n 
CBO NBQ 1YC sing 40 n n 
CBO OAX 1YC sing 41 n n 
O2' P2' 1YC sing 42 n n 
CBE NAR 1YC sing 43 n y 
NBQ CAL 1YC sing 44 n y 
CAL NAR 1YC doub 45 n y 
CBK OAX 1YC sing 46 n n 
CBK CAN 1YC sing 47 n n 
OP3 P2' 1YC sing 48 n n 
OP3 CAN 1YC sing 49 n n 
OP1 P2' 1YC doub 50 n n 
P2' OP2 1YC sing 51 n n 
NAT H1 1YC sing 52 n n 
NAA H2 1YC sing 53 n n 
NAA H3 1YC sing 54 n n 
CAL H4 1YC sing 55 n n 
CBO H5 1YC sing 56 n n 
CBK H6 1YC sing 57 n n 
CAN H7 1YC sing 58 n n 
CAN H8 1YC sing 59 n n 
OP2 H9 1YC sing 60 n n 
CBI H10 1YC sing 61 n n 
OAE H11 1YC sing 62 n n 
CBM H12 1YC sing 63 n n 
OAH H13 1YC sing 64 n n 
C5' H14 1YC sing 65 n n 
C5' H15 1YC sing 66 n n 
C4' H16 1YC sing 67 n n 
C3' H17 1YC sing 68 n n 
O3' H18 1YC sing 69 n n 
C2' H19 1YC sing 70 n n 
C1' H20 1YC sing 71 n n 
C8 H21 1YC sing 72 n n 
C2 H22 1YC sing 73 n n 
N6 H23 1YC sing 74 n n 
N6 H24 1YC sing 75 n n 
#
_atom_sites.entry_id                     5VDO 
_atom_sites.fract_transf_matrix[1][1]    0.004621 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001698 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020977 
_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]    0.011989 
_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 ZN A 1 601 601 ZN ZN . 
D 3 1YC A 1 602 1 1YC LIG . 
E 2 ZN B 1 601 601 ZN ZN . 
F 3 1YC B 1 602 2 1YC LIG . 
G 4 HOH A 1 701 1 HOH HOH . 
H 4 HOH B 1 701 2 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 O OAC 1YC . . . F 3 -24.9 3.139 24.472 1 138.35 ? OAC 1YC 602 B 1 
HETATM 2 C CBC 1YC . . . F 3 -24.825 3.318 25.636 1 134.34 ? CBC 1YC 602 B 1 
HETATM 3 N NAT 1YC . . . F 3 -24.379 4.571 26.139 1 136.67 ? NAT 1YC 602 B 1 
HETATM 4 C CBA 1YC . . . F 3 -24.288 4.786 27.576 1 136.98 ? CBA 1YC 602 B 1 
HETATM 5 N NAA 1YC . . . F 3 -23.838 6.057 28.094 1 137.77 ? NAA 1YC 602 B 1 
HETATM 6 N NAS 1YC . . . F 3 -24.657 3.71 28.51 1 134.63 ? NAS 1YC 602 B 1 
HETATM 7 C CBG 1YC . . . F 3 -25.12 2.409 27.989 1 129.3 ? CBG 1YC 602 B 1 
HETATM 8 C CBE 1YC . . . F 3 -25.209 2.194 26.616 1 127.27 ? CBE 1YC 602 B 1 
HETATM 9 N NAR 1YC . . . F 3 -25.657 0.931 26.422 1 119.03 ? NAR 1YC 602 B 1 
HETATM 10 C CAL 1YC . . . F 3 -25.849 0.343 27.675 1 120.83 ? CAL 1YC 602 B 1 
HETATM 11 N NBQ 1YC . . . F 3 -25.514 1.265 28.621 1 127.79 ? NBQ 1YC 602 B 1 
HETATM 12 C CBO 1YC . . . F 3 -25.57 1.065 30.128 1 130.9 ? CBO 1YC 602 B 1 
HETATM 13 O OAX 1YC . . . F 3 -24.225 0.485 30.338 1 137.17 ? OAX 1YC 602 B 1 
HETATM 14 C CBK 1YC . . . F 3 -24.442 -0.806 31.016 1 134.55 ? CBK 1YC 602 B 1 
HETATM 15 C CAN 1YC . . . F 3 -24.501 -1.918 30.004 1 137.13 ? CAN 1YC 602 B 1 
HETATM 16 O OP3 1YC . . . F 3 -25.498 -2.853 30.403 1 139.39 ? OP3 1YC 602 B 1 
HETATM 17 P P2' 1YC . . . F 3 -25.875 -4.132 29.361 1 147.59 ? P2' 1YC 602 B 1 
HETATM 18 O O2' 1YC . . . F 3 -27.109 -3.829 28.311 1 146.29 ? O2' 1YC 602 B 1 
HETATM 19 O OP2 1YC . . . F 3 -26.013 -5.48 30.073 1 153.21 -1 OP2 1YC 602 B 1 
HETATM 20 O OP1 1YC . . . F 3 -24.663 -4.281 28.486 1 152.15 ? OP1 1YC 602 B 1 
HETATM 21 C CBI 1YC . . . F 3 -25.729 -0.67 31.701 1 133.02 ? CBI 1YC 602 B 1 
HETATM 22 O OAE 1YC . . . F 3 -25.551 0.077 32.95 1 139.45 ? OAE 1YC 602 B 1 
HETATM 23 C CBM 1YC . . . F 3 -26.536 0.087 30.79 1 134.17 ? CBM 1YC 602 B 1 
HETATM 24 O OAZ 1YC . . . F 3 -27.562 0.774 31.473 1 140.06 ? OAZ 1YC 602 B 1 
HETATM 25 P PBS 1YC . . . F 3 -29.114 0.422 31.022 1 139.26 ? PBS 1YC 602 B 1 
HETATM 26 O OAH 1YC . . . F 3 -29.493 0.981 29.668 1 141.1 -1 OAH 1YC 602 B 1 
HETATM 27 O OAI 1YC . . . F 3 -29.988 1.167 32.009 1 142.92 ? OAI 1YC 602 B 1 
HETATM 28 O O5' 1YC . . . F 3 -29.514 -1.216 31.223 1 132.24 ? O5' 1YC 602 B 1 
HETATM 29 C C5' 1YC . . . F 3 -30.719 -1.72 30.595 1 131.5 ? C5' 1YC 602 B 1 
HETATM 30 C C4' 1YC . . . F 3 -30.327 -2.805 29.612 1 127.95 ? C4' 1YC 602 B 1 
HETATM 31 O O4' 1YC . . . F 3 -30.387 -2.306 28.272 1 130.28 ? O4' 1YC 602 B 1 
HETATM 32 C C3' 1YC . . . F 3 -28.898 -3.258 29.865 1 127.96 ? C3' 1YC 602 B 1 
HETATM 33 O O3' 1YC . . . F 3 -28.873 -4.668 30.041 1 118.93 ? O3' 1YC 602 B 1 
HETATM 34 C C2' 1YC . . . F 3 -28.156 -2.872 28.662 1 137.04 ? C2' 1YC 602 B 1 
HETATM 35 C C1' 1YC . . . F 3 -29.229 -2.894 27.6 1 130.51 ? C1' 1YC 602 B 1 
HETATM 36 N N9 1YC . . . F 3 -29.19 -2.092 26.346 1 119.24 ? N9 1YC 602 B 1 
HETATM 37 C C8 1YC . . . F 3 -29.105 -0.743 26.252 1 119.68 ? C8 1YC 602 B 1 
HETATM 38 N N7 1YC . . . F 3 -29.087 -0.416 24.951 1 120.75 ? N7 1YC 602 B 1 
HETATM 39 C C5 1YC . . . F 3 -29.157 -1.577 24.205 1 114.72 ? C5 1YC 602 B 1 
HETATM 40 C C4 1YC . . . F 3 -29.219 -2.622 25.075 1 112.96 ? C4 1YC 602 B 1 
HETATM 41 N N3 1YC . . . F 3 -29.296 -3.901 24.58 1 100.82 ? N3 1YC 602 B 1 
HETATM 42 C C2 1YC . . . F 3 -29.313 -4.134 23.262 1 100.1 ? C2 1YC 602 B 1 
HETATM 43 N N1 1YC . . . F 3 -29.253 -3.146 22.391 1 104.14 ? N1 1YC 602 B 1 
HETATM 44 C C6 1YC . . . F 3 -29.176 -1.87 22.795 1 108.66 ? C6 1YC 602 B 1 
HETATM 45 N N6 1YC . . . F 3 -29.111 -0.773 21.805 1 106.57 ? N6 1YC 602 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           45 
#