data_4RB4
#
_model_server_result.job_id            hnSIrDJ94pAK53sj3D2h-A 
_model_server_result.datetime_utc      '2024-12-21 12:36:05' 
_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          4rb4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":502}' 
#
_entry.id    4RB4 
#
_exptl.entry_id    4RB4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              619.368 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate' 
_entity.pdbx_number_of_molecules    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          101.26 
_cell.angle_gamma         90 
_cell.entry_id            4RB4 
_cell.length_a            88.292 
_cell.length_b            313.196 
_cell.length_c            164.695 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4RB4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 N N N 
? 3 P N N 
? 3 S N N 
? 3 U N N 
? 3 W N N 
? 3 Y N N 
? 3 AA N N 
? 3 CA N N 
? 3 EA N N 
? 3 HA N N 
? 3 KA N N 
? 3 MA 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 SG CYS 342 K CYS 342 1_555 M FE FE . K FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? 
metalc ? metalc2 B SG CYS 339 L CYS 339 1_555 O FE FE . L FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? 
metalc ? metalc3 B SG CYS 358 L CYS 358 1_555 O FE FE . L FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc4 B SG CYS 370 L CYS 370 1_555 O FE FE . L FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? 
metalc ? metalc5 C SG CYS 339 C CYS 339 1_555 Q FE FE . C FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? 
metalc ? metalc6 C SG CYS 342 C CYS 342 1_555 Q FE FE . C FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? 
metalc ? metalc7 D SG CYS 339 D CYS 339 1_555 T FE FE . D FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? 
metalc ? metalc8 D SG CYS 358 D CYS 358 1_555 T FE FE . D FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc9 E SG CYS 358 E CYS 358 1_555 V FE FE . E FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
metalc ? metalc10 F SG CYS 339 H CYS 339 1_555 X FE FE . H FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? 
metalc ? metalc11 F SG CYS 342 H CYS 342 1_555 X FE FE . H FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? 
metalc ? metalc12 F SG CYS 358 H CYS 358 1_555 X FE FE . H FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc13 G SG CYS 339 B CYS 339 1_555 Z FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? 
metalc ? metalc14 G SG CYS 342 B CYS 342 1_555 Z FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc15 G SG CYS 358 B CYS 358 1_555 Z FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc16 H SG CYS 339 F CYS 339 1_555 BA FE FE . F FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc17 H SG CYS 342 F CYS 342 1_555 BA FE FE . F FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
metalc ? metalc18 H SG CYS 358 F CYS 358 1_555 BA FE FE . F FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc19 I SG CYS 342 G CYS 342 1_555 DA FE FE . G FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? 
metalc ? metalc20 J SG CYS 358 I CYS 358 1_555 FA FE FE . I FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc21 J SG CYS 370 I CYS 370 1_555 FA FE FE . I FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc22 K SG CYS 339 J CYS 339 1_555 IA FE FE . J FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? 
metalc ? metalc23 L SG CYS 339 A CYS 339 1_555 LA FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? 
metalc ? metalc24 L SG CYS 358 A CYS 358 1_555 LA FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
#
_chem_comp.formula           'C17 H27 N5 O16 P2' 
_chem_comp.formula_weight    619.368 
_chem_comp.id                AQH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen 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
O2' C2D AQH sing 13 n n 
N1 C2 AQH doub 14 n y 
N1 C6 AQH sing 15 n y 
C2 N3 AQH sing 16 n y 
N6 C6 AQH sing 17 n n 
C6 C5 AQH doub 18 n y 
N3 C4 AQH doub 19 n y 
C5 C4 AQH sing 20 n y 
C5 N7 AQH sing 21 n y 
C4 N9 AQH sing 22 n y 
N7 C8 AQH doub 23 n y 
O3D C3D AQH sing 24 n n 
N9 C1D AQH sing 25 n n 
N9 C8 AQH sing 26 n y 
C1D C2D AQH sing 27 n n 
C1D O4D AQH sing 28 n n 
C2D C3D AQH sing 29 n n 
C3D C4D AQH sing 30 n n 
O4D C4D AQH sing 31 n n 
C4D C5D AQH sing 32 n n 
O2A PA AQH doub 33 n n 
C5D O5D AQH sing 34 n n 
O1B PB AQH doub 35 n n 
O5D PA AQH sing 36 n n 
O2B PA AQH sing 37 n n 
O2B PB AQH sing 38 n n 
PA O1A AQH sing 39 n n 
PB O3B AQH sing 40 n n 
PB O3A AQH sing 41 n n 
O3B C1' AQH sing 42 n n 
C1' O5' AQH sing 43 n n 
C1' C2' AQH sing 44 n n 
O5' C5' AQH sing 45 n n 
O6' C6' AQH sing 46 n n 
O C2' AQH sing 47 n n 
C2' C3' AQH sing 48 n n 
C5' C6' AQH sing 49 n n 
C5' C4' AQH sing 50 n n 
C6' C7' AQH sing 51 n n 
C3' C4' AQH sing 52 n n 
C3' O3' AQH sing 53 n n 
C4' O4' AQH sing 54 n n 
O7' C7' AQH sing 55 n n 
C7' H1 AQH sing 56 n n 
C7' H2 AQH sing 57 n n 
O7' H3 AQH sing 58 n n 
C6' H4 AQH sing 59 n n 
O6' H5 AQH sing 60 n n 
C5' H6 AQH sing 61 n n 
C4' H7 AQH sing 62 n n 
O4' H8 AQH sing 63 n n 
C3' H9 AQH sing 64 n n 
O3' H10 AQH sing 65 n n 
C2' H11 AQH sing 66 n n 
O2' H12 AQH sing 67 n n 
C1' H13 AQH sing 68 n n 
C1D H14 AQH sing 69 n n 
O1A H15 AQH sing 70 n n 
O3A H16 AQH sing 71 n n 
C2 H17 AQH sing 72 n n 
C2D H18 AQH sing 73 n n 
C3D H19 AQH sing 74 n n 
O3D H20 AQH sing 75 n n 
C4D H21 AQH sing 76 n n 
C5D H22 AQH sing 77 n n 
C5D H23 AQH sing 78 n n 
N6 H24 AQH sing 79 n n 
N6 H25 AQH sing 80 n n 
C8 H26 AQH sing 81 n n 
O H27 AQH sing 82 n n 
#
_atom_sites.entry_id                     4RB4 
_atom_sites.fract_transf_matrix[1][1]    0.011326 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002255 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.003193 
_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]    0.006191 
_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
M 2 FE K 1 501 1397 FE FE . 
N 3 AQH K 1 502 3001 AQH APH . 
O 2 FE L 1 501 1396 FE FE . 
P 3 AQH L 1 502 3002 AQH APH . 
Q 2 FE C 1 501 1399 FE FE . 
R 4 EDO C 1 502 1400 EDO EDO . 
S 3 AQH C 1 503 3001 AQH APH . 
T 2 FE D 1 501 1392 FE FE . 
U 3 AQH D 1 502 3001 AQH APH . 
V 2 FE E 1 501 1400 FE FE . 
W 3 AQH E 1 502 3001 AQH APH . 
X 2 FE H 1 501 1396 FE FE . 
Y 3 AQH H 1 502 3001 AQH APH . 
Z 2 FE B 1 501 1392 FE FE . 
AA 3 AQH B 1 502 3001 AQH APH . 
BA 2 FE F 1 501 1396 FE FE . 
CA 3 AQH F 1 502 3001 AQH APH . 
DA 2 FE G 1 501 1400 FE FE . 
EA 3 AQH G 1 502 3001 AQH APH . 
FA 2 FE I 1 501 1400 FE FE . 
GA 4 EDO I 1 502 1401 EDO EDO . 
HA 3 AQH I 1 503 3001 AQH APH . 
IA 2 FE J 1 501 1393 FE FE . 
JA 4 EDO J 1 502 1394 EDO EDO . 
KA 3 AQH J 1 503 3001 AQH APH . 
LA 2 FE A 1 501 1392 FE FE . 
MA 3 AQH A 1 502 3001 AQH APH . 
#
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 PA AQH . . . U 3 19.37 -13.327 18.679 0.85 150 ? PA AQH 502 D 1 
HETATM 2 P PB AQH . . . U 3 18.145 -12.062 16.487 0.85 150 ? PB AQH 502 D 1 
HETATM 3 C C7' AQH . . . U 3 14.168 -17.775 15.522 0.85 150 ? C7' AQH 502 D 1 
HETATM 4 O O7' AQH . . . U 3 14.402 -17.102 14.284 0.85 150 ? O7' AQH 502 D 1 
HETATM 5 C C6' AQH . . . U 3 14.338 -16.931 16.816 0.85 150 ? C6' AQH 502 D 1 
HETATM 6 O O6' AQH . . . U 3 13.946 -17.721 17.944 0.85 150 ? O6' AQH 502 D 1 
HETATM 7 C C5' AQH . . . U 3 15.775 -16.364 17.083 0.85 150 ? C5' AQH 502 D 1 
HETATM 8 O O5' AQH . . . U 3 15.839 -14.994 16.5 0.85 150 ? O5' AQH 502 D 1 
HETATM 9 C C4' AQH . . . U 3 16.938 -17.231 16.526 0.85 150 ? C4' AQH 502 D 1 
HETATM 10 O O4' AQH . . . U 3 16.833 -18.502 17.141 0.85 150 ? O4' AQH 502 D 1 
HETATM 11 C C3' AQH . . . U 3 18.301 -16.568 16.824 0.85 150 ? C3' AQH 502 D 1 
HETATM 12 O O3' AQH . . . U 3 19.364 -17.374 16.323 0.85 150 ? O3' AQH 502 D 1 
HETATM 13 C C2' AQH . . . U 3 18.298 -15.194 16.103 0.85 150 ? C2' AQH 502 D 1 
HETATM 14 O O2' AQH . . . U 3 18.046 -7.959 22.325 0.85 150 ? O2' AQH 502 D 1 
HETATM 15 C C1' AQH . . . U 3 17.147 -14.357 16.678 0.85 150 ? C1' AQH 502 D 1 
HETATM 16 C C1D AQH . . . U 3 19.58 -9.874 22.822 0.85 150 ? C1D AQH 502 D 1 
HETATM 17 N N1 AQH . . . U 3 22.898 -9.401 26.854 0.85 150 ? N1 AQH 502 D 1 
HETATM 18 O O1A AQH . . . U 3 18.504 -14.212 19.358 0.85 150 1 O1A AQH 502 D 1 
HETATM 19 O O3A AQH . . . U 3 17.713 -10.638 16.306 0.85 150 ? O3A AQH 502 D 1 
HETATM 20 C C2 AQH . . . U 3 21.542 -9.138 26.843 0.85 150 ? C2 AQH 502 D 1 
HETATM 21 C C2D AQH . . . U 3 19.337 -8.535 22.123 0.85 150 ? C2D AQH 502 D 1 
HETATM 22 O O2A AQH . . . U 3 20.302 -14.134 17.891 0.85 150 ? O2A AQH 502 D 1 
HETATM 23 O O1B AQH . . . U 3 19.339 -12.326 15.739 0.85 150 1 O1B AQH 502 D 1 
HETATM 24 C C3D AQH . . . U 3 19.689 -8.846 20.693 0.85 150 ? C3D AQH 502 D 1 
HETATM 25 N N3 AQH . . . U 3 20.855 -9.335 25.654 0.85 150 ? N3 AQH 502 D 1 
HETATM 26 O O2B AQH . . . U 3 18.481 -12.351 17.91 0.85 150 ? O2B AQH 502 D 1 
HETATM 27 O O3B AQH . . . U 3 17.045 -13.2 16.14 0.85 150 ? O3B AQH 502 D 1 
HETATM 28 O O3D AQH . . . U 3 18.989 -8.036 19.733 0.85 150 ? O3D AQH 502 D 1 
HETATM 29 C C4 AQH . . . U 3 21.456 -9.783 24.47 0.85 150 ? C4 AQH 502 D 1 
HETATM 30 C C4D AQH . . . U 3 19.252 -10.248 20.564 0.85 150 ? C4D AQH 502 D 1 
HETATM 31 O O4D AQH . . . U 3 19.182 -10.849 21.872 0.85 150 ? O4D AQH 502 D 1 
HETATM 32 C C5 AQH . . . U 3 22.874 -10.065 24.455 0.85 150 ? C5 AQH 502 D 1 
HETATM 33 C C5D AQH . . . U 3 20.22 -10.907 19.595 0.85 150 ? C5D AQH 502 D 1 
HETATM 34 O O5D AQH . . . U 3 20.079 -12.372 19.693 0.85 150 ? O5D AQH 502 D 1 
HETATM 35 C C6 AQH . . . U 3 23.576 -9.858 25.692 0.85 150 ? C6 AQH 502 D 1 
HETATM 36 N N6 AQH . . . U 3 24.886 -10.107 25.723 0.85 150 ? N6 AQH 502 D 1 
HETATM 37 N N7 AQH . . . U 3 23.181 -10.465 23.238 0.85 150 ? N7 AQH 502 D 1 
HETATM 38 C C8 AQH . . . U 3 22.084 -10.455 22.502 0.85 150 ? C8 AQH 502 D 1 
HETATM 39 N N9 AQH . . . U 3 21.022 -10.038 23.25 0.85 150 ? N9 AQH 502 D 1 
HETATM 40 O O AQH . . . U 3 17.56 -15.124 14.753 0.85 150 ? O AQH 502 D 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           40 
#