data_8IY2
#
_model_server_result.job_id            q1zH0E8UsETffTPnNcswAw 
_model_server_result.datetime_utc      '2024-11-23 23:47:57' 
_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          8iy2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"FA","auth_seq_id":205}' 
#
_entry.id    8IY2 
#
_exptl.entry_id    8IY2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' 
_entity.pdbx_number_of_molecules    22 
_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            8IY2 
_cell.length_a            103.427 
_cell.length_b            103.427 
_cell.length_c            101.487 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8IY2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 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
? hexameric 6 author_defined_assembly 1 
? hexameric 6 author_defined_assembly 2 
? hexameric 6 author_defined_assembly 3 
? hexameric 6 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,G,H,I,J,K,L,M,N,TA 1 1 
A,G,H,I,J,K,L,M,N,TA 1 2 
A,G,H,I,J,K,L,M,N,TA 1 4 
A,G,H,I,J,K,L,M,N,TA 1 6 
A,G,H,I,J,K,L,M,N,TA 1 8 
A,G,H,I,J,K,L,M,N,TA 1 10 
B,O,P,Q,R,S,T,U,UA 2 1 
B,O,P,Q,R,S,T,U,UA 2 2 
B,O,P,Q,R,S,T,U,UA 2 4 
B,O,P,Q,R,S,T,U,UA 2 7 
B,O,P,Q,R,S,T,U,UA 2 9 
B,O,P,Q,R,S,T,U,UA 2 11 
C,D,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,VA,WA 3 1 
C,D,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,VA,WA 3 3 
C,D,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,VA,WA 3 5 
E,F,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,XA 4 1 
E,F,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,XA 4 3 
E,F,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,XA 4 5 
#
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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -51.7135 -89.570409 0 
4 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
5 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.7135 -89.570409 0 
6 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 101.487 
7 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 
8 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 101.487 
9 'crystal symmetry operation' 5_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
10 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 101.487 
11 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 N N N 
? 3 Q N N 
? 3 R N N 
? 3 S N N 
? 3 U N N 
? 3 X N N 
? 3 Y N N 
? 3 Z N N 
? 3 DA N N 
? 3 EA N N 
? 3 FA N N 
? 3 GA N N 
? 3 JA N N 
? 3 KA N N 
? 3 LA N N 
? 3 PA N N 
? 3 QA N N 
? 3 RA N N 
? 3 SA N N 
#
_chem_comp.formula           'C10 H14 N5 O7 P' 
_chem_comp.formula_weight    347.221 
_chem_comp.id                3AM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "3'-AMP" 
#
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
O1P P 3AM doub 1 n n 
P O2P 3AM sing 2 n n 
P O3P 3AM sing 3 n n 
P O3' 3AM sing 4 n n 
O2' C2' 3AM sing 5 n n 
C2' C3' 3AM sing 6 n n 
C2' C1' 3AM sing 7 n n 
C3' O3' 3AM sing 8 n n 
C3' C4' 3AM sing 9 n n 
C1' O4' 3AM sing 10 n n 
C1' N9 3AM sing 11 n n 
O4' C4' 3AM sing 12 n n 
C4' C5' 3AM sing 13 n n 
C5' O5' 3AM sing 14 n n 
N9 C8 3AM sing 15 n y 
N9 C4 3AM sing 16 n y 
C8 N7 3AM doub 17 n y 
N7 C5 3AM sing 18 n y 
C5 C6 3AM doub 19 n y 
C5 C4 3AM sing 20 n y 
C6 N6 3AM sing 21 n n 
C6 N1 3AM sing 22 n y 
C4 N3 3AM doub 23 n y 
N3 C2 3AM sing 24 n y 
C2 N1 3AM doub 25 n y 
O2P HO2P 3AM sing 26 n n 
O3P HO3P 3AM sing 27 n n 
O2' HO2' 3AM sing 28 n n 
C2' H2' 3AM sing 29 n n 
C3' H3' 3AM sing 30 n n 
C1' H1' 3AM sing 31 n n 
C4' H4' 3AM sing 32 n n 
C5' H5' 3AM sing 33 n n 
C5' "H5'A" 3AM sing 34 n n 
O5' HO5' 3AM sing 35 n n 
C8 H8 3AM sing 36 n n 
N6 HN6 3AM sing 37 n n 
N6 HN6A 3AM sing 38 n n 
C2 H2 3AM sing 39 n n 
#
_atom_sites.entry_id                     8IY2 
_atom_sites.fract_transf_matrix[1][1]    0.009669 
_atom_sites.fract_transf_matrix[1][2]    0.005582 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011164 
_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]    0.009853 
_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
G 2 EDO A 1 201 201 EDO EDO . 
H 2 EDO A 1 202 302 EDO EDO . 
I 2 EDO A 1 203 301 EDO EDO . 
J 3 3AM A 1 204 102 3AM AAA . 
K 3 3AM A 1 205 102 3AM AAA . 
L 3 3AM A 1 206 102 3AM AAA . 
M 4 3GP A 1 207 101 3GP 4BW . 
N 3 3AM A 1 208 101 3AM 4BW . 
O 2 EDO B 1 201 201 EDO EDO . 
P 2 EDO B 1 202 302 EDO EDO . 
Q 3 3AM B 1 203 102 3AM AAA . 
R 3 3AM B 1 204 102 3AM AAA . 
S 3 3AM B 1 205 102 3AM AAA . 
T 4 3GP B 1 206 101 3GP 4BW . 
U 3 3AM B 1 207 101 3AM 4BW . 
V 2 EDO C 1 201 201 EDO EDO . 
W 2 EDO C 1 202 302 EDO EDO . 
X 3 3AM C 1 203 101 3AM AAA . 
Y 3 3AM C 1 204 101 3AM AAA . 
Z 3 3AM C 1 205 101 3AM AAA . 
AA 4 3GP C 1 206 101 3GP 4BW . 
BA 2 EDO D 1 201 201 EDO EDO . 
CA 2 EDO D 1 202 302 EDO EDO . 
DA 3 3AM D 1 203 102 3AM AAA . 
EA 3 3AM D 1 204 102 3AM AAA . 
FA 3 3AM D 1 205 102 3AM AAA . 
GA 3 3AM D 1 206 101 3AM 4BW . 
HA 2 EDO E 1 201 201 EDO EDO . 
IA 2 EDO E 1 202 302 EDO EDO . 
JA 3 3AM E 1 203 102 3AM AAA . 
KA 3 3AM E 1 204 102 3AM AAA . 
LA 3 3AM E 1 205 102 3AM AAA . 
MA 4 3GP E 1 206 101 3GP 4BW . 
NA 2 EDO F 1 201 201 EDO EDO . 
OA 2 EDO F 1 202 302 EDO EDO . 
PA 3 3AM F 1 203 101 3AM AAA . 
QA 3 3AM F 1 204 101 3AM AAA . 
RA 3 3AM F 1 205 101 3AM AAA . 
SA 3 3AM F 1 206 101 3AM 4BW . 
TA 5 HOH A 1 301 1 HOH HOH . 
TA 5 HOH A 2 302 3 HOH HOH . 
TA 5 HOH A 3 303 25 HOH HOH . 
TA 5 HOH A 4 304 4 HOH HOH . 
TA 5 HOH A 5 305 5 HOH HOH . 
TA 5 HOH A 6 306 8 HOH HOH . 
TA 5 HOH A 7 307 7 HOH HOH . 
TA 5 HOH A 8 308 17 HOH HOH . 
TA 5 HOH A 9 309 12 HOH HOH . 
TA 5 HOH A 10 310 18 HOH HOH . 
TA 5 HOH A 11 311 20 HOH HOH . 
TA 5 HOH A 12 312 19 HOH HOH . 
TA 5 HOH A 13 313 16 HOH HOH . 
UA 5 HOH B 1 301 21 HOH HOH . 
UA 5 HOH B 2 302 27 HOH HOH . 
UA 5 HOH B 3 303 15 HOH HOH . 
UA 5 HOH B 4 304 26 HOH HOH . 
VA 5 HOH C 1 301 14 HOH HOH . 
WA 5 HOH D 1 301 6 HOH HOH . 
WA 5 HOH D 2 302 13 HOH HOH . 
WA 5 HOH D 3 303 11 HOH HOH . 
WA 5 HOH D 4 304 23 HOH HOH . 
WA 5 HOH D 5 305 24 HOH HOH . 
WA 5 HOH D 6 306 9 HOH HOH . 
XA 5 HOH F 1 301 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 P P 3AM . . . FA 3 -0.69 -63.609 45.804 0.33 37.52 ? P 3AM 205 D 1 
HETATM 2 O O2P 3AM . . . FA 3 -0.244 -63.175 44.45 0.33 37.72 ? O2P 3AM 205 D 1 
HETATM 3 O O3P 3AM . . . FA 3 -1.086 -65.032 46.003 0.33 38.05 ? O3P 3AM 205 D 1 
HETATM 4 O O2' 3AM . . . FA 3 0.543 -61.72 49.256 0.33 38.8 ? O2' 3AM 205 D 1 
HETATM 5 C C2' 3AM . . . FA 3 1.528 -61.561 48.256 0.33 38.81 ? C2' 3AM 205 D 1 
HETATM 6 C C3' 3AM . . . FA 3 1.048 -61.927 46.852 0.33 38.31 ? C3' 3AM 205 D 1 
HETATM 7 O O3' 3AM . . . FA 3 0.391 -63.184 46.913 0.33 38.18 ? O3' 3AM 205 D 1 
HETATM 8 C C1' 3AM . . . FA 3 2.669 -62.563 48.398 0.33 39.13 ? C1' 3AM 205 D 1 
HETATM 9 O O4' 3AM . . . FA 3 3.311 -62.555 47.128 0.33 38.71 ? O4' 3AM 205 D 1 
HETATM 10 C C4' 3AM . . . FA 3 2.367 -62.145 46.112 0.33 38.14 ? C4' 3AM 205 D 1 
HETATM 11 C C5' 3AM . . . FA 3 2.929 -60.951 45.378 0.33 38.05 ? C5' 3AM 205 D 1 
HETATM 12 O O5' 3AM . . . FA 3 3.164 -59.873 46.306 0.33 38.28 ? O5' 3AM 205 D 1 
HETATM 13 N N9 3AM . . . FA 3 3.663 -62.188 49.401 0.33 39.57 ? N9 3AM 205 D 1 
HETATM 14 C C8 3AM . . . FA 3 4.108 -60.921 49.676 0.33 39.83 ? C8 3AM 205 D 1 
HETATM 15 N N7 3AM . . . FA 3 5.014 -60.876 50.622 0.33 40.3 ? N7 3AM 205 D 1 
HETATM 16 C C5 3AM . . . FA 3 5.174 -62.203 50.993 0.33 40.67 ? C5 3AM 205 D 1 
HETATM 17 C C6 3AM . . . FA 3 5.998 -62.817 51.954 0.33 41.06 ? C6 3AM 205 D 1 
HETATM 18 N N6 3AM . . . FA 3 6.841 -62.148 52.738 0.33 40.35 ? N6 3AM 205 D 1 
HETATM 19 C C4 3AM . . . FA 3 4.348 -63.023 50.249 0.33 40.65 ? C4 3AM 205 D 1 
HETATM 20 N N3 3AM . . . FA 3 4.248 -64.36 50.35 0.33 40.46 ? N3 3AM 205 D 1 
HETATM 21 C C2 3AM . . . FA 3 5.067 -64.831 51.284 0.33 41 ? C2 3AM 205 D 1 
HETATM 22 N N1 3AM . . . FA 3 5.917 -64.165 52.075 0.33 41.18 ? N1 3AM 205 D 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           36 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           256 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           22 
#