data_5J61
#
_model_server_result.job_id            0OdbZe5rfhbny-2m1yfcjg 
_model_server_result.datetime_utc      '2024-11-15 08:38:25' 
_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          5j61 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":501}' 
#
_entry.id    5J61 
#
_exptl.entry_id    5J61 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              323.308 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "3'-deoxy-3'-(glycylamino)adenosine" 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          96.39 
_cell.angle_gamma         90 
_cell.entry_id            5J61 
_cell.length_a            57.156 
_cell.length_b            86.439 
_cell.length_c            138.163 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5J61 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,Q,R 1 1 
C,D,K,L,S,T 2 1 
E,F,M,N,U,V 3 1 
G,H,O,P,W,X 4 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
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
#
_chem_comp.formula           'C12 H17 N7 O4' 
_chem_comp.formula_weight    323.308 
_chem_comp.id                A3G 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "3'-deoxy-3'-(glycylamino)adenosine" 
_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
C O A3G doub 1 n n 
C N8 A3G sing 2 n n 
C CA A3G sing 3 n n 
N CA A3G sing 4 n n 
N1 C2 A3G doub 5 n y 
N1 C6 A3G sing 6 n y 
C2 N3 A3G sing 7 n y 
N3 C4 A3G doub 8 n y 
C4 C5 A3G sing 9 n y 
C4 N9 A3G sing 10 n y 
C5 C6 A3G doub 11 n y 
C5 N7 A3G sing 12 n y 
C6 N6 A3G sing 13 n n 
N7 C8 A3G doub 14 n y 
C8 N9 A3G sing 15 n y 
N8 C3' A3G sing 16 n n 
N9 C1' A3G sing 17 n n 
C1' C2' A3G sing 18 n n 
C1' O4' A3G sing 19 n n 
C2' O2' A3G sing 20 n n 
C2' C3' A3G sing 21 n n 
C3' C4' A3G sing 22 n n 
C4' O4' A3G sing 23 n n 
C4' C5' A3G sing 24 n n 
C5' O5' A3G sing 25 n n 
N HN A3G sing 26 n n 
N HNA A3G sing 27 n n 
C2 H2 A3G sing 28 n n 
N6 HN6 A3G sing 29 n n 
N6 HN6A A3G sing 30 n n 
C8 H8 A3G sing 31 n n 
N8 HN8 A3G sing 32 n n 
CA HA A3G sing 33 n n 
CA HAA A3G sing 34 n n 
C1' H1' A3G sing 35 n n 
C2' H2' A3G sing 36 n n 
O2' HO2' A3G sing 37 n n 
C3' H3' A3G sing 38 n n 
C4' H4' A3G sing 39 n n 
C5' H5' A3G sing 40 n n 
C5' "H5'A" A3G sing 41 n n 
O5' HO5' A3G sing 42 n n 
#
_atom_sites.entry_id                     5J61 
_atom_sites.fract_transf_matrix[1][1]    0.017496 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001958 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011569 
_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]    0.007283 
_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
I 2 A3G A 1 501 501 A3G A3G . 
J 2 A3G B 1 501 501 A3G A3G . 
K 2 A3G C 1 501 501 A3G A3G . 
L 2 A3G D 1 501 501 A3G A3G . 
M 2 A3G E 1 501 501 A3G A3G . 
N 2 A3G F 1 501 501 A3G A3G . 
O 2 A3G G 1 501 501 A3G A3G . 
P 2 A3G H 1 501 501 A3G A3G . 
Q 3 HOH A 1 601 10 HOH HOH . 
Q 3 HOH A 2 602 87 HOH HOH . 
Q 3 HOH A 3 603 6 HOH HOH . 
Q 3 HOH A 4 604 77 HOH HOH . 
Q 3 HOH A 5 605 122 HOH HOH . 
Q 3 HOH A 6 606 80 HOH HOH . 
Q 3 HOH A 7 607 112 HOH HOH . 
Q 3 HOH A 8 608 67 HOH HOH . 
Q 3 HOH A 9 609 66 HOH HOH . 
Q 3 HOH A 10 610 43 HOH HOH . 
Q 3 HOH A 11 611 20 HOH HOH . 
Q 3 HOH A 12 612 7 HOH HOH . 
Q 3 HOH A 13 613 126 HOH HOH . 
Q 3 HOH A 14 614 85 HOH HOH . 
Q 3 HOH A 15 615 5 HOH HOH . 
Q 3 HOH A 16 616 100 HOH HOH . 
Q 3 HOH A 17 617 58 HOH HOH . 
Q 3 HOH A 18 618 170 HOH HOH . 
Q 3 HOH A 19 619 53 HOH HOH . 
Q 3 HOH A 20 620 146 HOH HOH . 
Q 3 HOH A 21 621 14 HOH HOH . 
Q 3 HOH A 22 622 178 HOH HOH . 
Q 3 HOH A 23 623 150 HOH HOH . 
Q 3 HOH A 24 624 116 HOH HOH . 
Q 3 HOH A 25 625 171 HOH HOH . 
Q 3 HOH A 26 626 145 HOH HOH . 
Q 3 HOH A 27 627 172 HOH HOH . 
Q 3 HOH A 28 628 142 HOH HOH . 
Q 3 HOH A 29 629 177 HOH HOH . 
R 3 HOH B 1 601 19 HOH HOH . 
R 3 HOH B 2 602 137 HOH HOH . 
R 3 HOH B 3 603 162 HOH HOH . 
R 3 HOH B 4 604 106 HOH HOH . 
R 3 HOH B 5 605 74 HOH HOH . 
R 3 HOH B 6 606 83 HOH HOH . 
R 3 HOH B 7 607 18 HOH HOH . 
R 3 HOH B 8 608 57 HOH HOH . 
R 3 HOH B 9 609 73 HOH HOH . 
R 3 HOH B 10 610 64 HOH HOH . 
R 3 HOH B 11 611 69 HOH HOH . 
R 3 HOH B 12 612 3 HOH HOH . 
R 3 HOH B 13 613 38 HOH HOH . 
R 3 HOH B 14 614 94 HOH HOH . 
R 3 HOH B 15 615 36 HOH HOH . 
R 3 HOH B 16 616 81 HOH HOH . 
R 3 HOH B 17 617 143 HOH HOH . 
R 3 HOH B 18 618 82 HOH HOH . 
R 3 HOH B 19 619 1 HOH HOH . 
R 3 HOH B 20 620 144 HOH HOH . 
R 3 HOH B 21 621 11 HOH HOH . 
R 3 HOH B 22 622 151 HOH HOH . 
R 3 HOH B 23 623 17 HOH HOH . 
R 3 HOH B 24 624 141 HOH HOH . 
R 3 HOH B 25 625 175 HOH HOH . 
R 3 HOH B 26 626 99 HOH HOH . 
R 3 HOH B 27 627 156 HOH HOH . 
S 3 HOH C 1 601 51 HOH HOH . 
S 3 HOH C 2 602 35 HOH HOH . 
S 3 HOH C 3 603 4 HOH HOH . 
S 3 HOH C 4 604 40 HOH HOH . 
S 3 HOH C 5 605 8 HOH HOH . 
S 3 HOH C 6 606 166 HOH HOH . 
S 3 HOH C 7 607 25 HOH HOH . 
S 3 HOH C 8 608 89 HOH HOH . 
S 3 HOH C 9 609 110 HOH HOH . 
S 3 HOH C 10 610 109 HOH HOH . 
S 3 HOH C 11 611 75 HOH HOH . 
S 3 HOH C 12 612 96 HOH HOH . 
S 3 HOH C 13 613 52 HOH HOH . 
S 3 HOH C 14 614 72 HOH HOH . 
S 3 HOH C 15 615 105 HOH HOH . 
S 3 HOH C 16 616 124 HOH HOH . 
S 3 HOH C 17 617 111 HOH HOH . 
S 3 HOH C 18 618 113 HOH HOH . 
S 3 HOH C 19 619 130 HOH HOH . 
S 3 HOH C 20 620 131 HOH HOH . 
S 3 HOH C 21 621 129 HOH HOH . 
T 3 HOH D 1 601 29 HOH HOH . 
T 3 HOH D 2 602 45 HOH HOH . 
T 3 HOH D 3 603 34 HOH HOH . 
T 3 HOH D 4 604 23 HOH HOH . 
T 3 HOH D 5 605 98 HOH HOH . 
T 3 HOH D 6 606 90 HOH HOH . 
T 3 HOH D 7 607 88 HOH HOH . 
T 3 HOH D 8 608 71 HOH HOH . 
T 3 HOH D 9 609 46 HOH HOH . 
T 3 HOH D 10 610 59 HOH HOH . 
T 3 HOH D 11 611 44 HOH HOH . 
U 3 HOH E 1 601 93 HOH HOH . 
U 3 HOH E 2 602 39 HOH HOH . 
U 3 HOH E 3 603 13 HOH HOH . 
U 3 HOH E 4 604 70 HOH HOH . 
U 3 HOH E 5 605 78 HOH HOH . 
U 3 HOH E 6 606 76 HOH HOH . 
U 3 HOH E 7 607 21 HOH HOH . 
U 3 HOH E 8 608 152 HOH HOH . 
U 3 HOH E 9 609 79 HOH HOH . 
U 3 HOH E 10 610 48 HOH HOH . 
U 3 HOH E 11 611 139 HOH HOH . 
U 3 HOH E 12 612 84 HOH HOH . 
U 3 HOH E 13 613 132 HOH HOH . 
U 3 HOH E 14 614 61 HOH HOH . 
U 3 HOH E 15 615 121 HOH HOH . 
U 3 HOH E 16 616 138 HOH HOH . 
U 3 HOH E 17 617 22 HOH HOH . 
U 3 HOH E 18 618 147 HOH HOH . 
U 3 HOH E 19 619 56 HOH HOH . 
U 3 HOH E 20 620 176 HOH HOH . 
U 3 HOH E 21 621 128 HOH HOH . 
U 3 HOH E 22 622 174 HOH HOH . 
V 3 HOH F 1 601 54 HOH HOH . 
V 3 HOH F 2 602 37 HOH HOH . 
V 3 HOH F 3 603 32 HOH HOH . 
V 3 HOH F 4 604 47 HOH HOH . 
V 3 HOH F 5 605 91 HOH HOH . 
V 3 HOH F 6 606 50 HOH HOH . 
V 3 HOH F 7 607 2 HOH HOH . 
V 3 HOH F 8 608 179 HOH HOH . 
V 3 HOH F 9 609 28 HOH HOH . 
V 3 HOH F 10 610 24 HOH HOH . 
V 3 HOH F 11 611 107 HOH HOH . 
V 3 HOH F 12 612 134 HOH HOH . 
V 3 HOH F 13 613 140 HOH HOH . 
V 3 HOH F 14 614 153 HOH HOH . 
V 3 HOH F 15 615 115 HOH HOH . 
V 3 HOH F 16 616 26 HOH HOH . 
V 3 HOH F 17 617 49 HOH HOH . 
V 3 HOH F 18 618 55 HOH HOH . 
V 3 HOH F 19 619 68 HOH HOH . 
V 3 HOH F 20 620 102 HOH HOH . 
V 3 HOH F 21 621 154 HOH HOH . 
V 3 HOH F 22 622 41 HOH HOH . 
V 3 HOH F 23 623 9 HOH HOH . 
V 3 HOH F 24 624 169 HOH HOH . 
V 3 HOH F 25 625 173 HOH HOH . 
V 3 HOH F 26 626 135 HOH HOH . 
V 3 HOH F 27 627 136 HOH HOH . 
V 3 HOH F 28 628 31 HOH HOH . 
V 3 HOH F 29 629 133 HOH HOH . 
V 3 HOH F 30 630 95 HOH HOH . 
W 3 HOH G 1 601 120 HOH HOH . 
W 3 HOH G 2 602 118 HOH HOH . 
W 3 HOH G 3 603 65 HOH HOH . 
W 3 HOH G 4 604 167 HOH HOH . 
W 3 HOH G 5 605 42 HOH HOH . 
W 3 HOH G 6 606 16 HOH HOH . 
W 3 HOH G 7 607 60 HOH HOH . 
W 3 HOH G 8 608 127 HOH HOH . 
W 3 HOH G 9 609 119 HOH HOH . 
W 3 HOH G 10 610 86 HOH HOH . 
W 3 HOH G 11 611 155 HOH HOH . 
W 3 HOH G 12 612 123 HOH HOH . 
W 3 HOH G 13 613 15 HOH HOH . 
W 3 HOH G 14 614 103 HOH HOH . 
W 3 HOH G 15 615 117 HOH HOH . 
W 3 HOH G 16 616 97 HOH HOH . 
W 3 HOH G 17 617 157 HOH HOH . 
W 3 HOH G 18 618 114 HOH HOH . 
W 3 HOH G 19 619 101 HOH HOH . 
W 3 HOH G 20 620 161 HOH HOH . 
W 3 HOH G 21 621 158 HOH HOH . 
X 3 HOH H 1 601 148 HOH HOH . 
X 3 HOH H 2 602 108 HOH HOH . 
X 3 HOH H 3 603 33 HOH HOH . 
X 3 HOH H 4 604 62 HOH HOH . 
X 3 HOH H 5 605 12 HOH HOH . 
X 3 HOH H 6 606 149 HOH HOH . 
X 3 HOH H 7 607 104 HOH HOH . 
X 3 HOH H 8 608 163 HOH HOH . 
X 3 HOH H 9 609 92 HOH HOH . 
X 3 HOH H 10 610 27 HOH HOH . 
X 3 HOH H 11 611 30 HOH HOH . 
X 3 HOH H 12 612 63 HOH HOH . 
X 3 HOH H 13 613 159 HOH HOH . 
X 3 HOH H 14 614 160 HOH HOH . 
X 3 HOH H 15 615 164 HOH HOH . 
X 3 HOH H 16 616 125 HOH HOH . 
X 3 HOH H 17 617 165 HOH HOH . 
X 3 HOH H 18 618 168 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 C C A3G . . . M 2 10.179 3.481 40.859 1 91.16 ? C A3G 501 E 1 
HETATM 2 N N A3G . . . M 2 11.986 2.925 39.219 1 91.13 ? N A3G 501 E 1 
HETATM 3 O O A3G . . . M 2 10.229 2.544 41.847 1 83.33 ? O A3G 501 E 1 
HETATM 4 N N1 A3G . . . M 2 5.618 2.17 46.663 1 73.01 ? N1 A3G 501 E 1 
HETATM 5 C C2 A3G . . . M 2 6.468 3.153 46.37 1 67.7 ? C2 A3G 501 E 1 
HETATM 6 N N3 A3G . . . M 2 6.437 3.748 45.185 1 69.16 ? N3 A3G 501 E 1 
HETATM 7 C C4 A3G . . . M 2 5.544 3.381 44.241 1 72.06 ? C4 A3G 501 E 1 
HETATM 8 C C5 A3G . . . M 2 4.641 2.368 44.522 1 71.3 ? C5 A3G 501 E 1 
HETATM 9 C C6 A3G . . . M 2 4.689 1.756 45.769 1 72.45 ? C6 A3G 501 E 1 
HETATM 10 N N6 A3G . . . M 2 3.824 0.778 46.069 1 71.92 ? N6 A3G 501 E 1 
HETATM 11 N N7 A3G . . . M 2 3.884 2.192 43.445 1 74.38 ? N7 A3G 501 E 1 
HETATM 12 C C8 A3G . . . M 2 4.275 3.06 42.514 1 72.92 ? C8 A3G 501 E 1 
HETATM 13 N N8 A3G . . . M 2 9.059 4.079 40.446 1 89.89 ? N8 A3G 501 E 1 
HETATM 14 N N9 A3G . . . M 2 5.294 3.782 42.989 1 77.61 ? N9 A3G 501 E 1 
HETATM 15 C CA A3G . . . M 2 11.5 3.908 40.201 1 92.32 ? CA A3G 501 E 1 
HETATM 16 C C1' A3G . . . M 2 6.003 4.875 42.229 1 79.72 ? C1' A3G 501 E 1 
HETATM 17 C C2' A3G . . . M 2 7.526 4.719 42.232 1 78.12 ? C2' A3G 501 E 1 
HETATM 18 O O2' A3G . . . M 2 8.161 5.992 41.986 1 69.98 ? O2' A3G 501 E 1 
HETATM 19 C C3' A3G . . . M 2 7.749 3.775 41.052 1 84.53 ? C3' A3G 501 E 1 
HETATM 20 C C4' A3G . . . M 2 6.583 4.06 40.078 1 80.86 ? C4' A3G 501 E 1 
HETATM 21 O O4' A3G . . . M 2 5.615 4.872 40.807 1 80.51 ? O4' A3G 501 E 1 
HETATM 22 C C5' A3G . . . M 2 5.892 2.764 39.605 1 79.94 ? C5' A3G 501 E 1 
HETATM 23 O O5' A3G . . . M 2 5.253 2.984 38.346 1 79.61 ? O5' A3G 501 E 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           248 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           23 
#