data_6M13
#
_model_server_result.job_id            K4AHR28vCpsWrKFNr6iNdw 
_model_server_result.datetime_utc      '2024-10-12 08:24:42' 
_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          6m13 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":802}' 
#
_entry.id    6M13 
#
_exptl.entry_id    6M13 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              1165.593 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate' 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            6M13 
_cell.length_a            59.45 
_cell.length_b            111.36 
_cell.length_c            263.86 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6M13 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_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,F,G,H,I 
_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 D N N 
? 3 G N N 
#
_chem_comp.formula           'C30 H40 N15 O25 P5' 
_chem_comp.formula_weight    1165.593 
_chem_comp.id                25L 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "2'-5'-oligoadenylate trimer" 
#
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 25L doub 1 n y 
N1 C6 25L sing 2 n y 
C2 N3 25L sing 3 n y 
N3 C4 25L doub 4 n y 
C4 C5 25L sing 5 n y 
C4 N9 25L sing 6 n y 
C5 C6 25L doub 7 n y 
C5 N7 25L sing 8 n y 
C6 N6 25L sing 9 n n 
N7 C8 25L doub 10 n y 
C8 N9 25L sing 11 n y 
N9 C1' 25L sing 12 n n 
C1' C2' 25L sing 13 n n 
C1' O4' 25L sing 14 n n 
C2' O2' 25L sing 15 n n 
C2' C3' 25L sing 16 n n 
C3' O3' 25L sing 17 n n 
C3' C4' 25L sing 18 n n 
C4' O4' 25L sing 19 n n 
C4' C5' 25L sing 20 n n 
C5' O5' 25L sing 21 n n 
O5' PCU 25L sing 22 n n 
NAB CBV 25L sing 23 n n 
NAC CBW 25L sing 24 n n 
OAD PCS 25L doub 25 n n 
OAE PCT 25L doub 26 n n 
OAF PCU 25L doub 27 n n 
OAG PCV 25L doub 28 n n 
OAH PCW 25L doub 29 n n 
OAK CCF 25L sing 30 n n 
OAL CCG 25L sing 31 n n 
OAM PCT 25L sing 32 n n 
OAN PCS 25L sing 33 n n 
OAO PCS 25L sing 34 n n 
OAP PCU 25L sing 35 n n 
OAQ PCV 25L sing 36 n n 
OAR PCW 25L sing 37 n n 
CAT NBC 25L doub 38 n y 
CAT NBF 25L sing 39 n y 
CAU NBD 25L doub 40 n y 
CAU NBG 25L sing 41 n y 
CAW NBI 25L doub 42 n y 
CAW NCQ 25L sing 43 n y 
CAX NBJ 25L doub 44 n y 
CAX NCR 25L sing 45 n y 
CAY OBK 25L sing 46 n n 
CAY CCI 25L sing 47 n n 
CBA OBM 25L sing 48 n n 
CBA CCJ 25L sing 49 n n 
NBC CBV 25L sing 50 n y 
NBD CBW 25L sing 51 n y 
NBF CCB 25L doub 52 n y 
NBG CCC 25L doub 53 n y 
NBI CBY 25L sing 54 n y 
NBJ CBZ 25L sing 55 n y 
OBK PCT 25L sing 56 n n 
OBM PCV 25L sing 57 n n 
OBO CCI 25L sing 58 n n 
OBO CCN 25L sing 59 n n 
OBP CCJ 25L sing 60 n n 
OBP CCO 25L sing 61 n n 
OBQ CCK 25L sing 62 n n 
OBQ PCV 25L sing 63 n n 
OBR CCL 25L sing 64 n n 
OBR PCU 25L sing 65 n n 
OBS PCS 25L sing 66 n n 
OBS PCW 25L sing 67 n n 
OBT PCT 25L sing 68 n n 
OBT PCW 25L sing 69 n n 
CBV CBY 25L doub 70 n y 
CBW CBZ 25L doub 71 n y 
CBY CCB 25L sing 72 n y 
CBZ CCC 25L sing 73 n y 
CCB NCQ 25L sing 74 n y 
CCC NCR 25L sing 75 n y 
CCF CCI 25L sing 76 n n 
CCF CCK 25L sing 77 n n 
CCG CCJ 25L sing 78 n n 
CCG CCL 25L sing 79 n n 
CCK CCN 25L sing 80 n n 
CCL CCO 25L sing 81 n n 
CCN NCQ 25L sing 82 n n 
CCO NCR 25L sing 83 n n 
C2 H2 25L sing 84 n n 
N6 HN6 25L sing 85 n n 
N6 HN6A 25L sing 86 n n 
C8 H8 25L sing 87 n n 
C1' H1' 25L sing 88 n n 
C2' H2' 25L sing 89 n n 
O2' HO2' 25L sing 90 n n 
C3' H3' 25L sing 91 n n 
O3' HO3' 25L sing 92 n n 
C4' H4' 25L sing 93 n n 
C5' H5' 25L sing 94 n n 
C5' "H5'A" 25L sing 95 n n 
NAB HNAB 25L sing 96 n n 
NAB HNAA 25L sing 97 n n 
NAC HNAC 25L sing 98 n n 
NAC HNAD 25L sing 99 n n 
OAK HOAK 25L sing 100 n n 
OAL HOAL 25L sing 101 n n 
OAM HOAM 25L sing 102 n n 
OAN HOAN 25L sing 103 n n 
OAO HOAO 25L sing 104 n n 
OAP HOAP 25L sing 105 n n 
OAQ HOAQ 25L sing 106 n n 
OAR HOAR 25L sing 107 n n 
CAT HAT 25L sing 108 n n 
CAU HAU 25L sing 109 n n 
CAW HAW 25L sing 110 n n 
CAX HAX 25L sing 111 n n 
CAY HAY 25L sing 112 n n 
CAY HAYA 25L sing 113 n n 
CBA HBA 25L sing 114 n n 
CBA HBAA 25L sing 115 n n 
CCF HCF 25L sing 116 n n 
CCG HCG 25L sing 117 n n 
CCI HCI 25L sing 118 n n 
CCJ HCJ 25L sing 119 n n 
CCK HCK 25L sing 120 n n 
CCL HCL 25L sing 121 n n 
CCN HCN 25L sing 122 n n 
CCO HCO 25L sing 123 n n 
#
_atom_sites.entry_id                     6M13 
_atom_sites.fract_transf_matrix[1][1]    0.016821 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00898 
_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]    0.00379 
_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 BWC a 1 801 801 BWC DRG . 
D 3 25L a 1 802 904 25L 25L . 
E 4 PO4 a 1 803 1 PO4 PO4 . 
F 2 BWC b 1 901 901 BWC DRG . 
G 3 25L b 1 902 905 25L 25L . 
H 5 HOH a 1 901 2 HOH HOH . 
H 5 HOH a 2 902 4 HOH HOH . 
H 5 HOH a 3 903 10 HOH HOH . 
H 5 HOH a 4 904 5 HOH HOH . 
H 5 HOH a 5 905 3 HOH HOH . 
H 5 HOH a 6 906 8 HOH HOH . 
H 5 HOH a 7 907 9 HOH HOH . 
I 5 HOH b 1 1001 6 HOH HOH . 
I 5 HOH b 2 1002 1 HOH HOH . 
I 5 HOH b 3 1003 7 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 N N1 25L . . . D 3 -28.229 -3.113 -27.967 1 83.95 ? N1 25L 802 a 1 
HETATM 2 C C2 25L . . . D 3 -27.705 -2.704 -29.151 1 89.67 ? C2 25L 802 a 1 
HETATM 3 N N3 25L . . . D 3 -27.088 -1.477 -29.233 1 79.29 ? N3 25L 802 a 1 
HETATM 4 C C4 25L . . . D 3 -27.005 -0.68 -28.143 1 82.36 ? C4 25L 802 a 1 
HETATM 5 C C5 25L . . . D 3 -27.535 -1.08 -26.98 1 91.05 ? C5 25L 802 a 1 
HETATM 6 C C6 25L . . . D 3 -28.15 -2.314 -26.881 1 94.95 ? C6 25L 802 a 1 
HETATM 7 N N6 25L . . . D 3 -28.778 -2.914 -25.679 1 101.71 ? N6 25L 802 a 1 
HETATM 8 N N7 25L . . . D 3 -27.324 -0.125 -26.087 1 91.05 ? N7 25L 802 a 1 
HETATM 9 C C8 25L . . . D 3 -26.662 0.873 -26.708 1 97.84 ? C8 25L 802 a 1 
HETATM 10 N N9 25L . . . D 3 -26.47 0.544 -27.976 1 87.66 ? N9 25L 802 a 1 
HETATM 11 C C1' 25L . . . D 3 -25.804 1.254 -29.037 1 81.13 ? C1' 25L 802 a 1 
HETATM 12 C C2' 25L . . . D 3 -25.636 2.569 -28.933 1 75.7 ? C2' 25L 802 a 1 
HETATM 13 O O2' 25L . . . D 3 -26.027 3.155 -30.236 1 89.65 ? O2' 25L 802 a 1 
HETATM 14 C C3' 25L . . . D 3 -24.138 2.868 -28.686 1 78.77 ? C3' 25L 802 a 1 
HETATM 15 O O3' 25L . . . D 3 -23.712 4.043 -29.18 1 70.84 ? O3' 25L 802 a 1 
HETATM 16 C C4' 25L . . . D 3 -23.495 1.643 -29.411 1 74.35 ? C4' 25L 802 a 1 
HETATM 17 O O4' 25L . . . D 3 -24.301 0.624 -29.152 1 76.04 ? O4' 25L 802 a 1 
HETATM 18 C C5' 25L . . . D 3 -22.066 1.442 -28.861 1 67.08 ? C5' 25L 802 a 1 
HETATM 19 O O5' 25L . . . D 3 -22.051 1.901 -27.499 1 71.06 ? O5' 25L 802 a 1 
HETATM 20 N NAB 25L . . . D 3 -17.677 4.87 -18.379 1 78.31 ? NAB 25L 802 a 1 
HETATM 21 N NAC 25L . . . D 3 -20.127 6.391 -20.171 1 69.23 ? NAC 25L 802 a 1 
HETATM 22 O OAE 25L . . . D 3 -9.827 8.42 -21.165 1 75.67 ? OAE 25L 802 a 1 
HETATM 23 O OAF 25L . . . D 3 -22.038 1.396 -25.03 1 65.46 ? OAF 25L 802 a 1 
HETATM 24 O OAG 25L . . . D 3 -14.497 5.904 -28.19 1 63.99 ? OAG 25L 802 a 1 
HETATM 25 O OAK 25L . . . D 3 -12.446 7.898 -24.837 1 87.38 ? OAK 25L 802 a 1 
HETATM 26 O OAL 25L . . . D 3 -18.81 2.506 -28.287 1 63.73 ? OAL 25L 802 a 1 
HETATM 27 O OAM 25L . . . D 3 -11.458 7.949 -19.311 1 62.73 ? OAM 25L 802 a 1 
HETATM 28 O OAP 25L . . . D 3 -21.278 -0.5 -26.597 1 77.12 ? OAP 25L 802 a 1 
HETATM 29 O OAQ 25L . . . D 3 -16.111 7.382 -26.841 1 69.28 ? OAQ 25L 802 a 1 
HETATM 30 C CAT 25L . . . D 3 -16.672 2.626 -20.936 1 82.32 ? CAT 25L 802 a 1 
HETATM 31 C CAU 25L . . . D 3 -20.302 2.93 -20.899 1 72.27 ? CAU 25L 802 a 1 
HETATM 32 C CAW 25L . . . D 3 -15.472 6.837 -21.706 1 81.76 ? CAW 25L 802 a 1 
HETATM 33 C CAX 25L . . . D 3 -18.505 5.211 -24.263 1 74.28 ? CAX 25L 802 a 1 
HETATM 34 C CAY 25L . . . D 3 -11.228 5.93 -22.615 1 88.09 ? CAY 25L 802 a 1 
HETATM 35 C CBA 25L . . . D 3 -15.922 3.614 -27.224 1 65.63 ? CBA 25L 802 a 1 
HETATM 36 N NBC 25L . . . D 3 -17.173 3.195 -19.811 1 80.16 ? NBC 25L 802 a 1 
HETATM 37 N NBD 25L . . . D 3 -20.363 4.164 -20.363 1 72.76 ? NBD 25L 802 a 1 
HETATM 38 N NBF 25L . . . D 3 -16.029 3.377 -21.868 1 80.67 ? NBF 25L 802 a 1 
HETATM 39 N NBG 25L . . . D 3 -19.788 2.743 -22.13 1 76.75 ? NBG 25L 802 a 1 
HETATM 40 N NBI 25L . . . D 3 -16.163 6.583 -20.575 1 81.1 ? NBI 25L 802 a 1 
HETATM 41 N NBJ 25L . . . D 3 -18.89 5.914 -23.181 1 71.4 ? NBJ 25L 802 a 1 
HETATM 42 O OBK 25L . . . D 3 -11.774 6.735 -21.547 1 74.44 ? OBK 25L 802 a 1 
HETATM 43 O OBM 25L . . . D 3 -16.216 4.882 -26.621 1 77.36 ? OBM 25L 802 a 1 
HETATM 44 O OBO 25L . . . D 3 -13.185 4.849 -23.404 1 88.38 ? OBO 25L 802 a 1 
HETATM 45 O OBP 25L . . . D 3 -17.04 2.733 -25.452 1 86.44 ? OBP 25L 802 a 1 
HETATM 46 O OBQ 25L . . . D 3 -14.086 6.291 -25.759 1 81.03 ? OBQ 25L 802 a 1 
HETATM 47 O OBR 25L . . . D 3 -19.773 1.399 -26.202 1 77.16 ? OBR 25L 802 a 1 
HETATM 48 O OBT 25L . . . D 3 -9.576 6.103 -20.176 1 71.54 ? OBT 25L 802 a 1 
HETATM 49 C CBV 25L . . . D 3 -17.062 4.508 -19.608 1 79.97 ? CBV 25L 802 a 1 
HETATM 50 C CBW 25L . . . D 3 -19.918 5.201 -21.028 1 72.87 ? CBW 25L 802 a 1 
HETATM 51 C CBY 25L . . . D 3 -16.413 5.27 -20.554 1 83.62 ? CBY 25L 802 a 1 
HETATM 52 C CBZ 25L . . . D 3 -19.394 5.026 -22.28 1 75.67 ? CBZ 25L 802 a 1 
HETATM 53 C CCB 25L . . . D 3 -15.886 4.722 -21.656 1 78.87 ? CCB 25L 802 a 1 
HETATM 54 C CCC 25L . . . D 3 -19.343 3.804 -22.814 1 78.96 ? CCC 25L 802 a 1 
HETATM 55 C CCF 25L . . . D 3 -13.078 7.157 -23.889 1 90.95 ? CCF 25L 802 a 1 
HETATM 56 C CCG 25L . . . D 3 -18.474 3.189 -27.206 1 67.18 ? CCG 25L 802 a 1 
HETATM 57 C CCI 25L . . . D 3 -12.287 5.775 -23.71 1 88.77 ? CCI 25L 802 a 1 
HETATM 58 C CCJ 25L . . . D 3 -17.041 2.702 -26.762 1 76.94 ? CCJ 25L 802 a 1 
HETATM 59 C CCK 25L . . . D 3 -14.423 6.653 -24.364 1 82.94 ? CCK 25L 802 a 1 
HETATM 60 C CCL 25L . . . D 3 -19.346 2.804 -26.008 1 70.62 ? CCL 25L 802 a 1 
HETATM 61 C CCN 25L . . . D 3 -14.648 5.521 -23.651 1 74.99 ? CCN 25L 802 a 1 
HETATM 62 C CCO 25L . . . D 3 -18.567 2.796 -24.931 1 74.87 ? CCO 25L 802 a 1 
HETATM 63 N NCQ 25L . . . D 3 -15.283 5.696 -22.382 1 70.96 ? NCQ 25L 802 a 1 
HETATM 64 N NCR 25L . . . D 3 -18.795 3.917 -24.059 1 76.58 ? NCR 25L 802 a 1 
HETATM 65 P PCT 25L . . . D 3 -10.662 7.353 -20.501 1 77.72 ? PCT 25L 802 a 1 
HETATM 66 P PCU 25L . . . D 3 -21.354 0.994 -26.282 1 73.41 ? PCU 25L 802 a 1 
HETATM 67 P PCV 25L . . . D 3 -15.228 6.145 -26.917 1 70.55 ? PCV 25L 802 a 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           67 
#