data_6M13
#
_model_server_result.job_id            G7F206m4ccnDO7kl5PCsMQ 
_model_server_result.datetime_utc      '2024-11-24 14:50:51' 
_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":"G","auth_seq_id":902}' 
#
_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 . . . G 3 -5.224 55.908 -18.799 1 133.96 ? N1 25L 902 b 1 
HETATM 2 C C2 25L . . . G 3 -4.667 55.292 -19.884 1 135.24 ? C2 25L 902 b 1 
HETATM 3 N N3 25L . . . G 3 -5.294 54.209 -20.466 1 139.1 ? N3 25L 902 b 1 
HETATM 4 C C4 25L . . . G 3 -6.469 53.746 -19.955 1 135.98 ? C4 25L 902 b 1 
HETATM 5 C C5 25L . . . G 3 -7.006 54.356 -18.887 1 137.61 ? C5 25L 902 b 1 
HETATM 6 C C6 25L . . . G 3 -6.396 55.445 -18.299 1 134.53 ? C6 25L 902 b 1 
HETATM 7 N N6 25L . . . G 3 -6.91 56.188 -17.126 1 114.96 ? N6 25L 902 b 1 
HETATM 8 N N7 25L . . . G 3 -8.13 53.728 -18.571 1 139.64 ? N7 25L 902 b 1 
HETATM 9 C C8 25L . . . G 3 -8.298 52.719 -19.429 1 129.11 ? C8 25L 902 b 1 
HETATM 10 N N9 25L . . . G 3 -7.274 52.715 -20.285 1 133.64 ? N9 25L 902 b 1 
HETATM 11 C C1' 25L . . . G 3 -7.068 51.821 -21.416 1 122.29 ? C1' 25L 902 b 1 
HETATM 12 C C2' 25L . . . G 3 -7.162 50.488 -21.221 1 107.77 ? C2' 25L 902 b 1 
HETATM 13 O O2' 25L . . . G 3 -5.983 49.838 -21.858 1 85.95 ? O2' 25L 902 b 1 
HETATM 14 C C3' 25L . . . G 3 -8.465 49.965 -21.888 1 90.38 ? C3' 25L 902 b 1 
HETATM 15 O O3' 25L . . . G 3 -8.336 48.735 -22.404 1 87.84 ? O3' 25L 902 b 1 
HETATM 16 C C4' 25L . . . G 3 -8.649 51.037 -22.997 1 82.97 ? C4' 25L 902 b 1 
HETATM 17 O O4' 25L . . . G 3 -8.26 52.179 -22.491 1 92.66 ? O4' 25L 902 b 1 
HETATM 18 C C5' 25L . . . G 3 -10.141 51.073 -23.329 1 73.18 ? C5' 25L 902 b 1 
HETATM 19 O O5' 25L . . . G 3 -10.753 52.074 -22.529 1 71.7 ? O5' 25L 902 b 1 
HETATM 20 N NAB 25L . . . G 3 -20.853 48.847 -20.132 1 136.09 ? NAB 25L 902 b 1 
HETATM 21 N NAC 25L . . . G 3 -18.551 46.963 -19.635 1 78.41 ? NAC 25L 902 b 1 
HETATM 22 O OAE 25L . . . G 3 -25.765 46.162 -27.17 1 94.2 ? OAE 25L 902 b 1 
HETATM 23 O OAF 25L . . . G 3 -13.037 51.452 -21.356 1 105.71 ? OAF 25L 902 b 1 
HETATM 24 O OAG 25L . . . G 3 -15.7 46.666 -28.915 1 103.21 ? OAG 25L 902 b 1 
HETATM 25 O OAK 25L . . . G 3 -19.136 45.035 -28.059 1 87.64 ? OAK 25L 902 b 1 
HETATM 26 O OAL 25L . . . G 3 -12.642 49.611 -25.865 1 83.65 ? OAL 25L 902 b 1 
HETATM 27 O OAM 25L . . . G 3 -24.224 44.414 -28.053 1 83.32 ? OAM 25L 902 b 1 
HETATM 28 O OAP 25L . . . G 3 -13.04 53.419 -22.81 1 91.58 ? OAP 25L 902 b 1 
HETATM 29 O OAQ 25L . . . G 3 -15.934 45.265 -26.887 1 81.11 ? OAQ 25L 902 b 1 
HETATM 30 C CAT 25L . . . G 3 -19.999 50.822 -22.923 1 139.39 ? CAT 25L 902 b 1 
HETATM 31 C CAU 25L . . . G 3 -17.229 50.262 -19.631 1 115.88 ? CAU 25L 902 b 1 
HETATM 32 C CAW 25L . . . G 3 -19.877 46.434 -23.77 1 120.06 ? CAW 25L 902 b 1 
HETATM 33 C CAX 25L . . . G 3 -16.122 47.977 -23.291 1 108.71 ? CAX 25L 902 b 1 
HETATM 34 C CAY 25L . . . G 3 -22.023 45.877 -26.256 1 80.11 ? CAY 25L 902 b 1 
HETATM 35 C CBA 25L . . . G 3 -15.782 49.098 -26.761 1 90.27 ? CBA 25L 902 b 1 
HETATM 36 N NBC 25L . . . G 3 -20.36 50.375 -21.708 1 139.44 ? NBC 25L 902 b 1 
HETATM 37 N NBD 25L . . . G 3 -17.857 49.097 -19.337 1 107.16 ? NBD 25L 902 b 1 
HETATM 38 N NBF 25L . . . G 3 -19.743 49.948 -23.934 1 141.47 ? NBF 25L 902 b 1 
HETATM 39 N NBG 25L . . . G 3 -16.532 50.388 -20.803 1 121.53 ? NBG 25L 902 b 1 
HETATM 40 N NBI 25L . . . G 3 -20.212 46.825 -22.538 1 132.7 ? NBI 25L 902 b 1 
HETATM 41 N NBJ 25L . . . G 3 -16.889 47.353 -22.381 1 97.19 ? NBJ 25L 902 b 1 
HETATM 42 O OBK 25L . . . G 3 -23.237 46.485 -26.648 1 78.45 ? OBK 25L 902 b 1 
HETATM 43 O OBM 25L . . . G 3 -15.29 47.76 -26.658 1 80.32 ? OBM 25L 902 b 1 
HETATM 44 O OBO 25L . . . G 3 -20.609 47.641 -26.793 1 81.07 ? OBO 25L 902 b 1 
HETATM 45 O OBP 25L . . . G 3 -15.741 50.586 -24.97 1 95.4 ? OBP 25L 902 b 1 
HETATM 46 O OBQ 25L . . . G 3 -17.769 47.042 -27.548 1 84.56 ? OBQ 25L 902 b 1 
HETATM 47 O OBR 25L . . . G 3 -12.965 51.1 -23.826 1 79.39 ? OBR 25L 902 b 1 
HETATM 48 O OBT 25L . . . G 3 -24.423 44.578 -25.45 1 109.32 ? OBT 25L 902 b 1 
HETATM 49 C CBV 25L . . . G 3 -20.461 49.055 -21.486 1 137.58 ? CBV 25L 902 b 1 
HETATM 50 C CBW 25L . . . G 3 -17.776 48.091 -20.19 1 108.6 ? CBW 25L 902 b 1 
HETATM 51 C CBY 25L . . . G 3 -20.194 48.163 -22.51 1 132.78 ? CBY 25L 902 b 1 
HETATM 52 C CBZ 25L . . . G 3 -17.083 48.228 -21.37 1 112.7 ? CBZ 25L 902 b 1 
HETATM 53 C CCB 25L . . . G 3 -19.847 48.602 -23.709 1 128.95 ? CCB 25L 902 b 1 
HETATM 54 C CCC 25L . . . G 3 -16.467 49.372 -21.663 1 107.47 ? CCC 25L 902 b 1 
HETATM 55 C CCF 25L . . . G 3 -19.581 45.583 -26.921 1 84.17 ? CCF 25L 902 b 1 
HETATM 56 C CCG 25L . . . G 3 -13.75 49.334 -25.192 1 90.65 ? CCG 25L 902 b 1 
HETATM 57 C CCI 25L . . . G 3 -20.887 46.427 -27.147 1 82.35 ? CCI 25L 902 b 1 
HETATM 58 C CCJ 25L . . . G 3 -14.956 50.053 -25.909 1 91.62 ? CCJ 25L 902 b 1 
HETATM 59 C CCK 25L . . . G 3 -18.566 46.581 -26.402 1 90.39 ? CCK 25L 902 b 1 
HETATM 60 C CCL 25L . . . G 3 -13.803 49.909 -23.76 1 90.78 ? CCL 25L 902 b 1 
HETATM 61 C CCN 25L . . . G 3 -19.258 47.609 -25.913 1 94.31 ? CCN 25L 902 b 1 
HETATM 62 C CCO 25L . . . G 3 -15.084 50.257 -23.531 1 95.89 ? CCO 25L 902 b 1 
HETATM 63 N NCQ 25L . . . G 3 -19.642 47.528 -24.511 1 119.31 ? NCQ 25L 902 b 1 
HETATM 64 N NCR 25L . . . G 3 -15.854 49.226 -22.864 1 106.8 ? NCR 25L 902 b 1 
HETATM 65 P PCT 25L . . . G 3 -24.467 45.412 -26.896 1 94.96 ? PCT 25L 902 b 1 
HETATM 66 P PCU 25L . . . G 3 -12.446 52.032 -22.587 1 90.27 ? PCU 25L 902 b 1 
HETATM 67 P PCV 25L . . . G 3 -16.149 46.649 -27.483 1 83.46 ? PCV 25L 902 b 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           67 
#