data_7ZVL
#
_model_server_result.job_id            8FY4aNxEV2nL3Li7oouYMA 
_model_server_result.datetime_utc      '2025-07-05 15:16:30' 
_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          7zvl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":701}' 
#
_entry.id    7ZVL 
#
_exptl.entry_id    7ZVL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              297.334 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-DEOXY-5'-METHYLTHIOADENOSINE" 
_entity.pdbx_number_of_molecules    1 
_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            7ZVL 
_cell.length_a            100.576 
_cell.length_b            138.392 
_cell.length_c            178.493 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7ZVL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 B SG CYS 180 B CYS 172 1_555 B SG CYS 194 B CYS 186 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.75 ? 
disulf ? disulf2 B SG CYS 216 B CYS 208 1_555 B SG CYS 255 B CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
#
_chem_comp.formula           'C11 H15 N5 O3 S' 
_chem_comp.formula_weight    297.334 
_chem_comp.id                MTA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-DEOXY-5'-METHYLTHIOADENOSINE" 
_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
CS S5' MTA sing 250 n n 
CS HCS1 MTA sing 251 n n 
CS HCS2 MTA sing 252 n n 
CS HCS3 MTA sing 253 n n 
S5' C5' MTA sing 254 n n 
C5' C4' MTA sing 255 n n 
C5' "H5'1" MTA sing 256 n n 
C5' "H5'2" MTA sing 257 n n 
C4' O4' MTA sing 258 n n 
C4' C3' MTA sing 259 n n 
C4' H4' MTA sing 260 n n 
O4' C1' MTA sing 261 n n 
C2' O2' MTA sing 262 n n 
C2' C3' MTA sing 263 n n 
C2' C1' MTA sing 264 n n 
C2' H2' MTA sing 265 n n 
O2' HO2' MTA sing 266 n n 
C3' O3' MTA sing 267 n n 
C3' H3' MTA sing 268 n n 
O3' H3T MTA sing 269 n n 
C1' N9 MTA sing 270 n n 
C1' H1' MTA sing 271 n n 
N9 C8 MTA sing 272 n y 
N9 C4 MTA sing 273 n y 
C8 N7 MTA doub 274 n y 
C8 H8 MTA sing 275 n n 
N7 C5 MTA sing 276 n y 
C5 C6 MTA sing 277 n y 
C5 C4 MTA doub 278 n y 
C6 N6 MTA sing 279 n n 
C6 N1 MTA doub 280 n y 
N6 H61 MTA sing 281 n n 
N6 H62 MTA sing 282 n n 
N1 C2 MTA sing 283 n y 
C2 N3 MTA doub 284 n y 
C2 H2 MTA sing 285 n n 
N3 C4 MTA sing 286 n y 
#
_atom_sites.entry_id                     7ZVL 
_atom_sites.fract_transf_matrix[1][1]    0.009943 
_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]    0.007226 
_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]    0.005602 
_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 3 MTA A 1 701 1000 MTA MTA . 
D 4 UNL A 1 702 1001 UNL UNL . 
E 5 GOL A 1 703 2 GOL GOL . 
F 6 CL A 1 704 1 CL CL . 
G 5 GOL B 1 401 1 GOL GOL . 
H 7 HOH A 1 801 60 HOH HOH . 
H 7 HOH A 2 802 46 HOH HOH . 
H 7 HOH A 3 803 110 HOH HOH . 
H 7 HOH A 4 804 59 HOH HOH . 
H 7 HOH A 5 805 64 HOH HOH . 
H 7 HOH A 6 806 34 HOH HOH . 
H 7 HOH A 7 807 56 HOH HOH . 
H 7 HOH A 8 808 63 HOH HOH . 
H 7 HOH A 9 809 74 HOH HOH . 
H 7 HOH A 10 810 44 HOH HOH . 
H 7 HOH A 11 811 61 HOH HOH . 
H 7 HOH A 12 812 72 HOH HOH . 
H 7 HOH A 13 813 47 HOH HOH . 
H 7 HOH A 14 814 78 HOH HOH . 
H 7 HOH A 15 815 76 HOH HOH . 
H 7 HOH A 16 816 45 HOH HOH . 
H 7 HOH A 17 817 50 HOH HOH . 
H 7 HOH A 18 818 6 HOH HOH . 
H 7 HOH A 19 819 38 HOH HOH . 
H 7 HOH A 20 820 66 HOH HOH . 
H 7 HOH A 21 821 83 HOH HOH . 
H 7 HOH A 22 822 41 HOH HOH . 
H 7 HOH A 23 823 97 HOH HOH . 
H 7 HOH A 24 824 129 HOH HOH . 
H 7 HOH A 25 825 75 HOH HOH . 
H 7 HOH A 26 826 69 HOH HOH . 
H 7 HOH A 27 827 71 HOH HOH . 
H 7 HOH A 28 828 86 HOH HOH . 
H 7 HOH A 29 829 35 HOH HOH . 
H 7 HOH A 30 830 37 HOH HOH . 
H 7 HOH A 31 831 85 HOH HOH . 
H 7 HOH A 32 832 5 HOH HOH . 
H 7 HOH A 33 833 77 HOH HOH . 
H 7 HOH A 34 834 80 HOH HOH . 
H 7 HOH A 35 835 103 HOH HOH . 
H 7 HOH A 36 836 49 HOH HOH . 
H 7 HOH A 37 837 57 HOH HOH . 
H 7 HOH A 38 838 70 HOH HOH . 
H 7 HOH A 39 839 58 HOH HOH . 
H 7 HOH A 40 840 94 HOH HOH . 
H 7 HOH A 41 841 134 HOH HOH . 
H 7 HOH A 42 842 53 HOH HOH . 
H 7 HOH A 43 843 62 HOH HOH . 
H 7 HOH A 44 844 91 HOH HOH . 
H 7 HOH A 45 845 33 HOH HOH . 
H 7 HOH A 46 846 82 HOH HOH . 
H 7 HOH A 47 847 55 HOH HOH . 
H 7 HOH A 48 848 84 HOH HOH . 
H 7 HOH A 49 849 42 HOH HOH . 
H 7 HOH A 50 850 81 HOH HOH . 
H 7 HOH A 51 851 88 HOH HOH . 
H 7 HOH A 52 852 7 HOH HOH . 
H 7 HOH A 53 853 126 HOH HOH . 
H 7 HOH A 54 854 48 HOH HOH . 
H 7 HOH A 55 855 36 HOH HOH . 
H 7 HOH A 56 856 117 HOH HOH . 
H 7 HOH A 57 857 95 HOH HOH . 
H 7 HOH A 58 858 109 HOH HOH . 
H 7 HOH A 59 859 79 HOH HOH . 
H 7 HOH A 60 860 104 HOH HOH . 
H 7 HOH A 61 861 116 HOH HOH . 
H 7 HOH A 62 862 68 HOH HOH . 
H 7 HOH A 63 863 124 HOH HOH . 
H 7 HOH A 64 864 119 HOH HOH . 
H 7 HOH A 65 865 96 HOH HOH . 
H 7 HOH A 66 866 89 HOH HOH . 
H 7 HOH A 67 867 3 HOH HOH . 
H 7 HOH A 68 868 65 HOH HOH . 
H 7 HOH A 69 869 102 HOH HOH . 
H 7 HOH A 70 870 40 HOH HOH . 
H 7 HOH A 71 871 105 HOH HOH . 
H 7 HOH A 72 872 108 HOH HOH . 
H 7 HOH A 73 873 123 HOH HOH . 
H 7 HOH A 74 874 90 HOH HOH . 
H 7 HOH A 75 875 115 HOH HOH . 
H 7 HOH A 76 876 1 HOH HOH . 
H 7 HOH A 77 877 122 HOH HOH . 
H 7 HOH A 78 878 25 HOH HOH . 
H 7 HOH A 79 879 114 HOH HOH . 
H 7 HOH A 80 880 93 HOH HOH . 
H 7 HOH A 81 881 43 HOH HOH . 
H 7 HOH A 82 882 112 HOH HOH . 
H 7 HOH A 83 883 67 HOH HOH . 
H 7 HOH A 84 884 4 HOH HOH . 
H 7 HOH A 85 885 73 HOH HOH . 
H 7 HOH A 86 886 106 HOH HOH . 
H 7 HOH A 87 887 125 HOH HOH . 
H 7 HOH A 88 888 132 HOH HOH . 
H 7 HOH A 89 889 52 HOH HOH . 
H 7 HOH A 90 890 131 HOH HOH . 
H 7 HOH A 91 891 99 HOH HOH . 
H 7 HOH A 92 892 101 HOH HOH . 
H 7 HOH A 93 893 92 HOH HOH . 
H 7 HOH A 94 894 100 HOH HOH . 
H 7 HOH A 95 895 135 HOH HOH . 
H 7 HOH A 96 896 39 HOH HOH . 
H 7 HOH A 97 897 121 HOH HOH . 
H 7 HOH A 98 898 133 HOH HOH . 
H 7 HOH A 99 899 118 HOH HOH . 
H 7 HOH A 100 900 120 HOH HOH . 
H 7 HOH A 101 901 107 HOH HOH . 
H 7 HOH A 102 902 98 HOH HOH . 
H 7 HOH A 103 903 2 HOH HOH . 
H 7 HOH A 104 904 51 HOH HOH . 
H 7 HOH A 105 905 54 HOH HOH . 
H 7 HOH A 106 906 87 HOH HOH . 
H 7 HOH A 107 907 111 HOH HOH . 
H 7 HOH A 108 908 128 HOH HOH . 
H 7 HOH A 109 909 113 HOH HOH . 
H 7 HOH A 110 910 127 HOH HOH . 
H 7 HOH A 111 911 130 HOH HOH . 
I 7 HOH B 1 501 18 HOH HOH . 
I 7 HOH B 2 502 13 HOH HOH . 
I 7 HOH B 3 503 17 HOH HOH . 
I 7 HOH B 4 504 12 HOH HOH . 
I 7 HOH B 5 505 15 HOH HOH . 
I 7 HOH B 6 506 20 HOH HOH . 
I 7 HOH B 7 507 30 HOH HOH . 
I 7 HOH B 8 508 24 HOH HOH . 
I 7 HOH B 9 509 14 HOH HOH . 
I 7 HOH B 10 510 11 HOH HOH . 
I 7 HOH B 11 511 16 HOH HOH . 
I 7 HOH B 12 512 10 HOH HOH . 
I 7 HOH B 13 513 8 HOH HOH . 
I 7 HOH B 14 514 19 HOH HOH . 
I 7 HOH B 15 515 29 HOH HOH . 
I 7 HOH B 16 516 28 HOH HOH . 
I 7 HOH B 17 517 9 HOH HOH . 
I 7 HOH B 18 518 21 HOH HOH . 
I 7 HOH B 19 519 26 HOH HOH . 
I 7 HOH B 20 520 23 HOH HOH . 
I 7 HOH B 21 521 22 HOH HOH . 
I 7 HOH B 22 522 27 HOH HOH . 
I 7 HOH B 23 523 32 HOH HOH . 
I 7 HOH B 24 524 31 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 CS MTA . . . C 3 21.434 -39.301 -6.41 1 37.56 ? CS MTA 701 A 1 
HETATM 2 S S5' MTA . . . C 3 20.125 -40.454 -6.316 1 36.08 ? S5' MTA 701 A 1 
HETATM 3 C C5' MTA . . . C 3 18.921 -39.17 -6.056 1 35.98 ? C5' MTA 701 A 1 
HETATM 4 C C4' MTA . . . C 3 19.112 -38.419 -4.74 1 36.52 ? C4' MTA 701 A 1 
HETATM 5 O O4' MTA . . . C 3 18.095 -37.426 -4.638 1 36.7 ? O4' MTA 701 A 1 
HETATM 6 C C2' MTA . . . C 3 17.555 -38.885 -2.968 1 35.68 ? C2' MTA 701 A 1 
HETATM 7 O O2' MTA . . . C 3 17.422 -39.018 -1.512 1 36.11 ? O2' MTA 701 A 1 
HETATM 8 C C3' MTA . . . C 3 18.938 -39.287 -3.516 1 36.05 ? C3' MTA 701 A 1 
HETATM 9 O O3' MTA . . . C 3 20.074 -39.062 -2.641 1 36.86 ? O3' MTA 701 A 1 
HETATM 10 C C1' MTA . . . C 3 17.378 -37.458 -3.439 1 35.98 ? C1' MTA 701 A 1 
HETATM 11 N N9 MTA . . . C 3 15.994 -37.126 -3.721 1 35.3 ? N9 MTA 701 A 1 
HETATM 12 C C8 MTA . . . C 3 15.158 -37.788 -4.478 1 34.63 ? C8 MTA 701 A 1 
HETATM 13 N N7 MTA . . . C 3 13.963 -37.186 -4.503 1 34.48 ? N7 MTA 701 A 1 
HETATM 14 C C5 MTA . . . C 3 14.041 -36.117 -3.774 1 35.26 ? C5 MTA 701 A 1 
HETATM 15 C C6 MTA . . . C 3 13.125 -35.057 -3.351 1 35.93 ? C6 MTA 701 A 1 
HETATM 16 N N6 MTA . . . C 3 11.86 -35.034 -3.76 1 35.86 ? N6 MTA 701 A 1 
HETATM 17 N N1 MTA . . . C 3 13.575 -34.073 -2.569 1 36.8 ? N1 MTA 701 A 1 
HETATM 18 C C2 MTA . . . C 3 14.844 -34.104 -2.122 1 37.51 ? C2 MTA 701 A 1 
HETATM 19 N N3 MTA . . . C 3 15.732 -35.084 -2.448 1 37.16 ? N3 MTA 701 A 1 
HETATM 20 C C4 MTA . . . C 3 15.39 -36.081 -3.276 1 35.87 ? C4 MTA 701 A 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           397 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           20 
#