data_6ZD5
#
_model_server_result.job_id            bPVIJAHvgkfWbbQwhsTpQw 
_model_server_result.datetime_utc      '2024-10-19 05:27:53' 
_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          6zd5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":606}' 
#
_entry.id    6ZD5 
#
_exptl.entry_id    6ZD5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              281.268 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-methyladenosine 
_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          105.765 
_cell.angle_gamma         90 
_cell.entry_id            6ZD5 
_cell.length_a            39.82 
_cell.length_b            103.4 
_cell.length_c            42.49 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6ZD5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,L 1 1 
B,I,J,K,M 2 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 H N N 
? 3 K N N 
#
_chem_comp.formula           'C11 H15 N5 O4' 
_chem_comp.formula_weight    281.268 
_chem_comp.id                6MD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-methyladenosine 
_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
C2 N1 6MD doub 1 n y 
C2 N3 6MD sing 2 n y 
N1 C6 6MD sing 3 n y 
N3 C4 6MD doub 4 n y 
CZ N6 6MD sing 5 n n 
C6 N6 6MD sing 6 n n 
C6 C5 6MD doub 7 n y 
C4 C5 6MD sing 8 n y 
C4 N9 6MD sing 9 n y 
C4' O4' 6MD sing 10 n n 
C4' C5' 6MD sing 11 n n 
C4' C3' 6MD sing 12 n n 
O4' C1' 6MD sing 13 n n 
C5 N7 6MD sing 14 n y 
C5' O5' 6MD sing 15 n n 
O3' C3' 6MD sing 16 n n 
C1' N9 6MD sing 17 n n 
C1' C2' 6MD sing 18 n n 
N9 C8 6MD sing 19 n y 
C3' C2' 6MD sing 20 n n 
C2' O2' 6MD sing 21 n n 
N7 C8 6MD doub 22 n y 
O5' H1 6MD sing 23 n n 
C5' H2 6MD sing 24 n n 
C5' H3 6MD sing 25 n n 
C4' H4 6MD sing 26 n n 
C3' H5 6MD sing 27 n n 
O3' H6 6MD sing 28 n n 
C2' H7 6MD sing 29 n n 
O2' H8 6MD sing 30 n n 
C1' H9 6MD sing 31 n n 
C8 H10 6MD sing 32 n n 
N6 H11 6MD sing 33 n n 
C2 H12 6MD sing 34 n n 
CZ H13 6MD sing 35 n n 
CZ H14 6MD sing 36 n n 
CZ H15 6MD sing 37 n n 
#
_atom_sites.entry_id                     6ZD5 
_atom_sites.fract_transf_matrix[1][1]    0.025113 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00709 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009671 
_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]    0.024455 
_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 SO4 A 1 601 1 SO4 SO4 . 
D 2 SO4 A 1 602 4 SO4 SO4 . 
E 2 SO4 A 1 603 6 SO4 SO4 . 
F 2 SO4 A 1 604 7 SO4 SO4 . 
G 2 SO4 A 1 605 8 SO4 SO4 . 
H 3 6MD A 1 606 601 6MD 6MD . 
I 2 SO4 B 1 601 2 SO4 SO4 . 
J 2 SO4 B 1 602 5 SO4 SO4 . 
K 3 6MD B 1 603 602 6MD 6MD . 
L 4 HOH A 1 701 85 HOH HOH . 
L 4 HOH A 2 702 24 HOH HOH . 
L 4 HOH A 3 703 68 HOH HOH . 
L 4 HOH A 4 704 119 HOH HOH . 
L 4 HOH A 5 705 30 HOH HOH . 
L 4 HOH A 6 706 67 HOH HOH . 
L 4 HOH A 7 707 114 HOH HOH . 
L 4 HOH A 8 708 41 HOH HOH . 
L 4 HOH A 9 709 120 HOH HOH . 
L 4 HOH A 10 710 39 HOH HOH . 
L 4 HOH A 11 711 69 HOH HOH . 
L 4 HOH A 12 712 25 HOH HOH . 
L 4 HOH A 13 713 136 HOH HOH . 
L 4 HOH A 14 714 65 HOH HOH . 
L 4 HOH A 15 715 98 HOH HOH . 
L 4 HOH A 16 716 95 HOH HOH . 
L 4 HOH A 17 717 36 HOH HOH . 
L 4 HOH A 18 718 161 HOH HOH . 
L 4 HOH A 19 719 73 HOH HOH . 
L 4 HOH A 20 720 6 HOH HOH . 
L 4 HOH A 21 721 91 HOH HOH . 
L 4 HOH A 22 722 38 HOH HOH . 
L 4 HOH A 23 723 117 HOH HOH . 
L 4 HOH A 24 724 93 HOH HOH . 
L 4 HOH A 25 725 4 HOH HOH . 
L 4 HOH A 26 726 127 HOH HOH . 
L 4 HOH A 27 727 166 HOH HOH . 
L 4 HOH A 28 728 23 HOH HOH . 
L 4 HOH A 29 729 16 HOH HOH . 
L 4 HOH A 30 730 75 HOH HOH . 
L 4 HOH A 31 731 5 HOH HOH . 
L 4 HOH A 32 732 31 HOH HOH . 
L 4 HOH A 33 733 48 HOH HOH . 
L 4 HOH A 34 734 92 HOH HOH . 
L 4 HOH A 35 735 44 HOH HOH . 
L 4 HOH A 36 736 35 HOH HOH . 
L 4 HOH A 37 737 27 HOH HOH . 
L 4 HOH A 38 738 50 HOH HOH . 
L 4 HOH A 39 739 46 HOH HOH . 
L 4 HOH A 40 740 176 HOH HOH . 
L 4 HOH A 41 741 89 HOH HOH . 
L 4 HOH A 42 742 87 HOH HOH . 
L 4 HOH A 43 743 60 HOH HOH . 
L 4 HOH A 44 744 101 HOH HOH . 
L 4 HOH A 45 745 177 HOH HOH . 
L 4 HOH A 46 746 168 HOH HOH . 
L 4 HOH A 47 747 111 HOH HOH . 
L 4 HOH A 48 748 7 HOH HOH . 
L 4 HOH A 49 749 40 HOH HOH . 
L 4 HOH A 50 750 22 HOH HOH . 
L 4 HOH A 51 751 121 HOH HOH . 
L 4 HOH A 52 752 148 HOH HOH . 
L 4 HOH A 53 753 131 HOH HOH . 
L 4 HOH A 54 754 116 HOH HOH . 
L 4 HOH A 55 755 164 HOH HOH . 
L 4 HOH A 56 756 18 HOH HOH . 
L 4 HOH A 57 757 51 HOH HOH . 
L 4 HOH A 58 758 33 HOH HOH . 
L 4 HOH A 59 759 17 HOH HOH . 
L 4 HOH A 60 760 163 HOH HOH . 
L 4 HOH A 61 761 105 HOH HOH . 
L 4 HOH A 62 762 26 HOH HOH . 
L 4 HOH A 63 763 94 HOH HOH . 
L 4 HOH A 64 764 139 HOH HOH . 
L 4 HOH A 65 765 79 HOH HOH . 
L 4 HOH A 66 766 144 HOH HOH . 
L 4 HOH A 67 767 135 HOH HOH . 
L 4 HOH A 68 768 71 HOH HOH . 
L 4 HOH A 69 769 47 HOH HOH . 
L 4 HOH A 70 770 129 HOH HOH . 
L 4 HOH A 71 771 34 HOH HOH . 
L 4 HOH A 72 772 147 HOH HOH . 
L 4 HOH A 73 773 113 HOH HOH . 
L 4 HOH A 74 774 80 HOH HOH . 
L 4 HOH A 75 775 13 HOH HOH . 
L 4 HOH A 76 776 32 HOH HOH . 
L 4 HOH A 77 777 172 HOH HOH . 
L 4 HOH A 78 778 180 HOH HOH . 
L 4 HOH A 79 779 132 HOH HOH . 
L 4 HOH A 80 780 182 HOH HOH . 
L 4 HOH A 81 781 167 HOH HOH . 
L 4 HOH A 82 782 115 HOH HOH . 
L 4 HOH A 83 783 156 HOH HOH . 
L 4 HOH A 84 784 181 HOH HOH . 
L 4 HOH A 85 785 59 HOH HOH . 
L 4 HOH A 86 786 64 HOH HOH . 
L 4 HOH A 87 787 143 HOH HOH . 
L 4 HOH A 88 788 146 HOH HOH . 
L 4 HOH A 89 789 110 HOH HOH . 
L 4 HOH A 90 790 154 HOH HOH . 
L 4 HOH A 91 791 151 HOH HOH . 
L 4 HOH A 92 792 37 HOH HOH . 
L 4 HOH A 93 793 175 HOH HOH . 
L 4 HOH A 94 794 96 HOH HOH . 
M 4 HOH B 1 701 45 HOH HOH . 
M 4 HOH B 2 702 11 HOH HOH . 
M 4 HOH B 3 703 70 HOH HOH . 
M 4 HOH B 4 704 149 HOH HOH . 
M 4 HOH B 5 705 160 HOH HOH . 
M 4 HOH B 6 706 81 HOH HOH . 
M 4 HOH B 7 707 97 HOH HOH . 
M 4 HOH B 8 708 55 HOH HOH . 
M 4 HOH B 9 709 2 HOH HOH . 
M 4 HOH B 10 710 9 HOH HOH . 
M 4 HOH B 11 711 42 HOH HOH . 
M 4 HOH B 12 712 15 HOH HOH . 
M 4 HOH B 13 713 104 HOH HOH . 
M 4 HOH B 14 714 63 HOH HOH . 
M 4 HOH B 15 715 49 HOH HOH . 
M 4 HOH B 16 716 183 HOH HOH . 
M 4 HOH B 17 717 52 HOH HOH . 
M 4 HOH B 18 718 138 HOH HOH . 
M 4 HOH B 19 719 21 HOH HOH . 
M 4 HOH B 20 720 62 HOH HOH . 
M 4 HOH B 21 721 54 HOH HOH . 
M 4 HOH B 22 722 142 HOH HOH . 
M 4 HOH B 23 723 8 HOH HOH . 
M 4 HOH B 24 724 158 HOH HOH . 
M 4 HOH B 25 725 56 HOH HOH . 
M 4 HOH B 26 726 76 HOH HOH . 
M 4 HOH B 27 727 19 HOH HOH . 
M 4 HOH B 28 728 83 HOH HOH . 
M 4 HOH B 29 729 14 HOH HOH . 
M 4 HOH B 30 730 3 HOH HOH . 
M 4 HOH B 31 731 53 HOH HOH . 
M 4 HOH B 32 732 1 HOH HOH . 
M 4 HOH B 33 733 29 HOH HOH . 
M 4 HOH B 34 734 82 HOH HOH . 
M 4 HOH B 35 735 122 HOH HOH . 
M 4 HOH B 36 736 77 HOH HOH . 
M 4 HOH B 37 737 57 HOH HOH . 
M 4 HOH B 38 738 109 HOH HOH . 
M 4 HOH B 39 739 174 HOH HOH . 
M 4 HOH B 40 740 58 HOH HOH . 
M 4 HOH B 41 741 100 HOH HOH . 
M 4 HOH B 42 742 12 HOH HOH . 
M 4 HOH B 43 743 28 HOH HOH . 
M 4 HOH B 44 744 106 HOH HOH . 
M 4 HOH B 45 745 159 HOH HOH . 
M 4 HOH B 46 746 157 HOH HOH . 
M 4 HOH B 47 747 78 HOH HOH . 
M 4 HOH B 48 748 108 HOH HOH . 
M 4 HOH B 49 749 66 HOH HOH . 
M 4 HOH B 50 750 152 HOH HOH . 
M 4 HOH B 51 751 125 HOH HOH . 
M 4 HOH B 52 752 99 HOH HOH . 
M 4 HOH B 53 753 134 HOH HOH . 
M 4 HOH B 54 754 86 HOH HOH . 
M 4 HOH B 55 755 141 HOH HOH . 
M 4 HOH B 56 756 20 HOH HOH . 
M 4 HOH B 57 757 72 HOH HOH . 
M 4 HOH B 58 758 133 HOH HOH . 
M 4 HOH B 59 759 102 HOH HOH . 
M 4 HOH B 60 760 150 HOH HOH . 
M 4 HOH B 61 761 43 HOH HOH . 
M 4 HOH B 62 762 118 HOH HOH . 
M 4 HOH B 63 763 130 HOH HOH . 
M 4 HOH B 64 764 90 HOH HOH . 
M 4 HOH B 65 765 170 HOH HOH . 
M 4 HOH B 66 766 178 HOH HOH . 
M 4 HOH B 67 767 61 HOH HOH . 
M 4 HOH B 68 768 112 HOH HOH . 
M 4 HOH B 69 769 84 HOH HOH . 
M 4 HOH B 70 770 179 HOH HOH . 
M 4 HOH B 71 771 10 HOH HOH . 
M 4 HOH B 72 772 155 HOH HOH . 
M 4 HOH B 73 773 137 HOH HOH . 
M 4 HOH B 74 774 103 HOH HOH . 
M 4 HOH B 75 775 173 HOH HOH . 
M 4 HOH B 76 776 128 HOH HOH . 
M 4 HOH B 77 777 140 HOH HOH . 
M 4 HOH B 78 778 74 HOH HOH . 
M 4 HOH B 79 779 171 HOH HOH . 
M 4 HOH B 80 780 162 HOH HOH . 
M 4 HOH B 81 781 169 HOH HOH . 
M 4 HOH B 82 782 153 HOH HOH . 
M 4 HOH B 83 783 124 HOH HOH . 
M 4 HOH B 84 784 165 HOH HOH . 
M 4 HOH B 85 785 107 HOH HOH . 
M 4 HOH B 86 786 88 HOH HOH . 
M 4 HOH B 87 787 123 HOH HOH . 
M 4 HOH B 88 788 126 HOH HOH . 
M 4 HOH B 89 789 145 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 O O5' 6MD . . . H 3 6.533 31.367 -26.716 1 42.17 ? O5' 6MD 606 A 1 
HETATM 2 C C5' 6MD . . . H 3 5.32 31.203 -27.43 1 31.94 ? C5' 6MD 606 A 1 
HETATM 3 C C4' 6MD . . . H 3 4.142 31.129 -26.494 1 27.59 ? C4' 6MD 606 A 1 
HETATM 4 O O4' 6MD . . . H 3 3.606 29.792 -26.539 1 29.05 ? O4' 6MD 606 A 1 
HETATM 5 C C3' 6MD . . . H 3 4.448 31.356 -25.023 1 26.63 ? C3' 6MD 606 A 1 
HETATM 6 O O3' 6MD . . . H 3 4.475 32.727 -24.672 1 33.76 ? O3' 6MD 606 A 1 
HETATM 7 C C2' 6MD . . . H 3 3.341 30.588 -24.31 1 25.93 ? C2' 6MD 606 A 1 
HETATM 8 O O2' 6MD . . . H 3 2.187 31.406 -24.163 1 18.85 ? O2' 6MD 606 A 1 
HETATM 9 C C1' 6MD . . . H 3 3.035 29.457 -25.303 1 25.32 ? C1' 6MD 606 A 1 
HETATM 10 N N9 6MD . . . H 3 3.576 28.149 -24.877 1 23.68 ? N9 6MD 606 A 1 
HETATM 11 C C8 6MD . . . H 3 4.516 27.921 -23.952 1 24.43 ? C8 6MD 606 A 1 
HETATM 12 N N7 6MD . . . H 3 4.696 26.599 -23.869 1 18.84 ? N7 6MD 606 A 1 
HETATM 13 C C5 6MD . . . H 3 3.863 25.999 -24.739 1 19.52 ? C5 6MD 606 A 1 
HETATM 14 C C6 6MD . . . H 3 3.634 24.673 -25.062 1 19.27 ? C6 6MD 606 A 1 
HETATM 15 N N6 6MD . . . H 3 4.337 23.562 -24.449 1 19.2 ? N6 6MD 606 A 1 
HETATM 16 N N1 6MD . . . H 3 2.737 24.341 -25.983 1 19.1 ? N1 6MD 606 A 1 
HETATM 17 C C2 6MD . . . H 3 2.04 25.313 -26.616 1 21.75 ? C2 6MD 606 A 1 
HETATM 18 N N3 6MD . . . H 3 2.259 26.616 -26.301 1 22.82 ? N3 6MD 606 A 1 
HETATM 19 C C4 6MD . . . H 3 3.175 26.957 -25.366 1 22.1 ? C4 6MD 606 A 1 
HETATM 20 C CZ 6MD . . . H 3 4.159 22.219 -24.979 1 18.15 ? CZ 6MD 606 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           20 
#