data_5IHE
#
_model_server_result.job_id            Vb6tPEyYUu4BNwe8FpR-JQ 
_model_server_result.datetime_utc      '2024-10-28 02:24:29' 
_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          5ihe 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":701}' 
#
_entry.id    5IHE 
#
_exptl.entry_id    5IHE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              331.222 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" 
_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            5IHE 
_cell.length_a            85.969 
_cell.length_b            91.415 
_cell.length_c            145.209 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5IHE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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,O 1 1 
B,I,J,K,L,M,N,P 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
? 2 C N N 
? 2 I N 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
metalc ? metalc1 A OD1 ASP 216 A ASP 360 1_555 D FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
metalc ? metalc2 A NE2 HIS 218 A HIS 362 1_555 D FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
metalc ? metalc3 A O GLU 241 A GLU 385 1_555 H CA CA . A CA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.086 ? 
metalc ? metalc4 A OD2 ASP 260 A ASP 404 1_555 D FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? 
metalc ? metalc5 A OD2 ASP 260 A ASP 404 1_555 E ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc6 A OD1 ASN 306 A ASN 450 1_555 E ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc7 A NE2 HIS 353 A HIS 497 1_555 E ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc8 A ND1 HIS 416 A HIS 560 1_555 E ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc9 A NE2 HIS 418 A HIS 562 1_555 D FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc10 C O1P D5M . A D5M 701 1_555 D FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc11 C O1P D5M . A D5M 701 1_555 E ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? 
metalc ? metalc12 B OD1 ASP 216 B ASP 360 1_555 J FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? 
metalc ? metalc13 B NE2 HIS 218 B HIS 362 1_555 J FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? 
metalc ? metalc14 B OD2 ASP 260 B ASP 404 1_555 J FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 
metalc ? metalc15 B OD2 ASP 260 B ASP 404 1_555 K ZN ZN . B ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc16 B OD1 ASN 306 B ASN 450 1_555 K ZN ZN . B ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc17 B NE2 HIS 353 B HIS 497 1_555 K ZN ZN . B ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc18 B OE2 GLU 400 B GLU 544 1_555 L CA CA . B CA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc19 B ND1 HIS 416 B HIS 560 1_555 K ZN ZN . B ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc20 B NE2 HIS 418 B HIS 562 1_555 J FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc21 I O1P D5M . B D5M 701 1_555 K ZN ZN . B ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
#
_chem_comp.formula           'C10 H14 N5 O6 P' 
_chem_comp.formula_weight    331.222 
_chem_comp.id                D5M 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" 
_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
O5' C5' D5M sing 89 n n 
O5' P D5M sing 90 n n 
C5' C4' D5M sing 91 n n 
C5' "H5'1" D5M sing 92 n n 
C5' "H5'2" D5M sing 93 n n 
C4' O4' D5M sing 94 n n 
C4' C3' D5M sing 95 n n 
C4' H4' D5M sing 96 n n 
O4' C1' D5M sing 97 n n 
C3' O3' D5M sing 98 n n 
C3' C2' D5M sing 99 n n 
C3' H1 D5M sing 100 n n 
O3' H3' D5M sing 101 n n 
C2' C1' D5M sing 102 n n 
C2' "H2'1" D5M sing 103 n n 
C2' "H2'2" D5M sing 104 n n 
C1' N9 D5M sing 105 n n 
C1' H1' D5M sing 106 n n 
N9 C8 D5M sing 107 n y 
N9 C4 D5M sing 108 n y 
C8 N7 D5M doub 109 n y 
C8 H8 D5M sing 110 n n 
N7 C5 D5M sing 111 n y 
C5 C6 D5M sing 112 n y 
C5 C4 D5M doub 113 n y 
C6 N6 D5M sing 114 n n 
C6 N1 D5M doub 115 n y 
N6 HN61 D5M sing 116 n n 
N6 HN62 D5M sing 117 n n 
N1 C2 D5M sing 118 n y 
C2 N3 D5M doub 119 n y 
C2 H2 D5M sing 120 n n 
N3 C4 D5M sing 121 n y 
P O1P D5M doub 122 n n 
P O3P D5M sing 123 n n 
P O2P D5M sing 124 n n 
O3P H3P D5M sing 125 n n 
O2P H2P D5M sing 126 n n 
#
_atom_sites.entry_id                     5IHE 
_atom_sites.fract_transf_matrix[1][1]    0.011632 
_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]    0.010939 
_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]    0.006887 
_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 D5M A 1 701 1 D5M D5M . 
D 3 FE A 1 702 3 FE FE . 
E 4 ZN A 1 703 4 ZN ZN . 
F 5 CA A 1 704 3 CA CA . 
G 6 ACT A 1 705 1 ACT ACT . 
H 5 CA A 1 706 1 CA CA . 
I 2 D5M B 1 701 2 D5M D5M . 
J 3 FE B 1 702 1 FE FE . 
K 4 ZN B 1 703 2 ZN ZN . 
L 5 CA B 1 704 2 CA CA . 
M 6 ACT B 1 705 2 ACT ACT . 
N 7 EDO B 1 706 1 EDO EDO . 
O 8 HOH A 1 801 29 HOH HOH . 
O 8 HOH A 2 802 28 HOH HOH . 
O 8 HOH A 3 803 57 HOH HOH . 
O 8 HOH A 4 804 25 HOH HOH . 
O 8 HOH A 5 805 121 HOH HOH . 
O 8 HOH A 6 806 50 HOH HOH . 
O 8 HOH A 7 807 58 HOH HOH . 
O 8 HOH A 8 808 112 HOH HOH . 
O 8 HOH A 9 809 22 HOH HOH . 
O 8 HOH A 10 810 6 HOH HOH . 
O 8 HOH A 11 811 8 HOH HOH . 
O 8 HOH A 12 812 18 HOH HOH . 
O 8 HOH A 13 813 3 HOH HOH . 
O 8 HOH A 14 814 11 HOH HOH . 
O 8 HOH A 15 815 125 HOH HOH . 
O 8 HOH A 16 816 126 HOH HOH . 
O 8 HOH A 17 817 128 HOH HOH . 
O 8 HOH A 18 818 5 HOH HOH . 
O 8 HOH A 19 819 44 HOH HOH . 
O 8 HOH A 20 820 127 HOH HOH . 
O 8 HOH A 21 821 9 HOH HOH . 
O 8 HOH A 22 822 56 HOH HOH . 
O 8 HOH A 23 823 116 HOH HOH . 
O 8 HOH A 24 824 23 HOH HOH . 
O 8 HOH A 25 825 80 HOH HOH . 
O 8 HOH A 26 826 26 HOH HOH . 
O 8 HOH A 27 827 21 HOH HOH . 
O 8 HOH A 28 828 62 HOH HOH . 
O 8 HOH A 29 829 123 HOH HOH . 
O 8 HOH A 30 830 33 HOH HOH . 
O 8 HOH A 31 831 35 HOH HOH . 
O 8 HOH A 32 832 15 HOH HOH . 
O 8 HOH A 33 833 42 HOH HOH . 
O 8 HOH A 34 834 10 HOH HOH . 
O 8 HOH A 35 835 55 HOH HOH . 
O 8 HOH A 36 836 51 HOH HOH . 
O 8 HOH A 37 837 13 HOH HOH . 
P 8 HOH B 1 801 120 HOH HOH . 
P 8 HOH B 2 802 129 HOH HOH . 
P 8 HOH B 3 803 34 HOH HOH . 
P 8 HOH B 4 804 106 HOH HOH . 
P 8 HOH B 5 805 74 HOH HOH . 
P 8 HOH B 6 806 104 HOH HOH . 
P 8 HOH B 7 807 70 HOH HOH . 
P 8 HOH B 8 808 87 HOH HOH . 
P 8 HOH B 9 809 102 HOH HOH . 
P 8 HOH B 10 810 86 HOH HOH . 
P 8 HOH B 11 811 119 HOH HOH . 
P 8 HOH B 12 812 124 HOH HOH . 
P 8 HOH B 13 813 90 HOH HOH . 
P 8 HOH B 14 814 108 HOH HOH . 
P 8 HOH B 15 815 4 HOH HOH . 
P 8 HOH B 16 816 122 HOH HOH . 
P 8 HOH B 17 817 98 HOH HOH . 
P 8 HOH B 18 818 67 HOH HOH . 
P 8 HOH B 19 819 94 HOH HOH . 
P 8 HOH B 20 820 69 HOH HOH . 
P 8 HOH B 21 821 97 HOH HOH . 
P 8 HOH B 22 822 76 HOH HOH . 
P 8 HOH B 23 823 115 HOH HOH . 
P 8 HOH B 24 824 68 HOH HOH . 
P 8 HOH B 25 825 89 HOH HOH . 
P 8 HOH B 26 826 91 HOH HOH . 
P 8 HOH B 27 827 77 HOH HOH . 
P 8 HOH B 28 828 95 HOH HOH . 
P 8 HOH B 29 829 73 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' D5M . . . I 2 43.251 45.796 87.819 1 89.39 ? O5' D5M 701 B 1 
HETATM 2 C C5' D5M . . . I 2 43.164 44.427 88.273 1 89.77 ? C5' D5M 701 B 1 
HETATM 3 C C4' D5M . . . I 2 41.712 44.031 88.425 1 91.65 ? C4' D5M 701 B 1 
HETATM 4 O O4' D5M . . . I 2 41.068 44.896 89.385 1 93.32 ? O4' D5M 701 B 1 
HETATM 5 C C3' D5M . . . I 2 40.83 44.057 87.174 1 91.41 ? C3' D5M 701 B 1 
HETATM 6 O O3' D5M . . . I 2 39.869 43.001 87.235 1 93.56 ? O3' D5M 701 B 1 
HETATM 7 C C2' D5M . . . I 2 40.119 45.398 87.283 1 89.78 ? C2' D5M 701 B 1 
HETATM 8 C C1' D5M . . . I 2 39.967 45.567 88.786 1 90.59 ? C1' D5M 701 B 1 
HETATM 9 N N9 D5M . . . I 2 39.963 46.946 89.26 1 88.7 ? N9 D5M 701 B 1 
HETATM 10 C C8 D5M . . . I 2 41.027 47.801 89.374 1 88.34 ? C8 D5M 701 B 1 
HETATM 11 N N7 D5M . . . I 2 40.722 48.974 89.873 1 87.99 ? N7 D5M 701 B 1 
HETATM 12 C C5 D5M . . . I 2 39.357 48.89 90.096 1 88.41 ? C5 D5M 701 B 1 
HETATM 13 C C6 D5M . . . I 2 38.417 49.814 90.59 1 90.2 ? C6 D5M 701 B 1 
HETATM 14 N N6 D5M . . . I 2 38.727 51.063 90.963 1 89.53 ? N6 D5M 701 B 1 
HETATM 15 N N1 D5M . . . I 2 37.127 49.416 90.672 1 91.09 ? N1 D5M 701 B 1 
HETATM 16 C C2 D5M . . . I 2 36.806 48.177 90.277 1 89.86 ? C2 D5M 701 B 1 
HETATM 17 N N3 D5M . . . I 2 37.602 47.22 89.79 1 88.68 ? N3 D5M 701 B 1 
HETATM 18 C C4 D5M . . . I 2 38.874 47.643 89.723 1 88.36 ? C4 D5M 701 B 1 
HETATM 19 P P D5M . . . I 2 44.578 46.696 87.698 1 88.88 ? P D5M 701 B 1 
HETATM 20 O O1P D5M . . . I 2 44.968 46.667 86.239 1 89.12 ? O1P D5M 701 B 1 
HETATM 21 O O3P D5M . . . I 2 44.109 48.141 88.028 1 86.81 ? O3P D5M 701 B 1 
HETATM 22 O O2P D5M . . . I 2 45.689 46.205 88.587 1 90.24 ? O2P D5M 701 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           22 
#