data_4EG3
#
_model_server_result.job_id            fA8j-_mogHUc2iwZoVFUHw 
_model_server_result.datetime_utc      '2024-12-02 20:32:09' 
_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          4eg3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":805}' 
#
_entry.id    4EG3 
#
_exptl.entry_id    4EG3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              478.417 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate' 
_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            4EG3 
_cell.length_a            85.477 
_cell.length_b            105.908 
_cell.length_c            208.445 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4EG3 
_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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_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,I,J,P 1 1 
B,K,L,M,N,O,Q 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 J N N 
? 3 O 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
covale ? covale1 A C HIS 238 A HIS 469 1_555 A N CAS 239 A CAS 470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale2 A C CAS 239 A CAS 470 1_555 A N VAL 240 A VAL 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale3 B C HIS 238 B HIS 469 1_555 B N CAS 239 B CAS 470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale4 B C CAS 239 B CAS 470 1_555 B N VAL 240 B VAL 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
#
_chem_comp.formula           'C15 H23 N6 O8 P S' 
_chem_comp.formula_weight    478.417 
_chem_comp.id                ME8 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     L-methionine-AMP;methionyl-adenylate 
#
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 ME8 sing 252 n y 
O1 P1 ME8 sing 253 n n 
O1 C9 ME8 sing 254 n n 
P1 O5' ME8 sing 255 n n 
C2 H2 ME8 sing 256 n n 
N2 CA ME8 sing 257 n n 
N2 HN2 ME8 sing 258 n n 
N2 HN2A ME8 sing 259 n n 
N3 C2 ME8 doub 260 n y 
C4 N3 ME8 sing 261 n y 
C5 C4 ME8 doub 262 n y 
C5 C6 ME8 sing 263 n y 
C6 N1 ME8 doub 264 n y 
N6 C6 ME8 sing 265 n n 
N6 HN6 ME8 sing 266 n n 
N6 HN6A ME8 sing 267 n n 
N7 C5 ME8 sing 268 n y 
C8 N7 ME8 doub 269 n y 
C8 N9 ME8 sing 270 n y 
C9 O ME8 doub 271 n n 
N9 C4 ME8 sing 272 n y 
N9 C1' ME8 sing 273 n n 
CA C9 ME8 sing 274 n n 
CA CB ME8 sing 275 n n 
CA HA ME8 sing 276 n n 
CB HB ME8 sing 277 n n 
CB HBA ME8 sing 278 n n 
CE SD ME8 sing 279 n n 
CE HE ME8 sing 280 n n 
CE HEA ME8 sing 281 n n 
CE HEB ME8 sing 282 n n 
CG CB ME8 sing 283 n n 
CG SD ME8 sing 284 n n 
CG HG ME8 sing 285 n n 
CG HGA ME8 sing 286 n n 
C1' C2' ME8 sing 287 n n 
C1' H1' ME8 sing 288 n n 
O1S P1 ME8 doub 289 n n 
C2' O2' ME8 sing 290 n n 
C2' H2' ME8 sing 291 n n 
O2' HO2' ME8 sing 292 n n 
O2S P1 ME8 sing 293 n n 
O2S HO2S ME8 sing 294 n n 
C3' C2' ME8 sing 295 n n 
C3' O3' ME8 sing 296 n n 
C3' H3' ME8 sing 297 n n 
O3' HO3' ME8 sing 298 n n 
C4' C3' ME8 sing 299 n n 
C4' O4' ME8 sing 300 n n 
C4' H4' ME8 sing 301 n n 
O4' C1' ME8 sing 302 n n 
C5' C4' ME8 sing 303 n n 
C5' H5' ME8 sing 304 n n 
C5' "H5'A" ME8 sing 305 n n 
O5' C5' ME8 sing 306 n n 
C8 H8 ME8 sing 307 n n 
#
_atom_sites.entry_id                     4EG3 
_atom_sites.fract_transf_matrix[1][1]    0.011699 
_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]    0.009442 
_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]    0.004797 
_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 GOL A 1 801 900 GOL GOL . 
D 2 GOL A 1 802 901 GOL GOL . 
E 2 GOL A 1 803 903 GOL GOL . 
F 2 GOL A 1 804 904 GOL GOL . 
G 2 GOL A 1 805 905 GOL GOL . 
H 2 GOL A 1 806 906 GOL GOL . 
I 2 GOL A 1 807 907 GOL GOL . 
J 3 ME8 A 1 808 800 ME8 ME8 . 
K 2 GOL B 1 801 900 GOL GOL . 
L 2 GOL B 1 802 901 GOL GOL . 
M 2 GOL B 1 803 902 GOL GOL . 
N 2 GOL B 1 804 903 GOL GOL . 
O 3 ME8 B 1 805 800 ME8 ME8 . 
P 4 HOH A 1 901 1000 HOH HOH . 
P 4 HOH A 2 902 1001 HOH HOH . 
P 4 HOH A 3 903 1002 HOH HOH . 
P 4 HOH A 4 904 1003 HOH HOH . 
P 4 HOH A 5 905 1004 HOH HOH . 
P 4 HOH A 6 906 1005 HOH HOH . 
P 4 HOH A 7 907 1006 HOH HOH . 
P 4 HOH A 8 908 1007 HOH HOH . 
P 4 HOH A 9 909 1008 HOH HOH . 
P 4 HOH A 10 910 1009 HOH HOH . 
P 4 HOH A 11 911 1010 HOH HOH . 
P 4 HOH A 12 912 1011 HOH HOH . 
P 4 HOH A 13 913 1012 HOH HOH . 
P 4 HOH A 14 914 1013 HOH HOH . 
P 4 HOH A 15 915 1014 HOH HOH . 
P 4 HOH A 16 916 1015 HOH HOH . 
P 4 HOH A 17 917 1016 HOH HOH . 
P 4 HOH A 18 918 1017 HOH HOH . 
P 4 HOH A 19 919 1018 HOH HOH . 
P 4 HOH A 20 920 1019 HOH HOH . 
P 4 HOH A 21 921 1020 HOH HOH . 
P 4 HOH A 22 922 1021 HOH HOH . 
P 4 HOH A 23 923 1022 HOH HOH . 
P 4 HOH A 24 924 1023 HOH HOH . 
P 4 HOH A 25 925 1025 HOH HOH . 
P 4 HOH A 26 926 1026 HOH HOH . 
P 4 HOH A 27 927 1027 HOH HOH . 
P 4 HOH A 28 928 1028 HOH HOH . 
P 4 HOH A 29 929 1029 HOH HOH . 
P 4 HOH A 30 930 1030 HOH HOH . 
P 4 HOH A 31 931 1031 HOH HOH . 
P 4 HOH A 32 932 1032 HOH HOH . 
P 4 HOH A 33 933 1033 HOH HOH . 
P 4 HOH A 34 934 1034 HOH HOH . 
P 4 HOH A 35 935 1035 HOH HOH . 
P 4 HOH A 36 936 1036 HOH HOH . 
P 4 HOH A 37 937 1037 HOH HOH . 
P 4 HOH A 38 938 1038 HOH HOH . 
P 4 HOH A 39 939 1039 HOH HOH . 
P 4 HOH A 40 940 1040 HOH HOH . 
Q 4 HOH B 1 901 1024 HOH HOH . 
Q 4 HOH B 2 902 1000 HOH HOH . 
Q 4 HOH B 3 903 1001 HOH HOH . 
Q 4 HOH B 4 904 1002 HOH HOH . 
Q 4 HOH B 5 905 1003 HOH HOH . 
Q 4 HOH B 6 906 1004 HOH HOH . 
Q 4 HOH B 7 907 1005 HOH HOH . 
Q 4 HOH B 8 908 1006 HOH HOH . 
Q 4 HOH B 9 909 1007 HOH HOH . 
Q 4 HOH B 10 910 1008 HOH HOH . 
Q 4 HOH B 11 911 1009 HOH HOH . 
Q 4 HOH B 12 912 1010 HOH HOH . 
Q 4 HOH B 13 913 1011 HOH HOH . 
Q 4 HOH B 14 914 1012 HOH HOH . 
Q 4 HOH B 15 915 1013 HOH HOH . 
Q 4 HOH B 16 916 1014 HOH HOH . 
Q 4 HOH B 17 917 1015 HOH HOH . 
Q 4 HOH B 18 918 1016 HOH HOH . 
Q 4 HOH B 19 919 1017 HOH HOH . 
Q 4 HOH B 20 920 1018 HOH HOH . 
Q 4 HOH B 21 921 1019 HOH HOH . 
Q 4 HOH B 22 922 1020 HOH HOH . 
Q 4 HOH B 23 923 1021 HOH HOH . 
Q 4 HOH B 24 924 1022 HOH HOH . 
Q 4 HOH B 25 925 1023 HOH HOH . 
Q 4 HOH B 26 926 1024 HOH HOH . 
Q 4 HOH B 27 927 1025 HOH HOH . 
Q 4 HOH B 28 928 1026 HOH HOH . 
Q 4 HOH B 29 929 1027 HOH HOH . 
Q 4 HOH B 30 930 1028 HOH HOH . 
Q 4 HOH B 31 931 1029 HOH HOH . 
Q 4 HOH B 32 932 1030 HOH HOH . 
Q 4 HOH B 33 933 1031 HOH HOH . 
Q 4 HOH B 34 934 1032 HOH HOH . 
Q 4 HOH B 35 935 1033 HOH HOH . 
Q 4 HOH B 36 936 1034 HOH HOH . 
Q 4 HOH B 37 937 1035 HOH HOH . 
Q 4 HOH B 38 938 1036 HOH HOH . 
Q 4 HOH B 39 939 1037 HOH HOH . 
Q 4 HOH B 40 940 1038 HOH HOH . 
Q 4 HOH B 41 941 1039 HOH HOH . 
Q 4 HOH B 42 942 1040 HOH HOH . 
Q 4 HOH B 43 943 1041 HOH HOH . 
Q 4 HOH B 44 944 1042 HOH HOH . 
Q 4 HOH B 45 945 1043 HOH HOH . 
Q 4 HOH B 46 946 1044 HOH HOH . 
Q 4 HOH B 47 947 1045 HOH HOH . 
Q 4 HOH B 48 948 1046 HOH HOH . 
Q 4 HOH B 49 949 1047 HOH HOH . 
Q 4 HOH B 50 950 1048 HOH HOH . 
Q 4 HOH B 51 951 1049 HOH HOH . 
Q 4 HOH B 52 952 1050 HOH HOH . 
Q 4 HOH B 53 953 1051 HOH HOH . 
Q 4 HOH B 54 954 1052 HOH HOH . 
Q 4 HOH B 55 955 1053 HOH HOH . 
Q 4 HOH B 56 956 1054 HOH HOH . 
Q 4 HOH B 57 957 1055 HOH HOH . 
Q 4 HOH B 58 958 1056 HOH HOH . 
Q 4 HOH B 59 959 1057 HOH HOH . 
Q 4 HOH B 60 960 1058 HOH HOH . 
Q 4 HOH B 61 961 1059 HOH HOH . 
Q 4 HOH B 62 962 1060 HOH HOH . 
Q 4 HOH B 63 963 1061 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 O ME8 . . . O 3 -37.905 11.604 8.548 1 41.82 ? O ME8 805 B 1 
HETATM 2 N N1 ME8 . . . O 3 -35.99 2.978 2.132 1 58.78 ? N1 ME8 805 B 1 
HETATM 3 O O1 ME8 . . . O 3 -36.576 10.315 10.019 1 43.75 ? O1 ME8 805 B 1 
HETATM 4 P P1 ME8 . . . O 3 -37.078 8.809 9.657 1 45.31 ? P1 ME8 805 B 1 
HETATM 5 C C2 ME8 . . . O 3 -35.029 3.88 1.919 1 58.21 ? C2 ME8 805 B 1 
HETATM 6 N N2 ME8 . . . O 3 -35.939 12.74 11.28 1 39.46 ? N2 ME8 805 B 1 
HETATM 7 N N3 ME8 . . . O 3 -34.81 4.868 2.795 1 58.25 ? N3 ME8 805 B 1 
HETATM 8 C C4 ME8 . . . O 3 -35.56 4.972 3.911 1 56.9 ? C4 ME8 805 B 1 
HETATM 9 C C5 ME8 . . . O 3 -36.562 4.05 4.146 1 56.75 ? C5 ME8 805 B 1 
HETATM 10 C C6 ME8 . . . O 3 -36.763 3.041 3.231 1 58.33 ? C6 ME8 805 B 1 
HETATM 11 N N6 ME8 . . . O 3 -37.73 2.126 3.434 1 60.6 ? N6 ME8 805 B 1 
HETATM 12 N N7 ME8 . . . O 3 -37.15 4.359 5.307 1 57.6 ? N7 ME8 805 B 1 
HETATM 13 C C8 ME8 . . . O 3 -36.518 5.46 5.78 1 58.6 ? C8 ME8 805 B 1 
HETATM 14 C C9 ME8 . . . O 3 -37.045 11.587 9.428 1 42.52 ? C9 ME8 805 B 1 
HETATM 15 N N9 ME8 . . . O 3 -35.544 5.833 4.926 1 55.8 ? N9 ME8 805 B 1 
HETATM 16 C CA ME8 . . . O 3 -36.474 12.903 9.929 1 40.83 ? CA ME8 805 B 1 
HETATM 17 C CB ME8 . . . O 3 -35.392 13.435 8.978 1 39.16 ? CB ME8 805 B 1 
HETATM 18 S SD ME8 . . . O 3 -33.642 15.464 8.366 1 38.54 ? SD ME8 805 B 1 
HETATM 19 C CE ME8 . . . O 3 -33.115 17.065 8.905 1 36.26 ? CE ME8 805 B 1 
HETATM 20 C CG ME8 . . . O 3 -34.837 14.772 9.473 1 38.4 ? CG ME8 805 B 1 
HETATM 21 C C1' ME8 . . . O 3 -34.607 6.987 5.066 1 51.79 ? C1' ME8 805 B 1 
HETATM 22 O O1S ME8 . . . O 3 -36.586 7.892 10.712 1 42.89 ? O1S ME8 805 B 1 
HETATM 23 C C2' ME8 . . . O 3 -34.882 8.054 4.034 1 50.47 ? C2' ME8 805 B 1 
HETATM 24 O O2' ME8 . . . O 3 -33.754 8.942 3.986 1 49.26 ? O2' ME8 805 B 1 
HETATM 25 O O2S ME8 . . . O 3 -38.687 8.683 9.416 1 42.76 ? O2S ME8 805 B 1 
HETATM 26 C C3' ME8 . . . O 3 -36.089 8.749 4.619 1 48.84 ? C3' ME8 805 B 1 
HETATM 27 O O3' ME8 . . . O 3 -36.31 10.058 4.091 1 47.24 ? O3' ME8 805 B 1 
HETATM 28 C C4' ME8 . . . O 3 -35.681 8.799 6.079 1 48.55 ? C4' ME8 805 B 1 
HETATM 29 O O4' ME8 . . . O 3 -34.813 7.676 6.298 1 50.08 ? O4' ME8 805 B 1 
HETATM 30 C C5' ME8 . . . O 3 -36.849 8.759 7.041 1 47.43 ? C5' ME8 805 B 1 
HETATM 31 O O5' ME8 . . . O 3 -36.295 8.447 8.311 1 45.09 ? O5' ME8 805 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           254 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           31 
#