data_3MF2 # _model_server_result.job_id aSkcfSqVaYD0aUVgfbYJTQ _model_server_result.datetime_utc '2024-11-15 06:25:22' _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 3mf2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1010}' # _entry.id 3MF2 # _exptl.entry_id 3MF2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE 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 3MF2 _cell.length_a 127.67 _cell.length_b 100.24 _cell.length_c 50.23 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MF2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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,J _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 H 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 disulf ? disulf1 A SG CYS 113 A CYS 93 1_555 B SG CYS 113 B CYS 93 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 113 A CYS 93 1_555 B SG CYS 113 B CYS 93 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.067 ? metalc ? metalc1 A SG CYS 151 A CYS 131 1_555 C ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc2 A OE1 GLU 196 A GLU 176 1_555 C ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc3 A SG CYS 299 A CYS 279 1_555 C ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc4 I O HOH . A HOH 384 1_555 C ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc5 B SG CYS 151 B CYS 131 1_555 G ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc6 B OE1 GLU 196 B GLU 176 1_555 G ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc7 B SG CYS 299 B CYS 279 1_555 G ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc8 J O HOH . B HOH 376 1_555 G ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE 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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 3MF2 _atom_sites.fract_transf_matrix[1][1] 0.007833 _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] 0.009976 _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] 0.019908 _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 ZN A 1 1000 1000 ZN ZN . D 3 AMP A 1 1010 1010 AMP AMP . E 4 GOL A 1 1011 1011 GOL GOL . F 4 GOL A 1 327 1011 GOL GOL . G 2 ZN B 1 1000 1000 ZN ZN . H 3 AMP B 1 1010 1010 AMP AMP . I 5 HOH A 1 328 1 HOH HOH . I 5 HOH A 2 329 3 HOH HOH . I 5 HOH A 3 330 5 HOH HOH . I 5 HOH A 4 331 6 HOH HOH . I 5 HOH A 5 332 7 HOH HOH . I 5 HOH A 6 333 8 HOH HOH . I 5 HOH A 7 334 10 HOH HOH . I 5 HOH A 8 335 11 HOH HOH . I 5 HOH A 9 336 13 HOH HOH . I 5 HOH A 10 337 14 HOH HOH . I 5 HOH A 11 338 15 HOH HOH . I 5 HOH A 12 339 21 HOH HOH . I 5 HOH A 13 340 22 HOH HOH . I 5 HOH A 14 341 23 HOH HOH . I 5 HOH A 15 342 24 HOH HOH . I 5 HOH A 16 343 25 HOH HOH . I 5 HOH A 17 344 26 HOH HOH . I 5 HOH A 18 345 27 HOH HOH . I 5 HOH A 19 346 28 HOH HOH . I 5 HOH A 20 347 29 HOH HOH . I 5 HOH A 21 348 33 HOH HOH . I 5 HOH A 22 349 36 HOH HOH . I 5 HOH A 23 350 37 HOH HOH . I 5 HOH A 24 351 38 HOH HOH . I 5 HOH A 25 352 40 HOH HOH . I 5 HOH A 26 353 42 HOH HOH . I 5 HOH A 27 354 44 HOH HOH . I 5 HOH A 28 355 45 HOH HOH . I 5 HOH A 29 356 49 HOH HOH . I 5 HOH A 30 357 51 HOH HOH . I 5 HOH A 31 358 52 HOH HOH . I 5 HOH A 32 359 61 HOH HOH . I 5 HOH A 33 360 66 HOH HOH . I 5 HOH A 34 361 68 HOH HOH . I 5 HOH A 35 362 69 HOH HOH . I 5 HOH A 36 363 70 HOH HOH . I 5 HOH A 37 364 71 HOH HOH . I 5 HOH A 38 365 72 HOH HOH . I 5 HOH A 39 366 73 HOH HOH . I 5 HOH A 40 367 74 HOH HOH . I 5 HOH A 41 368 75 HOH HOH . I 5 HOH A 42 369 79 HOH HOH . I 5 HOH A 43 370 84 HOH HOH . I 5 HOH A 44 371 86 HOH HOH . I 5 HOH A 45 372 87 HOH HOH . I 5 HOH A 46 373 90 HOH HOH . I 5 HOH A 47 374 91 HOH HOH . I 5 HOH A 48 375 92 HOH HOH . I 5 HOH A 49 376 96 HOH HOH . I 5 HOH A 50 377 97 HOH HOH . I 5 HOH A 51 378 98 HOH HOH . I 5 HOH A 52 379 102 HOH HOH . I 5 HOH A 53 380 103 HOH HOH . I 5 HOH A 54 381 104 HOH HOH . I 5 HOH A 55 382 105 HOH HOH . I 5 HOH A 56 383 106 HOH HOH . I 5 HOH A 57 384 107 HOH HOH . I 5 HOH A 58 385 110 HOH HOH . I 5 HOH A 59 386 112 HOH HOH . I 5 HOH A 60 387 113 HOH HOH . I 5 HOH A 61 388 114 HOH HOH . I 5 HOH A 62 389 115 HOH HOH . I 5 HOH A 63 390 116 HOH HOH . I 5 HOH A 64 391 117 HOH HOH . I 5 HOH A 65 392 118 HOH HOH . I 5 HOH A 66 393 119 HOH HOH . I 5 HOH A 67 394 120 HOH HOH . I 5 HOH A 68 395 122 HOH HOH . I 5 HOH A 69 396 123 HOH HOH . I 5 HOH A 70 397 125 HOH HOH . I 5 HOH A 71 398 126 HOH HOH . I 5 HOH A 72 399 128 HOH HOH . I 5 HOH A 73 400 131 HOH HOH . I 5 HOH A 74 401 132 HOH HOH . I 5 HOH A 75 402 136 HOH HOH . I 5 HOH A 76 403 137 HOH HOH . I 5 HOH A 77 404 138 HOH HOH . I 5 HOH A 78 405 139 HOH HOH . I 5 HOH A 79 406 144 HOH HOH . I 5 HOH A 80 407 145 HOH HOH . I 5 HOH A 81 408 147 HOH HOH . I 5 HOH A 82 409 150 HOH HOH . I 5 HOH A 83 410 153 HOH HOH . I 5 HOH A 84 411 154 HOH HOH . I 5 HOH A 85 412 155 HOH HOH . I 5 HOH A 86 413 156 HOH HOH . I 5 HOH A 87 414 163 HOH HOH . I 5 HOH A 88 415 168 HOH HOH . I 5 HOH A 89 416 169 HOH HOH . I 5 HOH A 90 417 170 HOH HOH . J 5 HOH B 1 327 2 HOH HOH . J 5 HOH B 2 328 4 HOH HOH . J 5 HOH B 3 329 9 HOH HOH . J 5 HOH B 4 330 12 HOH HOH . J 5 HOH B 5 331 16 HOH HOH . J 5 HOH B 6 332 17 HOH HOH . J 5 HOH B 7 333 18 HOH HOH . J 5 HOH B 8 334 19 HOH HOH . J 5 HOH B 9 335 20 HOH HOH . J 5 HOH B 10 336 30 HOH HOH . J 5 HOH B 11 337 31 HOH HOH . J 5 HOH B 12 338 32 HOH HOH . J 5 HOH B 13 339 34 HOH HOH . J 5 HOH B 14 340 35 HOH HOH . J 5 HOH B 15 341 39 HOH HOH . J 5 HOH B 16 342 41 HOH HOH . J 5 HOH B 17 343 43 HOH HOH . J 5 HOH B 18 344 46 HOH HOH . J 5 HOH B 19 345 47 HOH HOH . J 5 HOH B 20 346 48 HOH HOH . J 5 HOH B 21 347 50 HOH HOH . J 5 HOH B 22 348 53 HOH HOH . J 5 HOH B 23 349 54 HOH HOH . J 5 HOH B 24 350 55 HOH HOH . J 5 HOH B 25 351 56 HOH HOH . J 5 HOH B 26 352 57 HOH HOH . J 5 HOH B 27 353 58 HOH HOH . J 5 HOH B 28 354 59 HOH HOH . J 5 HOH B 29 355 60 HOH HOH . J 5 HOH B 30 356 62 HOH HOH . J 5 HOH B 31 357 63 HOH HOH . J 5 HOH B 32 358 64 HOH HOH . J 5 HOH B 33 359 65 HOH HOH . J 5 HOH B 34 360 67 HOH HOH . J 5 HOH B 35 361 76 HOH HOH . J 5 HOH B 36 362 77 HOH HOH . J 5 HOH B 37 363 78 HOH HOH . J 5 HOH B 38 364 80 HOH HOH . J 5 HOH B 39 365 81 HOH HOH . J 5 HOH B 40 366 82 HOH HOH . J 5 HOH B 41 367 83 HOH HOH . J 5 HOH B 42 368 85 HOH HOH . J 5 HOH B 43 369 88 HOH HOH . J 5 HOH B 44 370 89 HOH HOH . J 5 HOH B 45 371 93 HOH HOH . J 5 HOH B 46 372 94 HOH HOH . J 5 HOH B 47 373 95 HOH HOH . J 5 HOH B 48 374 99 HOH HOH . J 5 HOH B 49 375 100 HOH HOH . J 5 HOH B 50 376 101 HOH HOH . J 5 HOH B 51 377 108 HOH HOH . J 5 HOH B 52 378 109 HOH HOH . J 5 HOH B 53 379 111 HOH HOH . J 5 HOH B 54 380 121 HOH HOH . J 5 HOH B 55 381 124 HOH HOH . J 5 HOH B 56 382 127 HOH HOH . J 5 HOH B 57 383 129 HOH HOH . J 5 HOH B 58 384 130 HOH HOH . J 5 HOH B 59 385 133 HOH HOH . J 5 HOH B 60 386 134 HOH HOH . J 5 HOH B 61 387 135 HOH HOH . J 5 HOH B 62 388 140 HOH HOH . J 5 HOH B 63 389 141 HOH HOH . J 5 HOH B 64 390 142 HOH HOH . J 5 HOH B 65 391 143 HOH HOH . J 5 HOH B 66 392 146 HOH HOH . J 5 HOH B 67 393 148 HOH HOH . J 5 HOH B 68 394 149 HOH HOH . J 5 HOH B 69 395 151 HOH HOH . J 5 HOH B 70 396 152 HOH HOH . J 5 HOH B 71 397 157 HOH HOH . J 5 HOH B 72 398 158 HOH HOH . J 5 HOH B 73 399 159 HOH HOH . J 5 HOH B 74 400 160 HOH HOH . J 5 HOH B 75 401 161 HOH HOH . J 5 HOH B 76 402 162 HOH HOH . J 5 HOH B 77 403 164 HOH HOH . J 5 HOH B 78 404 165 HOH HOH . J 5 HOH B 79 405 166 HOH HOH . J 5 HOH B 80 406 167 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 P P AMP . . . D 3 90.587 31.929 6.483 1 41.43 ? P AMP 1010 A 1 HETATM 2 O O1P AMP . . . D 3 90.696 30.554 7.048 1 42.42 ? O1P AMP 1010 A 1 HETATM 3 O O2P AMP . . . D 3 90.382 31.915 4.96 1 42.67 ? O2P AMP 1010 A 1 HETATM 4 O O3P AMP . . . D 3 89.499 32.753 7.13 1 40.65 ? O3P AMP 1010 A 1 HETATM 5 O O5' AMP . . . D 3 92.08 32.606 6.742 1 41.79 ? O5' AMP 1010 A 1 HETATM 6 C C5' AMP . . . D 3 92.325 33.351 7.952 1 39.12 ? C5' AMP 1010 A 1 HETATM 7 C C4' AMP . . . D 3 93.207 34.541 7.559 1 37.85 ? C4' AMP 1010 A 1 HETATM 8 O O4' AMP . . . D 3 94.469 34.05 7.001 1 37.68 ? O4' AMP 1010 A 1 HETATM 9 C C3' AMP . . . D 3 92.547 35.314 6.437 1 44.14 ? C3' AMP 1010 A 1 HETATM 10 O O3' AMP . . . D 3 91.643 36.224 7.022 1 46.08 ? O3' AMP 1010 A 1 HETATM 11 C C2' AMP . . . D 3 93.768 35.963 5.765 1 43.05 ? C2' AMP 1010 A 1 HETATM 12 O O2' AMP . . . D 3 94.028 37.162 6.542 1 46.51 ? O2' AMP 1010 A 1 HETATM 13 C C1' AMP . . . D 3 94.889 34.897 5.944 1 36.65 ? C1' AMP 1010 A 1 HETATM 14 N N9 AMP . . . D 3 95.016 34.19 4.696 1 38.51 ? N9 AMP 1010 A 1 HETATM 15 C C8 AMP . . . D 3 94.18 33.236 4.114 1 35.2 ? C8 AMP 1010 A 1 HETATM 16 N N7 AMP . . . D 3 94.601 32.867 2.904 1 39.42 ? N7 AMP 1010 A 1 HETATM 17 C C5 AMP . . . D 3 95.727 33.603 2.673 1 36.13 ? C5 AMP 1010 A 1 HETATM 18 C C6 AMP . . . D 3 96.606 33.671 1.588 1 33.14 ? C6 AMP 1010 A 1 HETATM 19 N N6 AMP . . . D 3 96.423 32.858 0.432 1 27.96 ? N6 AMP 1010 A 1 HETATM 20 N N1 AMP . . . D 3 97.66 34.608 1.665 1 29.66 ? N1 AMP 1010 A 1 HETATM 21 C C2 AMP . . . D 3 97.838 35.34 2.778 1 31.86 ? C2 AMP 1010 A 1 HETATM 22 N N3 AMP . . . D 3 97.05 35.32 3.934 1 34.33 ? N3 AMP 1010 A 1 HETATM 23 C C4 AMP . . . D 3 96.009 34.45 3.785 1 38.02 ? C4 AMP 1010 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 23 #