data_2DSD # _model_server_result.job_id GDzzVGSw1h0Zt0e4EMGH8Q _model_server_result.datetime_utc '2024-11-15 13:10:24' _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 2dsd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":402}' # _entry.id 2DSD # _exptl.entry_id 2DSD _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 121.68 _cell.angle_gamma 90 _cell.entry_id 2DSD _cell.length_a 112.076 _cell.length_b 40.156 _cell.length_c 100.124 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DSD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,K,L _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 F N N ? 3 J 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 OE2 GLU 114 A GLU 112 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? metalc ? metalc2 A OE2 GLU 114 A GLU 112 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? metalc ? metalc3 A OE1 GLU 118 A GLU 116 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc4 A OE2 GLU 118 A GLU 116 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc5 A OE2 GLU 118 A GLU 116 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc6 A OE1 GLU 168 A GLU 166 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc7 A OE2 GLU 168 A GLU 166 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc8 C MG MG . A MG 301 1_555 F O2P AMP . A AMP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc9 C MG MG . A MG 301 1_555 K O HOH . A HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? metalc ? metalc10 D MG MG . A MG 302 1_555 F O1P AMP . A AMP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? metalc ? metalc11 E MG MG . A MG 303 1_555 F O1P AMP . A AMP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc12 E MG MG . A MG 303 1_555 K O HOH . A HOH 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.081 ? metalc ? metalc13 B O ALA 98 B ALA 96 1_555 G MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc14 B OE1 GLU 114 B GLU 112 1_555 H MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc15 B OE2 GLU 114 B GLU 112 1_555 I MG MG . B MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc16 B OE1 GLU 118 B GLU 116 1_555 G MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc17 B OE1 GLU 118 B GLU 116 1_555 H MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc18 B OE1 GLU 168 B GLU 166 1_555 H MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc19 B OE2 GLU 168 B GLU 166 1_555 H MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.002 ? metalc ? metalc20 G MG MG . B MG 304 1_555 J O3P AMP . B AMP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc21 G MG MG . B MG 304 1_555 L O HOH . B HOH 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc22 G MG MG . B MG 304 1_555 L O HOH . B HOH 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? metalc ? metalc23 H MG MG . B MG 305 1_555 J O3P AMP . B AMP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc24 I MG MG . B MG 306 1_555 J O2P AMP . B AMP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? # _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 2DSD _atom_sites.fract_transf_matrix[1][1] 0.008923 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005505 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024903 _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] 0.011736 _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 MG A 1 301 301 MG MG . D 2 MG A 1 302 302 MG MG . E 2 MG A 1 303 303 MG MG . F 3 AMP A 1 401 401 AMP AMP . G 2 MG B 1 304 304 MG MG . H 2 MG B 1 305 305 MG MG . I 2 MG B 1 306 306 MG MG . J 3 AMP B 1 402 402 AMP AMP . K 4 HOH A 1 402 1 HOH HOH . K 4 HOH A 2 403 2 HOH HOH . K 4 HOH A 3 404 4 HOH HOH . K 4 HOH A 4 405 6 HOH HOH . K 4 HOH A 5 406 12 HOH HOH . K 4 HOH A 6 407 13 HOH HOH . K 4 HOH A 7 408 17 HOH HOH . K 4 HOH A 8 409 18 HOH HOH . K 4 HOH A 9 410 25 HOH HOH . K 4 HOH A 10 411 26 HOH HOH . K 4 HOH A 11 412 30 HOH HOH . K 4 HOH A 12 413 33 HOH HOH . K 4 HOH A 13 414 34 HOH HOH . K 4 HOH A 14 415 35 HOH HOH . K 4 HOH A 15 416 36 HOH HOH . K 4 HOH A 16 417 37 HOH HOH . K 4 HOH A 17 418 44 HOH HOH . K 4 HOH A 18 419 48 HOH HOH . K 4 HOH A 19 420 49 HOH HOH . K 4 HOH A 20 421 50 HOH HOH . K 4 HOH A 21 422 51 HOH HOH . K 4 HOH A 22 423 55 HOH HOH . K 4 HOH A 23 424 56 HOH HOH . K 4 HOH A 24 425 57 HOH HOH . K 4 HOH A 25 426 58 HOH HOH . K 4 HOH A 26 427 62 HOH HOH . K 4 HOH A 27 428 63 HOH HOH . K 4 HOH A 28 429 64 HOH HOH . K 4 HOH A 29 430 66 HOH HOH . K 4 HOH A 30 431 67 HOH HOH . K 4 HOH A 31 432 69 HOH HOH . K 4 HOH A 32 433 70 HOH HOH . K 4 HOH A 33 434 71 HOH HOH . K 4 HOH A 34 435 76 HOH HOH . K 4 HOH A 35 436 77 HOH HOH . K 4 HOH A 36 437 79 HOH HOH . K 4 HOH A 37 438 82 HOH HOH . K 4 HOH A 38 439 83 HOH HOH . K 4 HOH A 39 440 84 HOH HOH . K 4 HOH A 40 441 86 HOH HOH . K 4 HOH A 41 442 92 HOH HOH . K 4 HOH A 42 443 93 HOH HOH . K 4 HOH A 43 444 94 HOH HOH . K 4 HOH A 44 445 96 HOH HOH . L 4 HOH B 1 403 3 HOH HOH . L 4 HOH B 2 404 5 HOH HOH . L 4 HOH B 3 405 7 HOH HOH . L 4 HOH B 4 406 8 HOH HOH . L 4 HOH B 5 407 9 HOH HOH . L 4 HOH B 6 408 10 HOH HOH . L 4 HOH B 7 409 11 HOH HOH . L 4 HOH B 8 410 14 HOH HOH . L 4 HOH B 9 411 15 HOH HOH . L 4 HOH B 10 412 16 HOH HOH . L 4 HOH B 11 413 19 HOH HOH . L 4 HOH B 12 414 20 HOH HOH . L 4 HOH B 13 415 21 HOH HOH . L 4 HOH B 14 416 22 HOH HOH . L 4 HOH B 15 417 23 HOH HOH . L 4 HOH B 16 418 24 HOH HOH . L 4 HOH B 17 419 27 HOH HOH . L 4 HOH B 18 420 28 HOH HOH . L 4 HOH B 19 421 29 HOH HOH . L 4 HOH B 20 422 31 HOH HOH . L 4 HOH B 21 423 32 HOH HOH . L 4 HOH B 22 424 38 HOH HOH . L 4 HOH B 23 425 39 HOH HOH . L 4 HOH B 24 426 40 HOH HOH . L 4 HOH B 25 427 41 HOH HOH . L 4 HOH B 26 428 42 HOH HOH . L 4 HOH B 27 429 43 HOH HOH . L 4 HOH B 28 430 45 HOH HOH . L 4 HOH B 29 431 46 HOH HOH . L 4 HOH B 30 432 47 HOH HOH . L 4 HOH B 31 433 52 HOH HOH . L 4 HOH B 32 434 53 HOH HOH . L 4 HOH B 33 435 54 HOH HOH . L 4 HOH B 34 436 59 HOH HOH . L 4 HOH B 35 437 60 HOH HOH . L 4 HOH B 36 438 61 HOH HOH . L 4 HOH B 37 439 65 HOH HOH . L 4 HOH B 38 440 68 HOH HOH . L 4 HOH B 39 441 72 HOH HOH . L 4 HOH B 40 442 73 HOH HOH . L 4 HOH B 41 443 74 HOH HOH . L 4 HOH B 42 444 75 HOH HOH . L 4 HOH B 43 445 78 HOH HOH . L 4 HOH B 44 446 80 HOH HOH . L 4 HOH B 45 447 81 HOH HOH . L 4 HOH B 46 448 85 HOH HOH . L 4 HOH B 47 449 87 HOH HOH . L 4 HOH B 48 450 88 HOH HOH . L 4 HOH B 49 451 89 HOH HOH . L 4 HOH B 50 452 90 HOH HOH . L 4 HOH B 51 453 91 HOH HOH . L 4 HOH B 52 454 95 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 . . . J 3 -26.759 16.424 73.1 1 79.27 ? P AMP 402 B 1 HETATM 2 O O1P AMP . . . J 3 -25.446 16.344 72.39 1 78.45 ? O1P AMP 402 B 1 HETATM 3 O O2P AMP . . . J 3 -27.086 15.051 73.919 1 78.73 ? O2P AMP 402 B 1 HETATM 4 O O3P AMP . . . J 3 -28.001 16.665 72.07 1 79.96 ? O3P AMP 402 B 1 HETATM 5 O O5' AMP . . . J 3 -26.851 17.627 74.172 1 80.02 ? O5' AMP 402 B 1 HETATM 6 C C5' AMP . . . J 3 -26.01 17.539 75.325 1 81.51 ? C5' AMP 402 B 1 HETATM 7 C C4' AMP . . . J 3 -26.159 18.714 76.293 1 81.35 ? C4' AMP 402 B 1 HETATM 8 O O4' AMP . . . J 3 -25.259 18.514 77.38 1 80.57 ? O4' AMP 402 B 1 HETATM 9 C C3' AMP . . . J 3 -25.787 20.082 75.73 1 81.31 ? C3' AMP 402 B 1 HETATM 10 O O3' AMP . . . J 3 -26.895 20.65 75.034 1 81.52 ? O3' AMP 402 B 1 HETATM 11 C C2' AMP . . . J 3 -25.391 20.859 77.022 1 80.6 ? C2' AMP 402 B 1 HETATM 12 O O2' AMP . . . J 3 -26.542 21.497 77.66 1 82.16 ? O2' AMP 402 B 1 HETATM 13 C C1' AMP . . . J 3 -24.73 19.749 77.917 1 79.16 ? C1' AMP 402 B 1 HETATM 14 N N9 AMP . . . J 3 -23.237 19.699 77.72 1 76.35 ? N9 AMP 402 B 1 HETATM 15 C C8 AMP . . . J 3 -22.544 18.709 77.115 1 75.7 ? C8 AMP 402 B 1 HETATM 16 N N7 AMP . . . J 3 -21.238 19.005 77.1 1 74.61 ? N7 AMP 402 B 1 HETATM 17 C C5 AMP . . . J 3 -21.078 20.183 77.708 1 73.69 ? C5 AMP 402 B 1 HETATM 18 C C6 AMP . . . J 3 -19.927 20.975 77.99 1 72.63 ? C6 AMP 402 B 1 HETATM 19 N N6 AMP . . . J 3 -18.716 20.534 77.609 1 71.39 ? N6 AMP 402 B 1 HETATM 20 N N1 AMP . . . J 3 -20.034 22.208 78.665 1 71.34 ? N1 AMP 402 B 1 HETATM 21 C C2 AMP . . . J 3 -21.353 22.771 79.139 1 72.11 ? C2 AMP 402 B 1 HETATM 22 N N3 AMP . . . J 3 -22.501 21.872 78.799 1 72.55 ? N3 AMP 402 B 1 HETATM 23 C C4 AMP . . . J 3 -22.344 20.639 78.115 1 74.16 ? C4 AMP 402 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 23 #