data_4M7Y # _model_server_result.job_id HjOynpzl1lsz8aIQ3ayzrQ _model_server_result.datetime_utc '2024-10-10 15:19:22' _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 4m7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":302}' # _entry.id 4M7Y # _exptl.entry_id 4M7Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 101.17 _cell.angle_gamma 90 _cell.entry_id 4M7Y _cell.length_a 141.96 _cell.length_b 56.13 _cell.length_c 68.42 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M7Y _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 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,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA _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 R N N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 53 n n PB O2B ADP sing 54 n n PB O3B ADP sing 55 n n PB O3A ADP sing 56 n n O2B HOB2 ADP sing 57 n n O3B HOB3 ADP sing 58 n n PA O1A ADP doub 59 n n PA O2A ADP sing 60 n n PA O3A ADP sing 61 n n PA O5' ADP sing 62 n n O2A HOA2 ADP sing 63 n n O5' C5' ADP sing 64 n n C5' C4' ADP sing 65 n n C5' "H5'1" ADP sing 66 n n C5' "H5'2" ADP sing 67 n n C4' O4' ADP sing 68 n n C4' C3' ADP sing 69 n n C4' H4' ADP sing 70 n n O4' C1' ADP sing 71 n n C3' O3' ADP sing 72 n n C3' C2' ADP sing 73 n n C3' H3' ADP sing 74 n n O3' HO3' ADP sing 75 n n C2' O2' ADP sing 76 n n C2' C1' ADP sing 77 n n C2' H2' ADP sing 78 n n O2' HO2' ADP sing 79 n n C1' N9 ADP sing 80 n n C1' H1' ADP sing 81 n n N9 C8 ADP sing 82 n y N9 C4 ADP sing 83 n y C8 N7 ADP doub 84 n y C8 H8 ADP sing 85 n n N7 C5 ADP sing 86 n y C5 C6 ADP sing 87 n y C5 C4 ADP doub 88 n y C6 N6 ADP sing 89 n n C6 N1 ADP doub 90 n y N6 HN61 ADP sing 91 n n N6 HN62 ADP sing 92 n n N1 C2 ADP sing 93 n y C2 N3 ADP doub 94 n y C2 H2 ADP sing 95 n n N3 C4 ADP sing 96 n y # _atom_sites.entry_id 4M7Y _atom_sites.fract_transf_matrix[1][1] 0.007044 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00139 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017816 _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] 0.014898 _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 2GH A 1 301 301 2GH 2GH . D 3 ADP A 1 302 302 ADP ADP . E 4 PO4 A 1 303 4 PO4 PO4 . F 4 PO4 A 1 304 6 PO4 PO4 . G 5 UNX A 1 305 1 UNX UNX . H 5 UNX A 1 306 5 UNX UNX . I 5 UNX A 1 307 7 UNX UNX . J 5 UNX A 1 308 8 UNX UNX . K 5 UNX A 1 309 13 UNX UNX . L 5 UNX A 1 310 14 UNX UNX . M 5 UNX A 1 311 16 UNX UNX . N 5 UNX A 1 312 17 UNX UNX . O 5 UNX A 1 313 22 UNX UNX . P 5 UNX A 1 314 23 UNX UNX . Q 2 2GH B 1 301 301 2GH 2GH . R 3 ADP B 1 302 302 ADP ADP . S 4 PO4 B 1 303 2 PO4 PO4 . T 4 PO4 B 1 304 3 PO4 PO4 . U 4 PO4 B 1 305 5 PO4 PO4 . V 5 UNX B 1 306 7 UNX UNX . W 5 UNX B 1 307 9 UNX UNX . X 5 UNX B 1 308 10 UNX UNX . Y 5 UNX B 1 309 11 UNX UNX . Z 5 UNX B 1 310 12 UNX UNX . AA 4 PO4 B 1 311 7 PO4 PO4 . BA 4 PO4 B 1 312 8 PO4 PO4 . CA 5 UNX B 1 313 4 UNX UNX . DA 5 UNX B 1 314 6 UNX UNX . EA 5 UNX B 1 315 11 UNX UNX . FA 5 UNX B 1 316 12 UNX UNX . GA 5 UNX B 1 317 15 UNX UNX . HA 5 UNX B 1 318 18 UNX UNX . IA 5 UNX B 1 319 19 UNX UNX . JA 6 HOH A 1 401 2 HOH HOH . JA 6 HOH A 2 402 4 HOH HOH . JA 6 HOH A 3 403 7 HOH HOH . JA 6 HOH A 4 404 9 HOH HOH . JA 6 HOH A 5 405 10 HOH HOH . JA 6 HOH A 6 406 13 HOH HOH . JA 6 HOH A 7 407 14 HOH HOH . JA 6 HOH A 8 408 15 HOH HOH . JA 6 HOH A 9 409 16 HOH HOH . JA 6 HOH A 10 410 19 HOH HOH . JA 6 HOH A 11 411 20 HOH HOH . JA 6 HOH A 12 412 21 HOH HOH . JA 6 HOH A 13 413 22 HOH HOH . JA 6 HOH A 14 414 23 HOH HOH . JA 6 HOH A 15 415 24 HOH HOH . JA 6 HOH A 16 416 25 HOH HOH . JA 6 HOH A 17 417 27 HOH HOH . JA 6 HOH A 18 418 28 HOH HOH . JA 6 HOH A 19 419 29 HOH HOH . JA 6 HOH A 20 420 36 HOH HOH . JA 6 HOH A 21 421 37 HOH HOH . JA 6 HOH A 22 422 38 HOH HOH . JA 6 HOH A 23 423 39 HOH HOH . JA 6 HOH A 24 424 40 HOH HOH . JA 6 HOH A 25 425 42 HOH HOH . JA 6 HOH A 26 426 47 HOH HOH . JA 6 HOH A 27 427 49 HOH HOH . JA 6 HOH A 28 428 50 HOH HOH . JA 6 HOH A 29 429 51 HOH HOH . JA 6 HOH A 30 430 52 HOH HOH . JA 6 HOH A 31 431 53 HOH HOH . JA 6 HOH A 32 432 56 HOH HOH . JA 6 HOH A 33 433 60 HOH HOH . JA 6 HOH A 34 434 62 HOH HOH . JA 6 HOH A 35 435 63 HOH HOH . JA 6 HOH A 36 436 65 HOH HOH . JA 6 HOH A 37 437 66 HOH HOH . JA 6 HOH A 38 438 70 HOH HOH . JA 6 HOH A 39 439 71 HOH HOH . JA 6 HOH A 40 440 72 HOH HOH . JA 6 HOH A 41 441 73 HOH HOH . JA 6 HOH A 42 442 80 HOH HOH . JA 6 HOH A 43 443 81 HOH HOH . JA 6 HOH A 44 444 82 HOH HOH . JA 6 HOH A 45 445 83 HOH HOH . JA 6 HOH A 46 446 85 HOH HOH . JA 6 HOH A 47 447 87 HOH HOH . JA 6 HOH A 48 448 89 HOH HOH . JA 6 HOH A 49 449 90 HOH HOH . JA 6 HOH A 50 450 96 HOH HOH . JA 6 HOH A 51 451 98 HOH HOH . JA 6 HOH A 52 452 102 HOH HOH . JA 6 HOH A 53 453 110 HOH HOH . JA 6 HOH A 54 454 124 HOH HOH . JA 6 HOH A 55 455 125 HOH HOH . JA 6 HOH A 56 456 126 HOH HOH . JA 6 HOH A 57 457 127 HOH HOH . JA 6 HOH A 58 458 128 HOH HOH . JA 6 HOH A 59 459 129 HOH HOH . JA 6 HOH A 60 460 130 HOH HOH . JA 6 HOH A 61 461 131 HOH HOH . JA 6 HOH A 62 462 133 HOH HOH . JA 6 HOH A 63 463 135 HOH HOH . JA 6 HOH A 64 464 136 HOH HOH . JA 6 HOH A 65 465 137 HOH HOH . JA 6 HOH A 66 466 138 HOH HOH . JA 6 HOH A 67 467 140 HOH HOH . JA 6 HOH A 68 468 141 HOH HOH . JA 6 HOH A 69 469 142 HOH HOH . JA 6 HOH A 70 470 143 HOH HOH . JA 6 HOH A 71 471 144 HOH HOH . JA 6 HOH A 72 472 145 HOH HOH . JA 6 HOH A 73 473 146 HOH HOH . JA 6 HOH A 74 474 147 HOH HOH . JA 6 HOH A 75 475 148 HOH HOH . JA 6 HOH A 76 476 149 HOH HOH . JA 6 HOH A 77 477 150 HOH HOH . JA 6 HOH A 78 478 151 HOH HOH . JA 6 HOH A 79 479 153 HOH HOH . JA 6 HOH A 80 480 154 HOH HOH . JA 6 HOH A 81 481 155 HOH HOH . JA 6 HOH A 82 482 156 HOH HOH . JA 6 HOH A 83 483 157 HOH HOH . JA 6 HOH A 84 484 160 HOH HOH . JA 6 HOH A 85 485 162 HOH HOH . JA 6 HOH A 86 486 163 HOH HOH . JA 6 HOH A 87 487 164 HOH HOH . JA 6 HOH A 88 488 165 HOH HOH . JA 6 HOH A 89 489 179 HOH HOH . JA 6 HOH A 90 490 184 HOH HOH . JA 6 HOH A 91 491 185 HOH HOH . JA 6 HOH A 92 492 186 HOH HOH . JA 6 HOH A 93 493 187 HOH HOH . JA 6 HOH A 94 494 188 HOH HOH . JA 6 HOH A 95 495 191 HOH HOH . JA 6 HOH A 96 496 193 HOH HOH . JA 6 HOH A 97 497 194 HOH HOH . JA 6 HOH A 98 498 195 HOH HOH . JA 6 HOH A 99 499 196 HOH HOH . JA 6 HOH A 100 500 197 HOH HOH . JA 6 HOH A 101 501 201 HOH HOH . JA 6 HOH A 102 502 202 HOH HOH . JA 6 HOH A 103 503 203 HOH HOH . JA 6 HOH A 104 504 204 HOH HOH . JA 6 HOH A 105 505 207 HOH HOH . JA 6 HOH A 106 506 211 HOH HOH . JA 6 HOH A 107 507 213 HOH HOH . JA 6 HOH A 108 508 214 HOH HOH . JA 6 HOH A 109 509 215 HOH HOH . JA 6 HOH A 110 510 217 HOH HOH . JA 6 HOH A 111 511 218 HOH HOH . JA 6 HOH A 112 512 219 HOH HOH . JA 6 HOH A 113 513 220 HOH HOH . JA 6 HOH A 114 514 221 HOH HOH . JA 6 HOH A 115 515 222 HOH HOH . JA 6 HOH A 116 516 232 HOH HOH . JA 6 HOH A 117 517 233 HOH HOH . KA 6 HOH B 1 401 5 HOH HOH . KA 6 HOH B 2 402 6 HOH HOH . KA 6 HOH B 3 403 18 HOH HOH . KA 6 HOH B 4 404 26 HOH HOH . KA 6 HOH B 5 405 31 HOH HOH . KA 6 HOH B 6 406 32 HOH HOH . KA 6 HOH B 7 407 34 HOH HOH . KA 6 HOH B 8 408 35 HOH HOH . KA 6 HOH B 9 409 41 HOH HOH . KA 6 HOH B 10 410 43 HOH HOH . KA 6 HOH B 11 411 45 HOH HOH . KA 6 HOH B 12 412 46 HOH HOH . KA 6 HOH B 13 413 48 HOH HOH . KA 6 HOH B 14 414 54 HOH HOH . KA 6 HOH B 15 415 55 HOH HOH . KA 6 HOH B 16 416 59 HOH HOH . KA 6 HOH B 17 417 61 HOH HOH . KA 6 HOH B 18 418 64 HOH HOH . KA 6 HOH B 19 419 68 HOH HOH . KA 6 HOH B 20 420 74 HOH HOH . KA 6 HOH B 21 421 77 HOH HOH . KA 6 HOH B 22 422 79 HOH HOH . KA 6 HOH B 23 423 84 HOH HOH . KA 6 HOH B 24 424 86 HOH HOH . KA 6 HOH B 25 425 91 HOH HOH . KA 6 HOH B 26 426 92 HOH HOH . KA 6 HOH B 27 427 93 HOH HOH . KA 6 HOH B 28 428 94 HOH HOH . KA 6 HOH B 29 429 95 HOH HOH . KA 6 HOH B 30 430 97 HOH HOH . KA 6 HOH B 31 431 100 HOH HOH . KA 6 HOH B 32 432 101 HOH HOH . KA 6 HOH B 33 433 105 HOH HOH . KA 6 HOH B 34 434 107 HOH HOH . KA 6 HOH B 35 435 112 HOH HOH . KA 6 HOH B 36 436 114 HOH HOH . KA 6 HOH B 37 437 116 HOH HOH . KA 6 HOH B 38 438 132 HOH HOH . KA 6 HOH B 39 439 158 HOH HOH . KA 6 HOH B 40 440 159 HOH HOH . KA 6 HOH B 41 441 161 HOH HOH . KA 6 HOH B 42 442 166 HOH HOH . KA 6 HOH B 43 443 167 HOH HOH . KA 6 HOH B 44 444 168 HOH HOH . KA 6 HOH B 45 445 169 HOH HOH . KA 6 HOH B 46 446 170 HOH HOH . KA 6 HOH B 47 447 171 HOH HOH . KA 6 HOH B 48 448 172 HOH HOH . KA 6 HOH B 49 449 173 HOH HOH . KA 6 HOH B 50 450 174 HOH HOH . KA 6 HOH B 51 451 175 HOH HOH . KA 6 HOH B 52 452 177 HOH HOH . KA 6 HOH B 53 453 178 HOH HOH . KA 6 HOH B 54 454 181 HOH HOH . KA 6 HOH B 55 455 182 HOH HOH . KA 6 HOH B 56 456 190 HOH HOH . KA 6 HOH B 57 457 192 HOH HOH . KA 6 HOH B 58 458 198 HOH HOH . KA 6 HOH B 59 459 199 HOH HOH . KA 6 HOH B 60 460 200 HOH HOH . KA 6 HOH B 61 461 205 HOH HOH . KA 6 HOH B 62 462 206 HOH HOH . KA 6 HOH B 63 463 209 HOH HOH . KA 6 HOH B 64 464 210 HOH HOH . KA 6 HOH B 65 465 212 HOH HOH . KA 6 HOH B 66 466 223 HOH HOH . KA 6 HOH B 67 467 224 HOH HOH . KA 6 HOH B 68 468 225 HOH HOH . KA 6 HOH B 69 469 226 HOH HOH . KA 6 HOH B 70 470 227 HOH HOH . KA 6 HOH B 71 471 228 HOH HOH . KA 6 HOH B 72 472 229 HOH HOH . KA 6 HOH B 73 473 230 HOH HOH . KA 6 HOH B 74 474 231 HOH HOH . KA 6 HOH B 75 475 234 HOH HOH . KA 6 HOH B 76 476 235 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 PB ADP . . . R 3 -16.666 7.714 -52.163 1 24.2 ? PB ADP 302 B 1 HETATM 2 O O1B ADP . . . R 3 -17.685 8.335 -51.219 1 22.8 ? O1B ADP 302 B 1 HETATM 3 O O2B ADP . . . R 3 -16.692 6.177 -52.222 1 24.67 ? O2B ADP 302 B 1 HETATM 4 O O3B ADP . . . R 3 -16.664 8.35 -53.516 1 22.93 ? O3B ADP 302 B 1 HETATM 5 P PA ADP . . . R 3 -13.784 7.812 -51.952 1 24.17 ? PA ADP 302 B 1 HETATM 6 O O1A ADP . . . R 3 -13.78 7.603 -53.473 1 24.71 ? O1A ADP 302 B 1 HETATM 7 O O2A ADP . . . R 3 -13.154 6.754 -51.092 1 23.47 ? O2A ADP 302 B 1 HETATM 8 O O3A ADP . . . R 3 -15.274 8.108 -51.46 1 22.66 ? O3A ADP 302 B 1 HETATM 9 O O5' ADP . . . R 3 -13.066 9.236 -51.593 1 24.31 ? O5' ADP 302 B 1 HETATM 10 C C5' ADP . . . R 3 -13.64 10.491 -51.961 1 22.72 ? C5' ADP 302 B 1 HETATM 11 C C4' ADP . . . R 3 -12.623 11.566 -51.715 1 23.27 ? C4' ADP 302 B 1 HETATM 12 O O4' ADP . . . R 3 -11.415 11.271 -52.41 1 24.73 ? O4' ADP 302 B 1 HETATM 13 C C3' ADP . . . R 3 -13.011 12.96 -52.174 1 23.1 ? C3' ADP 302 B 1 HETATM 14 O O3' ADP . . . R 3 -13.797 13.563 -51.184 1 23.89 ? O3' ADP 302 B 1 HETATM 15 C C2' ADP . . . R 3 -11.679 13.629 -52.332 1 23.79 ? C2' ADP 302 B 1 HETATM 16 O O2' ADP . . . R 3 -11.171 14.076 -51.046 1 22.13 ? O2' ADP 302 B 1 HETATM 17 C C1' ADP . . . R 3 -10.787 12.495 -52.83 1 25.67 ? C1' ADP 302 B 1 HETATM 18 N N9 ADP . . . R 3 -10.524 12.508 -54.305 1 26.61 ? N9 ADP 302 B 1 HETATM 19 C C8 ADP . . . R 3 -9.484 11.852 -54.872 1 27.75 ? C8 ADP 302 B 1 HETATM 20 N N7 ADP . . . R 3 -9.466 12.057 -56.212 1 27.47 ? N7 ADP 302 B 1 HETATM 21 C C5 ADP . . . R 3 -10.49 12.842 -56.501 1 27.96 ? C5 ADP 302 B 1 HETATM 22 C C6 ADP . . . R 3 -10.999 13.424 -57.723 1 28.26 ? C6 ADP 302 B 1 HETATM 23 N N6 ADP . . . R 3 -10.402 13.164 -58.872 1 30.39 ? N6 ADP 302 B 1 HETATM 24 N N1 ADP . . . R 3 -12.072 14.193 -57.666 1 28.57 ? N1 ADP 302 B 1 HETATM 25 C C2 ADP . . . R 3 -12.685 14.457 -56.522 1 28.55 ? C2 ADP 302 B 1 HETATM 26 N N3 ADP . . . R 3 -12.269 13.946 -55.343 1 27.36 ? N3 ADP 302 B 1 HETATM 27 C C4 ADP . . . R 3 -11.186 13.143 -55.28 1 26.55 ? C4 ADP 302 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #