data_3SM9 # _model_server_result.job_id aW70yY6Qdcn5N9okUBfgCw _model_server_result.datetime_utc '2024-11-26 14:03:06' _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 3sm9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":485}' # _entry.id 3SM9 # _exptl.entry_id 3SM9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 353.369 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine _entity.pdbx_number_of_molecules 1 _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 3SM9 _cell.length_a 83.402 _cell.length_b 98.633 _cell.length_c 203.513 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SM9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 83.402 98.633 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 32 A CYS 32 1_555 A SG CYS 74 A CYS 74 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 A SG CYS 32 A CYS 32 1_555 A SG CYS 74 A CYS 74 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 A SG CYS 336 A CYS 336 1_555 A SG CYS 348 A CYS 348 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 336 A CYS 336 1_555 A SG CYS 348 A CYS 348 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf5 A SG CYS 387 A CYS 387 1_555 A SG CYS 394 A CYS 394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? # _chem_comp.formula 'C20 H19 N O5' _chem_comp.formula_weight 353.369 _chem_comp.id Z99 _chem_comp.mon_nstd_flag . _chem_comp.name 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(1S,2S)-2-[(2S)-2-amino-1-hydroxy-1-oxo-3-(9H-xanthen-9-yl)propan-2-yl]cyclopropane-1-carboxylic acid' # 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 NAA CAY Z99 sing 380 n n NAA HNAA Z99 sing 381 n n NAA HNAB Z99 sing 382 n n OAB CAQ Z99 doub 383 n n CAR OAC Z99 sing 384 n n OAC HOAC Z99 sing 385 n n CAQ OAD Z99 sing 386 n n OAD HOAD Z99 sing 387 n n OAE CAR Z99 doub 388 n n CAH CAF Z99 doub 389 n y CAF CAJ Z99 sing 390 n y CAF HAF Z99 sing 391 n n CAI CAG Z99 doub 392 n y CAG CAK Z99 sing 393 n y CAG HAG Z99 sing 394 n n CAL CAH Z99 sing 395 n y CAH HAH Z99 sing 396 n n CAM CAI Z99 sing 397 n y CAI HAI Z99 sing 398 n n CAS CAJ Z99 doub 399 n y CAJ HAJ Z99 sing 400 n n CAT CAK Z99 doub 401 n y CAK HAK Z99 sing 402 n n CAL CAU Z99 doub 403 n y CAL HAL Z99 sing 404 n n CAM CAV Z99 doub 405 n y CAM HAM Z99 sing 406 n n CAY CAN Z99 sing 407 n n CAN CAW Z99 sing 408 n n CAN HAN Z99 sing 409 n n CAN HANA Z99 sing 410 n n CAZ CAO Z99 sing 411 n n CAO CAX Z99 sing 412 n n CAO HAO Z99 sing 413 n n CAO HAOA Z99 sing 414 n n CAS OAP Z99 sing 415 n n CAT OAP Z99 sing 416 n n CAQ CAX Z99 sing 417 n n CAY CAR Z99 sing 418 n n CAU CAS Z99 sing 419 n y CAV CAT Z99 sing 420 n y CAW CAU Z99 sing 421 n n CAW CAV Z99 sing 422 n n CAW HAW Z99 sing 423 n n CAZ CAX Z99 sing 424 n n CAX HAX Z99 sing 425 n n CAZ CAY Z99 sing 426 n n CAZ HAZ Z99 sing 427 n n # _atom_sites.entry_id 3SM9 _atom_sites.fract_transf_matrix[1][1] 0.01199 _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] 0.010139 _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] 0.004914 _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 B 2 SO4 A 1 480 1 SO4 SO4 . C 2 SO4 A 1 481 2 SO4 SO4 . D 2 SO4 A 1 482 3 SO4 SO4 . E 2 SO4 A 1 483 4 SO4 SO4 . F 2 SO4 A 1 484 5 SO4 SO4 . G 3 Z99 A 1 485 1 Z99 Z99 . H 4 CL A 1 486 1 CL CL . I 4 CL A 1 487 1 CL CL . J 5 HOH A 1 488 1 HOH HOH . J 5 HOH A 2 489 2 HOH HOH . J 5 HOH A 3 490 3 HOH HOH . J 5 HOH A 4 491 4 HOH HOH . J 5 HOH A 5 492 5 HOH HOH . J 5 HOH A 6 493 6 HOH HOH . J 5 HOH A 7 494 7 HOH HOH . J 5 HOH A 8 495 12 HOH HOH . J 5 HOH A 9 496 17 HOH HOH . J 5 HOH A 10 497 18 HOH HOH . J 5 HOH A 11 498 19 HOH HOH . J 5 HOH A 12 499 22 HOH HOH . J 5 HOH A 13 500 23 HOH HOH . J 5 HOH A 14 501 25 HOH HOH . J 5 HOH A 15 502 29 HOH HOH . J 5 HOH A 16 503 30 HOH HOH . J 5 HOH A 17 504 32 HOH HOH . J 5 HOH A 18 505 34 HOH HOH . J 5 HOH A 19 506 36 HOH HOH . J 5 HOH A 20 507 41 HOH HOH . J 5 HOH A 21 508 48 HOH HOH . J 5 HOH A 22 509 54 HOH HOH . J 5 HOH A 23 510 74 HOH HOH . J 5 HOH A 24 511 76 HOH HOH . J 5 HOH A 25 512 86 HOH HOH . J 5 HOH A 26 513 92 HOH HOH . J 5 HOH A 27 514 147 HOH HOH . J 5 HOH A 28 515 225 HOH HOH . J 5 HOH A 29 516 227 HOH HOH . J 5 HOH A 30 517 239 HOH HOH . J 5 HOH A 31 518 240 HOH HOH . J 5 HOH A 32 519 241 HOH HOH . J 5 HOH A 33 520 242 HOH HOH . J 5 HOH A 34 521 243 HOH HOH . J 5 HOH A 35 522 244 HOH HOH . J 5 HOH A 36 523 245 HOH HOH . J 5 HOH A 37 524 247 HOH HOH . J 5 HOH A 38 525 248 HOH HOH . J 5 HOH A 39 526 249 HOH HOH . J 5 HOH A 40 527 250 HOH HOH . J 5 HOH A 41 528 251 HOH HOH . J 5 HOH A 42 529 252 HOH HOH . J 5 HOH A 43 530 253 HOH HOH . J 5 HOH A 44 531 255 HOH HOH . J 5 HOH A 45 532 257 HOH HOH . J 5 HOH A 46 533 259 HOH HOH . J 5 HOH A 47 534 260 HOH HOH . J 5 HOH A 48 535 261 HOH HOH . J 5 HOH A 49 536 262 HOH HOH . J 5 HOH A 50 537 264 HOH HOH . J 5 HOH A 51 538 265 HOH HOH . J 5 HOH A 52 539 266 HOH HOH . J 5 HOH A 53 540 267 HOH HOH . J 5 HOH A 54 541 268 HOH HOH . J 5 HOH A 55 542 269 HOH HOH . J 5 HOH A 56 543 270 HOH HOH . J 5 HOH A 57 544 271 HOH HOH . J 5 HOH A 58 545 272 HOH HOH . J 5 HOH A 59 546 274 HOH HOH . J 5 HOH A 60 547 275 HOH HOH . J 5 HOH A 61 548 276 HOH HOH . J 5 HOH A 62 549 278 HOH HOH . J 5 HOH A 63 550 279 HOH HOH . J 5 HOH A 64 551 280 HOH HOH . J 5 HOH A 65 552 281 HOH HOH . J 5 HOH A 66 553 282 HOH HOH . J 5 HOH A 67 554 283 HOH HOH . J 5 HOH A 68 555 291 HOH HOH . J 5 HOH A 69 556 292 HOH HOH . J 5 HOH A 70 557 294 HOH HOH . J 5 HOH A 71 558 297 HOH HOH . J 5 HOH A 72 559 298 HOH HOH . J 5 HOH A 73 560 302 HOH HOH . J 5 HOH A 74 561 303 HOH HOH . J 5 HOH A 75 562 307 HOH HOH . J 5 HOH A 76 563 308 HOH HOH . J 5 HOH A 77 564 309 HOH HOH . J 5 HOH A 78 565 313 HOH HOH . J 5 HOH A 79 566 314 HOH HOH . J 5 HOH A 80 567 316 HOH HOH . J 5 HOH A 81 568 318 HOH HOH . J 5 HOH A 82 569 320 HOH HOH . J 5 HOH A 83 570 323 HOH HOH . J 5 HOH A 84 571 324 HOH HOH . J 5 HOH A 85 572 325 HOH HOH . J 5 HOH A 86 573 326 HOH HOH . J 5 HOH A 87 574 327 HOH HOH . J 5 HOH A 88 575 328 HOH HOH . J 5 HOH A 89 576 330 HOH HOH . J 5 HOH A 90 577 331 HOH HOH . J 5 HOH A 91 578 334 HOH HOH . J 5 HOH A 92 579 335 HOH HOH . J 5 HOH A 93 580 336 HOH HOH . J 5 HOH A 94 581 338 HOH HOH . J 5 HOH A 95 582 339 HOH HOH . J 5 HOH A 96 583 341 HOH HOH . J 5 HOH A 97 584 342 HOH HOH . J 5 HOH A 98 585 343 HOH HOH . J 5 HOH A 99 586 344 HOH HOH . J 5 HOH A 100 587 345 HOH HOH . J 5 HOH A 101 588 347 HOH HOH . J 5 HOH A 102 589 348 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 N NAA Z99 . . . G 3 36.77 28.351 -31.556 1 34.38 ? NAA Z99 485 A 1 HETATM 2 O OAB Z99 . . . G 3 36.878 27.079 -36.285 1 42.23 ? OAB Z99 485 A 1 HETATM 3 O OAC Z99 . . . G 3 39.789 30.068 -32.595 1 46.88 ? OAC Z99 485 A 1 HETATM 4 O OAD Z99 . . . G 3 35.795 25.586 -35.051 1 38.66 ? OAD Z99 485 A 1 HETATM 5 O OAE Z99 . . . G 3 37.931 30.712 -31.544 1 49.55 ? OAE Z99 485 A 1 HETATM 6 C CAF Z99 . . . G 3 40.945 24.033 -28.305 1 36.79 ? CAF Z99 485 A 1 HETATM 7 C CAG Z99 . . . G 3 41.973 30.879 -28.957 1 48.32 ? CAG Z99 485 A 1 HETATM 8 C CAH Z99 . . . G 3 39.552 24.181 -28.304 1 38.43 ? CAH Z99 485 A 1 HETATM 9 C CAI Z99 . . . G 3 40.604 31.158 -28.959 1 44.87 ? CAI Z99 485 A 1 HETATM 10 C CAJ Z99 . . . G 3 41.745 25.08 -28.781 1 44.17 ? CAJ Z99 485 A 1 HETATM 11 C CAK Z99 . . . G 3 42.422 29.577 -29.218 1 46.93 ? CAK Z99 485 A 1 HETATM 12 C CAL Z99 . . . G 3 38.96 25.365 -28.765 1 48.66 ? CAL Z99 485 A 1 HETATM 13 C CAM Z99 . . . G 3 39.688 30.124 -29.174 1 41.11 ? CAM Z99 485 A 1 HETATM 14 C CAN Z99 . . . G 3 39.087 27.475 -31.388 1 39.12 ? CAN Z99 485 A 1 HETATM 15 C CAO Z99 . . . G 3 39.043 27.263 -34.362 1 30.74 ? CAO Z99 485 A 1 HETATM 16 O OAP Z99 . . . G 3 41.958 27.278 -29.735 1 46.93 ? OAP Z99 485 A 1 HETATM 17 C CAQ Z99 . . . G 3 36.695 26.434 -35.223 1 40.85 ? CAQ Z99 485 A 1 HETATM 18 C CAR Z99 . . . G 3 38.658 29.856 -32.094 1 41.68 ? CAR Z99 485 A 1 HETATM 19 C CAS Z99 . . . G 3 41.162 26.266 -29.254 1 43.15 ? CAS Z99 485 A 1 HETATM 20 C CAT Z99 . . . G 3 41.508 28.55 -29.47 1 50.07 ? CAT Z99 485 A 1 HETATM 21 C CAU Z99 . . . G 3 39.763 26.411 -29.233 1 42.36 ? CAU Z99 485 A 1 HETATM 22 C CAV Z99 . . . G 3 40.136 28.834 -29.494 1 43 ? CAV Z99 485 A 1 HETATM 23 C CAW Z99 . . . G 3 39.15 27.696 -29.819 1 41.05 ? CAW Z99 485 A 1 HETATM 24 C CAX Z99 . . . G 3 37.664 26.654 -34.037 1 43.05 ? CAX Z99 485 A 1 HETATM 25 C CAY Z99 . . . G 3 38.123 28.428 -32.162 1 41.22 ? CAY Z99 485 A 1 HETATM 26 C CAZ Z99 . . . G 3 37.969 28.118 -33.681 1 40.65 ? CAZ Z99 485 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #