data_8KDU # _model_server_result.job_id cDAU42-XWGomZQuegXon9w _model_server_result.datetime_utc '2024-10-14 05:17:15' _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 8kdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 8KDU # _exptl.entry_id 8KDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 278.307 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2~{R})-2-benzamido-5-carbamimidamido-pentanoic acid' _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 120 _cell.entry_id 8KDU _cell.length_a 131.116 _cell.length_b 131.116 _cell.length_c 71.424 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc1 A OE1 GLU 52 A GLU 70 1_555 G CA CA . A CA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc2 A O ASN 54 A ASN 72 1_555 G CA CA . A CA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc3 A O VAL 57 A VAL 75 1_555 G CA CA . A CA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 G CA CA . A CA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? # _chem_comp.formula 'C13 H18 N4 O3' _chem_comp.formula_weight 278.307 _chem_comp.id JNR _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{R})-2-benzamido-5-carbamimidamido-pentanoic acid' _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 C10 C9 JNR doub 233 n y C10 C11 JNR sing 234 n y C9 C8 JNR sing 235 n y C11 C12 JNR doub 236 n y C8 C7 JNR doub 237 n y C12 C7 JNR sing 238 n y C7 C6 JNR sing 239 n n N1 C1 JNR doub 240 n n C1 N3 JNR sing 241 n n C1 N2 JNR sing 242 n n N4 C6 JNR sing 243 n n N4 C5 JNR sing 244 n n C6 O1 JNR doub 245 n n N3 C2 JNR sing 246 n n C3 C2 JNR sing 247 n n C3 C4 JNR sing 248 n n C5 C4 JNR sing 249 n n C5 C13 JNR sing 250 n n O3 C13 JNR doub 251 n n C13 O2 JNR sing 252 n n N1 H1 JNR sing 253 n n C2 H3 JNR sing 254 n n C2 H4 JNR sing 255 n n C3 H5 JNR sing 256 n n C3 H6 JNR sing 257 n n C4 H7 JNR sing 258 n n C4 H8 JNR sing 259 n n C5 H9 JNR sing 260 n n N2 H10 JNR sing 261 n n N2 H11 JNR sing 262 n n N3 H12 JNR sing 263 n n N4 H13 JNR sing 264 n n C8 H14 JNR sing 265 n n C9 H15 JNR sing 266 n n C10 H16 JNR sing 267 n n C11 H17 JNR sing 268 n n C12 H18 JNR sing 269 n n O2 H2 JNR sing 270 n n # _atom_sites.entry_id 8KDU _atom_sites.fract_transf_matrix[1][1] 0.007627 _atom_sites.fract_transf_matrix[1][2] 0.004403 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008807 _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] 0.014001 _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 I4Q A 1 301 301 I4Q BZA . C 3 JNR A 1 302 302 JNR BA1 . D 4 ARG A 1 303 303 ARG ARG . E 5 GAI A 1 304 401 GAI GAI . F 6 SO4 A 1 305 2 SO4 SO4 . G 7 CA A 1 306 1 CA CA . H 8 CL A 1 307 1 CL CL . I 8 CL A 1 308 2 CL CL . J 8 CL A 1 309 3 CL CL . K 9 PEG A 1 310 301 PEG PEG . L 10 EOH A 1 311 303 EOH EOH . M 10 EOH A 1 312 305 EOH EOH . N 11 HOH A 1 401 196 HOH HOH . N 11 HOH A 2 402 183 HOH HOH . N 11 HOH A 3 403 31 HOH HOH . N 11 HOH A 4 404 65 HOH HOH . N 11 HOH A 5 405 111 HOH HOH . N 11 HOH A 6 406 100 HOH HOH . N 11 HOH A 7 407 142 HOH HOH . N 11 HOH A 8 408 47 HOH HOH . N 11 HOH A 9 409 117 HOH HOH . N 11 HOH A 10 410 186 HOH HOH . N 11 HOH A 11 411 11 HOH HOH . N 11 HOH A 12 412 94 HOH HOH . N 11 HOH A 13 413 98 HOH HOH . N 11 HOH A 14 414 76 HOH HOH . N 11 HOH A 15 415 86 HOH HOH . N 11 HOH A 16 416 181 HOH HOH . N 11 HOH A 17 417 192 HOH HOH . N 11 HOH A 18 418 109 HOH HOH . N 11 HOH A 19 419 92 HOH HOH . N 11 HOH A 20 420 63 HOH HOH . N 11 HOH A 21 421 118 HOH HOH . N 11 HOH A 22 422 154 HOH HOH . N 11 HOH A 23 423 68 HOH HOH . N 11 HOH A 24 424 123 HOH HOH . N 11 HOH A 25 425 64 HOH HOH . N 11 HOH A 26 426 96 HOH HOH . N 11 HOH A 27 427 163 HOH HOH . N 11 HOH A 28 428 43 HOH HOH . N 11 HOH A 29 429 190 HOH HOH . N 11 HOH A 30 430 36 HOH HOH . N 11 HOH A 31 431 143 HOH HOH . N 11 HOH A 32 432 58 HOH HOH . N 11 HOH A 33 433 153 HOH HOH . N 11 HOH A 34 434 113 HOH HOH . N 11 HOH A 35 435 93 HOH HOH . N 11 HOH A 36 436 172 HOH HOH . N 11 HOH A 37 437 69 HOH HOH . N 11 HOH A 38 438 157 HOH HOH . N 11 HOH A 39 439 13 HOH HOH . N 11 HOH A 40 440 72 HOH HOH . N 11 HOH A 41 441 9 HOH HOH . N 11 HOH A 42 442 16 HOH HOH . N 11 HOH A 43 443 38 HOH HOH . N 11 HOH A 44 444 197 HOH HOH . N 11 HOH A 45 445 202 HOH HOH . N 11 HOH A 46 446 104 HOH HOH . N 11 HOH A 47 447 99 HOH HOH . N 11 HOH A 48 448 25 HOH HOH . N 11 HOH A 49 449 83 HOH HOH . N 11 HOH A 50 450 74 HOH HOH . N 11 HOH A 51 451 188 HOH HOH . N 11 HOH A 52 452 107 HOH HOH . N 11 HOH A 53 453 81 HOH HOH . N 11 HOH A 54 454 122 HOH HOH . N 11 HOH A 55 455 39 HOH HOH . N 11 HOH A 56 456 23 HOH HOH . N 11 HOH A 57 457 171 HOH HOH . N 11 HOH A 58 458 146 HOH HOH . N 11 HOH A 59 459 160 HOH HOH . N 11 HOH A 60 460 136 HOH HOH . N 11 HOH A 61 461 149 HOH HOH . N 11 HOH A 62 462 119 HOH HOH . N 11 HOH A 63 463 19 HOH HOH . N 11 HOH A 64 464 6 HOH HOH . N 11 HOH A 65 465 59 HOH HOH . N 11 HOH A 66 466 150 HOH HOH . N 11 HOH A 67 467 7 HOH HOH . N 11 HOH A 68 468 22 HOH HOH . N 11 HOH A 69 469 44 HOH HOH . N 11 HOH A 70 470 42 HOH HOH . N 11 HOH A 71 471 61 HOH HOH . N 11 HOH A 72 472 71 HOH HOH . N 11 HOH A 73 473 125 HOH HOH . N 11 HOH A 74 474 184 HOH HOH . N 11 HOH A 75 475 137 HOH HOH . N 11 HOH A 76 476 162 HOH HOH . N 11 HOH A 77 477 37 HOH HOH . N 11 HOH A 78 478 53 HOH HOH . N 11 HOH A 79 479 24 HOH HOH . N 11 HOH A 80 480 78 HOH HOH . N 11 HOH A 81 481 178 HOH HOH . N 11 HOH A 82 482 12 HOH HOH . N 11 HOH A 83 483 176 HOH HOH . N 11 HOH A 84 484 90 HOH HOH . N 11 HOH A 85 485 20 HOH HOH . N 11 HOH A 86 486 35 HOH HOH . N 11 HOH A 87 487 67 HOH HOH . N 11 HOH A 88 488 101 HOH HOH . N 11 HOH A 89 489 210 HOH HOH . N 11 HOH A 90 490 165 HOH HOH . N 11 HOH A 91 491 164 HOH HOH . N 11 HOH A 92 492 102 HOH HOH . N 11 HOH A 93 493 170 HOH HOH . N 11 HOH A 94 494 21 HOH HOH . N 11 HOH A 95 495 73 HOH HOH . N 11 HOH A 96 496 191 HOH HOH . N 11 HOH A 97 497 87 HOH HOH . N 11 HOH A 98 498 158 HOH HOH . N 11 HOH A 99 499 145 HOH HOH . N 11 HOH A 100 500 4 HOH HOH . N 11 HOH A 101 501 34 HOH HOH . N 11 HOH A 102 502 18 HOH HOH . N 11 HOH A 103 503 32 HOH HOH . N 11 HOH A 104 504 124 HOH HOH . N 11 HOH A 105 505 114 HOH HOH . N 11 HOH A 106 506 8 HOH HOH . N 11 HOH A 107 507 33 HOH HOH . N 11 HOH A 108 508 17 HOH HOH . N 11 HOH A 109 509 77 HOH HOH . N 11 HOH A 110 510 195 HOH HOH . N 11 HOH A 111 511 79 HOH HOH . N 11 HOH A 112 512 41 HOH HOH . N 11 HOH A 113 513 66 HOH HOH . N 11 HOH A 114 514 161 HOH HOH . N 11 HOH A 115 515 46 HOH HOH . N 11 HOH A 116 516 206 HOH HOH . N 11 HOH A 117 517 75 HOH HOH . N 11 HOH A 118 518 5 HOH HOH . N 11 HOH A 119 519 54 HOH HOH . N 11 HOH A 120 520 200 HOH HOH . N 11 HOH A 121 521 138 HOH HOH . N 11 HOH A 122 522 2 HOH HOH . N 11 HOH A 123 523 62 HOH HOH . N 11 HOH A 124 524 30 HOH HOH . N 11 HOH A 125 525 51 HOH HOH . N 11 HOH A 126 526 28 HOH HOH . N 11 HOH A 127 527 116 HOH HOH . N 11 HOH A 128 528 82 HOH HOH . N 11 HOH A 129 529 189 HOH HOH . N 11 HOH A 130 530 175 HOH HOH . N 11 HOH A 131 531 105 HOH HOH . N 11 HOH A 132 532 179 HOH HOH . N 11 HOH A 133 533 27 HOH HOH . N 11 HOH A 134 534 187 HOH HOH . N 11 HOH A 135 535 140 HOH HOH . N 11 HOH A 136 536 144 HOH HOH . N 11 HOH A 137 537 209 HOH HOH . N 11 HOH A 138 538 156 HOH HOH . N 11 HOH A 139 539 148 HOH HOH . N 11 HOH A 140 540 177 HOH HOH . N 11 HOH A 141 541 84 HOH HOH . N 11 HOH A 142 542 106 HOH HOH . N 11 HOH A 143 543 155 HOH HOH . N 11 HOH A 144 544 215 HOH HOH . N 11 HOH A 145 545 48 HOH HOH . N 11 HOH A 146 546 49 HOH HOH . N 11 HOH A 147 547 55 HOH HOH . N 11 HOH A 148 548 180 HOH HOH . N 11 HOH A 149 549 141 HOH HOH . N 11 HOH A 150 550 115 HOH HOH . N 11 HOH A 151 551 80 HOH HOH . N 11 HOH A 152 552 182 HOH HOH . N 11 HOH A 153 553 50 HOH HOH . N 11 HOH A 154 554 151 HOH HOH . N 11 HOH A 155 555 135 HOH HOH . N 11 HOH A 156 556 166 HOH HOH . N 11 HOH A 157 557 95 HOH HOH . N 11 HOH A 158 558 214 HOH HOH . N 11 HOH A 159 559 152 HOH HOH . N 11 HOH A 160 560 126 HOH HOH . N 11 HOH A 161 561 60 HOH HOH . N 11 HOH A 162 562 103 HOH HOH . N 11 HOH A 163 563 85 HOH HOH . N 11 HOH A 164 564 121 HOH HOH . N 11 HOH A 165 565 167 HOH HOH . N 11 HOH A 166 566 14 HOH HOH . N 11 HOH A 167 567 205 HOH HOH . N 11 HOH A 168 568 213 HOH HOH . N 11 HOH A 169 569 198 HOH HOH . N 11 HOH A 170 570 132 HOH HOH . N 11 HOH A 171 571 52 HOH HOH . N 11 HOH A 172 572 129 HOH HOH . N 11 HOH A 173 573 199 HOH HOH . N 11 HOH A 174 574 168 HOH HOH . N 11 HOH A 175 575 203 HOH HOH . N 11 HOH A 176 576 174 HOH HOH . N 11 HOH A 177 577 57 HOH HOH . N 11 HOH A 178 578 201 HOH HOH . N 11 HOH A 179 579 97 HOH HOH . N 11 HOH A 180 580 110 HOH HOH . N 11 HOH A 181 581 147 HOH HOH . N 11 HOH A 182 582 173 HOH HOH . N 11 HOH A 183 583 212 HOH HOH . N 11 HOH A 184 584 89 HOH HOH . N 11 HOH A 185 585 131 HOH HOH . N 11 HOH A 186 586 207 HOH HOH . N 11 HOH A 187 587 204 HOH HOH . N 11 HOH A 188 588 208 HOH HOH . N 11 HOH A 189 589 134 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 N1 JNR . . . C 3 23.15 6.337 40.472 1 42.72 ? N1 JNR 302 A 1 HETATM 2 C C2 JNR . . . C 3 24.366 9.246 42.275 1 34.08 ? C2 JNR 302 A 1 HETATM 3 C C3 JNR . . . C 3 23.713 10.602 42.244 1 30.33 ? C3 JNR 302 A 1 HETATM 4 C C4 JNR . . . C 3 24.725 11.657 42.644 1 25.18 ? C4 JNR 302 A 1 HETATM 5 C C5 JNR . . . C 3 24.312 13.083 42.273 1 23.05 ? C5 JNR 302 A 1 HETATM 6 C C6 JNR . . . C 3 21.904 13.18 41.346 1 17.94 ? C6 JNR 302 A 1 HETATM 7 C C7 JNR . . . C 3 21.243 13.693 40.091 1 16.51 ? C7 JNR 302 A 1 HETATM 8 C C1 JNR . . . C 3 23.99 7.12 41.124 1 42.67 ? C1 JNR 302 A 1 HETATM 9 N N2 JNR . . . C 3 25.187 6.681 41.472 1 44.34 ? N2 JNR 302 A 1 HETATM 10 N N3 JNR . . . C 3 23.638 8.364 41.393 1 39.51 ? N3 JNR 302 A 1 HETATM 11 N N4 JNR . . . C 3 23.245 13.132 41.265 1 20.21 ? N4 JNR 302 A 1 HETATM 12 O O1 JNR . . . C 3 21.215 12.787 42.286 1 16.92 ? O1 JNR 302 A 1 HETATM 13 C C8 JNR . . . C 3 21.876 14.672 39.318 1 15.95 ? C8 JNR 302 A 1 HETATM 14 C C9 JNR . . . C 3 21.265 15.192 38.184 1 15.28 ? C9 JNR 302 A 1 HETATM 15 C C10 JNR . . . C 3 20.033 14.708 37.791 1 15.34 ? C10 JNR 302 A 1 HETATM 16 C C11 JNR . . . C 3 19.409 13.712 38.531 1 15.28 ? C11 JNR 302 A 1 HETATM 17 C C12 JNR . . . C 3 20.009 13.204 39.673 1 15.65 ? C12 JNR 302 A 1 HETATM 18 C C13 JNR . . . C 3 24.19 14.021 43.488 1 20.12 ? C13 JNR 302 A 1 HETATM 19 O O2 JNR . . . C 3 24.369 13.537 44.607 1 19.43 ? O2 JNR 302 A 1 HETATM 20 O O3 JNR . . . C 3 24.159 15.22 43.236 1 18.35 ? O3 JNR 302 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #