0.024767 0.000000 0.003599 -0.000000 0.011016 0.000000 0.000000 -0.000000 0.024668 0.00000 0.00000 0.00000 Fotinou, C. Rana, R. Djordjevic, S. Yelland, T. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 98.27 90.00 40.376 90.781 40.965 C15 H21 N5 O4 335.358 N-(benzenecarbonyl)glycyl-L-arginine non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 N C N 3 N N N 4 S C N 5 N C N 6 N C N 7 N C N 8 N O N 9 N O N 10 N O N 11 N C N 12 N C N 13 N N N 14 N C N 15 N N N 16 N C N 17 N N N 18 N O Y 19 N C Y 20 N C Y 21 N C Y 22 N C Y 23 N C Y 24 N C N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N N N 47 S C N 48 N C N 49 N O N 50 N C N 51 N O N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N N N 60 S C N 61 N C N 62 N O N 63 N C N 64 N C N 65 N C N 66 N N N 67 N C N 68 N N N 69 N N N 70 N O N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N N N 87 S C N 88 N C N 89 N O N 90 N C N 91 N C N 92 N O N 93 N N N 94 N O N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N N N 104 S C N 105 N C N 106 N O N 107 N C N 108 N C N 109 N O N 110 N O N 111 N O N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N N N 120 R C N 121 N C N 122 N O N 123 N C N 124 N S N 125 N O N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N N N 134 S C N 135 N C N 136 N O N 137 N C N 138 N C N 139 N C N 140 N O N 141 N N N 142 N O N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N N N 154 S C N 155 N C N 156 N O N 157 N C N 158 N C N 159 N C N 160 N O N 161 N O N 162 N O N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N N N 173 N C N 174 N C N 175 N O N 176 N O N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N N N 183 S C N 184 N C N 185 N O N 186 N C Y 187 N C Y 188 N N Y 189 N C Y 190 N C Y 191 N N N 192 N O N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N O N 204 N H N 205 N H N 206 N N N 207 S C N 208 N C N 209 N O N 210 S C N 211 N C N 212 N C N 213 N C N 214 N O N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N N N 229 S C N 230 N C N 231 N O N 232 N C N 233 N C N 234 N C N 235 N C N 236 N O N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N N N 251 S C N 252 N C N 253 N O N 254 N C N 255 N C N 256 N C N 257 N C N 258 N N N 259 N O N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N N N 276 S C N 277 N C N 278 N O N 279 N C N 280 N C N 281 N S N 282 N C N 283 N O N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N N N 296 S C N 297 N C N 298 N O N 299 N C Y 300 N C Y 301 N C Y 302 N C Y 303 N C Y 304 N C Y 305 N C N 306 N O N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N N N 319 S C N 320 N C N 321 N O N 322 N C N 323 N C N 324 N C N 325 N O N 326 N H N 327 N H N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N N N 336 S C N 337 N C N 338 N O N 339 N C N 340 N O N 341 N O N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N N N 350 S C N 351 N C N 352 N O N 353 R C N 354 N O N 355 N C N 356 N O N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N N N 367 S C N 368 N C N 369 N O N 370 N C Y 371 N C Y 372 N C Y 373 N C Y 374 N N Y 375 N C Y 376 N C Y 377 N C Y 378 N C Y 379 N C N 380 N O N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 N H N 391 N H N 392 N H N 393 N N N 394 S C N 395 N C N 396 N O N 397 N C Y 398 N C Y 399 N C Y 400 N C Y 401 N C Y 402 N C Y 403 N C N 404 N O N 405 N O N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N N N 418 S C N 419 N C N 420 N O N 421 N C N 422 N C N 423 N C N 424 N O N 425 N H N 426 N H N 427 N H N 428 N H N 429 N H N 430 N H N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 1 N doub Y 2 N doub Y 3 N sing N 4 N sing N 5 N sing Y 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N doub Y 11 N doub Y 12 N doub N 13 N sing N 14 N doub Y 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N doub N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N doub N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N doub N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N doub N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N doub N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N doub N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N doub N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N doub N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing Y 185 N sing Y 186 N doub Y 187 N doub N 188 N sing Y 189 N sing N 190 N sing Y 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N doub N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N doub N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N doub N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N doub N 289 N sing N 290 N sing N 291 N sing N 292 N sing Y 293 N doub Y 294 N sing Y 295 N sing N 296 N sing Y 297 N doub N 298 N sing Y 299 N doub N 300 N sing Y 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N doub N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N doub N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N doub N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N doub N 358 N sing N 359 N sing N 360 N sing N 361 N sing Y 362 N doub Y 363 N sing Y 364 N sing N 365 N sing Y 366 N doub Y 367 N sing Y 368 N sing N 369 N sing Y 370 N sing Y 371 N doub N 372 N sing Y 373 N doub N 374 N sing Y 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N doub N 386 N sing N 387 N sing N 388 N sing N 389 N sing Y 390 N doub Y 391 N sing Y 392 N sing N 393 N sing Y 394 N doub N 395 N sing Y 396 N doub N 397 N sing Y 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N doub N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing UK FEBS J. 1742-4658 285 1290 1304 10.1111/febs.14405 29430837 Architecture and hydration of the arginine-binding site of neuropilin-1. 2018 10.2210/pdb5jhk/pdb pdb_00005jhk 100 1 PIXEL 2015-02-18 DECTRIS PILATUS 6M-F SINGLE WAVELENGTH M x-ray 1 0.979 1.0 I04 Diamond 0.979 SYNCHROTRON DIAMOND BEAMLINE I04 17917.291 Neuropilin-1 2 man polymer 335.358 N-(benzenecarbonyl)glycyl-L-arginine 1 syn non-polymer 18.015 water 206 nat water Vascular endothelial cell growth factor 165 receptor no no GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKET KKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKET KKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT A,B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Human sample 1 158 NRP1, NRP, VEGF165R 9606 Homo sapiens 469008 Escherichia coli BL21(DE3) Rosetta-gami2-pLysS pET15B-TEV Plasmid Biological sequence pET15B-TEV-NRP1B1 1 2.07 40.69 VAPOR DIFFUSION, HANGING DROP 7.9 30%PEG3350+0,2M NH4Cl 293 citation citation_author citation citation_author chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Database references Data collection Database references Data collection Database references Refinement description 1 0 2017-05-24 1 1 2018-02-28 1 2 2018-04-25 1 3 2024-01-10 _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation.journal_volume _citation.page_first _citation.page_last _citation.title _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession N PDBE Y PDBE 2016-04-21 REL REL 6K8 N-(benzenecarbonyl)glycyl-L-arginine HOH water 1KEX PDB experimental model AR6 1 2 6K8 6K8 501 A HOH 82 3 HOH HOH 601 A HOH 117 3 HOH HOH 602 A HOH 85 3 HOH HOH 603 A HOH 92 3 HOH HOH 604 A HOH 121 3 HOH HOH 605 A HOH 6 3 HOH HOH 606 A HOH 78 3 HOH HOH 607 A HOH 113 3 HOH HOH 608 A HOH 103 3 HOH HOH 609 A HOH 189 3 HOH HOH 610 A HOH 38 3 HOH HOH 611 A HOH 129 3 HOH HOH 612 A HOH 178 3 HOH HOH 613 A HOH 146 3 HOH HOH 614 A HOH 70 3 HOH HOH 615 A HOH 106 3 HOH HOH 616 A HOH 173 3 HOH HOH 617 A HOH 171 3 HOH HOH 618 A HOH 8 3 HOH HOH 619 A HOH 2 3 HOH HOH 620 A HOH 184 3 HOH HOH 621 A HOH 81 3 HOH HOH 622 A HOH 80 3 HOH HOH 623 A HOH 51 3 HOH HOH 624 A HOH 23 3 HOH HOH 625 A HOH 158 3 HOH HOH 626 A HOH 77 3 HOH HOH 627 A HOH 194 3 HOH HOH 628 A HOH 91 3 HOH HOH 629 A HOH 137 3 HOH HOH 630 A HOH 159 3 HOH HOH 631 A HOH 13 3 HOH HOH 632 A HOH 79 3 HOH HOH 633 A HOH 110 3 HOH HOH 634 A HOH 125 3 HOH HOH 635 A HOH 132 3 HOH HOH 636 A HOH 87 3 HOH HOH 637 A HOH 154 3 HOH HOH 638 A HOH 166 3 HOH HOH 639 A HOH 65 3 HOH HOH 640 A HOH 163 3 HOH HOH 641 A HOH 102 3 HOH HOH 642 A HOH 83 3 HOH HOH 643 A HOH 104 3 HOH HOH 644 A HOH 29 3 HOH HOH 645 A HOH 98 3 HOH HOH 646 A HOH 181 3 HOH HOH 647 A HOH 111 3 HOH HOH 648 A HOH 93 3 HOH HOH 649 A HOH 130 3 HOH HOH 650 A HOH 107 3 HOH HOH 651 A HOH 127 3 HOH HOH 652 A HOH 170 3 HOH HOH 653 A HOH 26 3 HOH HOH 654 A HOH 46 3 HOH HOH 655 A HOH 52 3 HOH HOH 656 A HOH 72 3 HOH HOH 657 A HOH 64 3 HOH HOH 658 A HOH 60 3 HOH HOH 659 A HOH 97 3 HOH HOH 660 A HOH 94 3 HOH HOH 661 A HOH 57 3 HOH HOH 662 A HOH 12 3 HOH HOH 663 A HOH 116 3 HOH HOH 664 A HOH 101 3 HOH HOH 665 A HOH 96 3 HOH HOH 666 A HOH 119 3 HOH HOH 667 A HOH 63 3 HOH HOH 668 A HOH 73 3 HOH HOH 669 A HOH 47 3 HOH HOH 670 A HOH 168 3 HOH HOH 671 A HOH 128 3 HOH HOH 672 A HOH 54 3 HOH HOH 673 A HOH 149 3 HOH HOH 674 A HOH 114 3 HOH HOH 675 A HOH 161 3 HOH HOH 676 A HOH 35 3 HOH HOH 677 A HOH 150 3 HOH HOH 678 A HOH 58 3 HOH HOH 679 A HOH 156 3 HOH HOH 680 A HOH 55 3 HOH HOH 681 A HOH 175 3 HOH HOH 682 A HOH 27 3 HOH HOH 683 A HOH 109 3 HOH HOH 684 A HOH 188 3 HOH HOH 685 A HOH 142 3 HOH HOH 686 A HOH 185 3 HOH HOH 687 A HOH 180 3 HOH HOH 688 A HOH 21 3 HOH HOH 689 A HOH 122 3 HOH HOH 690 A HOH 124 3 HOH HOH 691 A HOH 190 3 HOH HOH 692 A HOH 141 3 HOH HOH 693 A HOH 196 3 HOH HOH 501 B HOH 49 3 HOH HOH 502 B HOH 138 3 HOH HOH 503 B HOH 179 3 HOH HOH 504 B HOH 22 3 HOH HOH 505 B HOH 147 3 HOH HOH 506 B HOH 135 3 HOH HOH 507 B HOH 120 3 HOH HOH 508 B HOH 174 3 HOH HOH 509 B HOH 1 3 HOH HOH 510 B HOH 59 3 HOH HOH 511 B HOH 75 3 HOH HOH 512 B HOH 43 3 HOH HOH 513 B HOH 15 3 HOH HOH 514 B HOH 153 3 HOH HOH 515 B HOH 62 3 HOH HOH 516 B HOH 11 3 HOH HOH 517 B HOH 99 3 HOH HOH 518 B HOH 9 3 HOH HOH 519 B HOH 17 3 HOH HOH 520 B HOH 67 3 HOH HOH 521 B HOH 61 3 HOH HOH 522 B HOH 84 3 HOH HOH 523 B HOH 136 3 HOH HOH 524 B HOH 4 3 HOH HOH 525 B HOH 31 3 HOH HOH 526 B HOH 66 3 HOH HOH 527 B HOH 7 3 HOH HOH 528 B HOH 5 3 HOH HOH 529 B HOH 30 3 HOH HOH 530 B HOH 16 3 HOH HOH 531 B HOH 40 3 HOH HOH 532 B HOH 76 3 HOH HOH 533 B HOH 88 3 HOH HOH 534 B HOH 157 3 HOH HOH 535 B HOH 105 3 HOH HOH 536 B HOH 152 3 HOH HOH 537 B HOH 162 3 HOH HOH 538 B HOH 140 3 HOH HOH 539 B HOH 34 3 HOH HOH 540 B HOH 151 3 HOH HOH 541 B HOH 155 3 HOH HOH 542 B HOH 74 3 HOH HOH 543 B HOH 33 3 HOH HOH 544 B HOH 118 3 HOH HOH 545 B HOH 89 3 HOH HOH 546 B HOH 164 3 HOH HOH 547 B HOH 18 3 HOH HOH 548 B HOH 45 3 HOH HOH 549 B HOH 24 3 HOH HOH 550 B HOH 95 3 HOH HOH 551 B HOH 86 3 HOH HOH 552 B HOH 123 3 HOH HOH 553 B HOH 198 3 HOH HOH 554 B HOH 71 3 HOH HOH 555 B HOH 41 3 HOH HOH 556 B HOH 206 3 HOH HOH 557 B HOH 36 3 HOH HOH 558 B HOH 44 3 HOH HOH 559 B HOH 42 3 HOH HOH 560 B HOH 167 3 HOH HOH 561 B HOH 48 3 HOH HOH 562 B HOH 169 3 HOH HOH 563 B HOH 28 3 HOH HOH 564 B HOH 112 3 HOH HOH 565 B HOH 172 3 HOH HOH 566 B HOH 134 3 HOH HOH 567 B HOH 68 3 HOH HOH 568 B HOH 126 3 HOH HOH 569 B HOH 14 3 HOH HOH 570 B HOH 177 3 HOH HOH 571 B HOH 19 3 HOH HOH 572 B HOH 176 3 HOH HOH 573 B HOH 100 3 HOH HOH 574 B HOH 160 3 HOH HOH 575 B HOH 25 3 HOH HOH 576 B HOH 133 3 HOH HOH 577 B HOH 148 3 HOH HOH 578 B HOH 186 3 HOH HOH 579 B HOH 108 3 HOH HOH 580 B HOH 131 3 HOH HOH 581 B HOH 32 3 HOH HOH 582 B HOH 192 3 HOH HOH 583 B HOH 37 3 HOH HOH 584 B HOH 50 3 HOH HOH 585 B HOH 3 3 HOH HOH 586 B HOH 204 3 HOH HOH 587 B HOH 139 3 HOH HOH 588 B HOH 205 3 HOH HOH 589 B HOH 183 3 HOH HOH 590 B HOH 187 3 HOH HOH 591 B HOH 195 3 HOH HOH 592 B HOH 197 3 HOH HOH 593 B HOH 53 3 HOH HOH 594 B HOH 145 3 HOH HOH 595 B HOH 69 3 HOH HOH 596 B HOH 144 3 HOH HOH 597 B HOH 56 3 HOH HOH 598 B HOH 203 3 HOH HOH 599 B HOH 182 3 HOH HOH 600 B HOH 200 3 HOH HOH 601 B HOH 202 3 HOH HOH 602 B HOH 90 3 HOH HOH 603 B HOH 115 3 HOH HOH 604 B HOH 39 3 HOH HOH 605 B HOH 201 3 HOH HOH 606 B HOH 10 3 HOH HOH 607 B HOH 191 3 HOH HOH 608 B HOH 20 3 HOH HOH 609 B HOH 165 3 HOH HOH 610 B HOH 143 3 HOH HOH 611 B HOH 193 3 HOH HOH 612 B HOH 199 3 HOH HOH 613 B n 1 270 A n 2 271 A n 3 272 A n 4 273 A LYS 274 n 5 LYS 274 A CYS 275 n 6 CYS 275 A MET 276 n 7 MET 276 A GLU 277 n 8 GLU 277 A ALA 278 n 9 ALA 278 A LEU 279 n 10 LEU 279 A GLY 280 n 11 GLY 280 A MET 281 n 12 MET 281 A GLU 282 n 13 GLU 282 A SER 283 n 14 SER 283 A GLY 284 n 15 GLY 284 A GLU 285 n 16 GLU 285 A ILE 286 n 17 ILE 286 A HIS 287 n 18 HIS 287 A SER 288 n 19 SER 288 A ASP 289 n 20 ASP 289 A GLN 290 n 21 GLN 290 A ILE 291 n 22 ILE 291 A THR 292 n 23 THR 292 A ALA 293 n 24 ALA 293 A SER 294 n 25 SER 294 A SER 295 n 26 SER 295 A GLN 296 n 27 GLN 296 A TYR 297 n 28 TYR 297 A SER 298 n 29 SER 298 A THR 299 n 30 THR 299 A ASN 300 n 31 ASN 300 A TRP 301 n 32 TRP 301 A SER 302 n 33 SER 302 A ALA 303 n 34 ALA 303 A GLU 304 n 35 GLU 304 A ARG 305 n 36 ARG 305 A SER 306 n 37 SER 306 A ARG 307 n 38 ARG 307 A LEU 308 n 39 LEU 308 A ASN 309 n 40 ASN 309 A TYR 310 n 41 TYR 310 A PRO 311 n 42 PRO 311 A GLU 312 n 43 GLU 312 A ASN 313 n 44 ASN 313 A GLY 314 n 45 GLY 314 A TRP 315 n 46 TRP 315 A THR 316 n 47 THR 316 A PRO 317 n 48 PRO 317 A GLY 318 n 49 GLY 318 A GLU 319 n 50 GLU 319 A ASP 320 n 51 ASP 320 A SER 321 n 52 SER 321 A TYR 322 n 53 TYR 322 A ARG 323 n 54 ARG 323 A GLU 324 n 55 GLU 324 A TRP 325 n 56 TRP 325 A ILE 326 n 57 ILE 326 A GLN 327 n 58 GLN 327 A VAL 328 n 59 VAL 328 A ASP 329 n 60 ASP 329 A LEU 330 n 61 LEU 330 A GLY 331 n 62 GLY 331 A LEU 332 n 63 LEU 332 A LEU 333 n 64 LEU 333 A ARG 334 n 65 ARG 334 A PHE 335 n 66 PHE 335 A VAL 336 n 67 VAL 336 A THR 337 n 68 THR 337 A ALA 338 n 69 ALA 338 A VAL 339 n 70 VAL 339 A GLY 340 n 71 GLY 340 A THR 341 n 72 THR 341 A GLN 342 n 73 GLN 342 A GLY 343 n 74 GLY 343 A ALA 344 n 75 ALA 344 A ILE 345 n 76 ILE 345 A SER 346 n 77 SER 346 A LYS 347 n 78 LYS 347 A GLU 348 n 79 GLU 348 A THR 349 n 80 THR 349 A LYS 350 n 81 LYS 350 A LYS 351 n 82 LYS 351 A LYS 352 n 83 LYS 352 A TYR 353 n 84 TYR 353 A TYR 354 n 85 TYR 354 A VAL 355 n 86 VAL 355 A LYS 356 n 87 LYS 356 A THR 357 n 88 THR 357 A TYR 358 n 89 TYR 358 A LYS 359 n 90 LYS 359 A ILE 360 n 91 ILE 360 A ASP 361 n 92 ASP 361 A VAL 362 n 93 VAL 362 A SER 363 n 94 SER 363 A SER 364 n 95 SER 364 A ASN 365 n 96 ASN 365 A GLY 366 n 97 GLY 366 A GLU 367 n 98 GLU 367 A ASP 368 n 99 ASP 368 A TRP 369 n 100 TRP 369 A ILE 370 n 101 ILE 370 A THR 371 n 102 THR 371 A ILE 372 n 103 ILE 372 A LYS 373 n 104 LYS 373 A GLU 374 n 105 GLU 374 A GLY 375 n 106 GLY 375 A ASN 376 n 107 ASN 376 A LYS 377 n 108 LYS 377 A PRO 378 n 109 PRO 378 A VAL 379 n 110 VAL 379 A LEU 380 n 111 LEU 380 A PHE 381 n 112 PHE 381 A GLN 382 n 113 GLN 382 A GLY 383 n 114 GLY 383 A ASN 384 n 115 ASN 384 A THR 385 n 116 THR 385 A ASN 386 n 117 ASN 386 A PRO 387 n 118 PRO 387 A THR 388 n 119 THR 388 A ASP 389 n 120 ASP 389 A VAL 390 n 121 VAL 390 A VAL 391 n 122 VAL 391 A VAL 392 n 123 VAL 392 A ALA 393 n 124 ALA 393 A VAL 394 n 125 VAL 394 A PHE 395 n 126 PHE 395 A PRO 396 n 127 PRO 396 A LYS 397 n 128 LYS 397 A PRO 398 n 129 PRO 398 A LEU 399 n 130 LEU 399 A ILE 400 n 131 ILE 400 A THR 401 n 132 THR 401 A ARG 402 n 133 ARG 402 A PHE 403 n 134 PHE 403 A VAL 404 n 135 VAL 404 A ARG 405 n 136 ARG 405 A ILE 406 n 137 ILE 406 A LYS 407 n 138 LYS 407 A PRO 408 n 139 PRO 408 A ALA 409 n 140 ALA 409 A THR 410 n 141 THR 410 A TRP 411 n 142 TRP 411 A GLU 412 n 143 GLU 412 A THR 413 n 144 THR 413 A GLY 414 n 145 GLY 414 A ILE 415 n 146 ILE 415 A SER 416 n 147 SER 416 A MET 417 n 148 MET 417 A ARG 418 n 149 ARG 418 A PHE 419 n 150 PHE 419 A GLU 420 n 151 GLU 420 A VAL 421 n 152 VAL 421 A TYR 422 n 153 TYR 422 A GLY 423 n 154 GLY 423 A CYS 424 n 155 CYS 424 A LYS 425 n 156 LYS 425 A ILE 426 n 157 ILE 426 A THR 427 n 158 THR 427 A GLY 270 n 1 GLY 270 B HIS 271 n 2 HIS 271 B MET 272 n 3 MET 272 B PHE 273 n 4 PHE 273 B LYS 274 n 5 LYS 274 B CYS 275 n 6 CYS 275 B MET 276 n 7 MET 276 B GLU 277 n 8 GLU 277 B ALA 278 n 9 ALA 278 B LEU 279 n 10 LEU 279 B GLY 280 n 11 GLY 280 B MET 281 n 12 MET 281 B GLU 282 n 13 GLU 282 B SER 283 n 14 SER 283 B GLY 284 n 15 GLY 284 B GLU 285 n 16 GLU 285 B ILE 286 n 17 ILE 286 B HIS 287 n 18 HIS 287 B SER 288 n 19 SER 288 B ASP 289 n 20 ASP 289 B GLN 290 n 21 GLN 290 B ILE 291 n 22 ILE 291 B THR 292 n 23 THR 292 B ALA 293 n 24 ALA 293 B SER 294 n 25 SER 294 B SER 295 n 26 SER 295 B GLN 296 n 27 GLN 296 B TYR 297 n 28 TYR 297 B SER 298 n 29 SER 298 B THR 299 n 30 THR 299 B ASN 300 n 31 ASN 300 B TRP 301 n 32 TRP 301 B SER 302 n 33 SER 302 B ALA 303 n 34 ALA 303 B GLU 304 n 35 GLU 304 B ARG 305 n 36 ARG 305 B SER 306 n 37 SER 306 B ARG 307 n 38 ARG 307 B LEU 308 n 39 LEU 308 B ASN 309 n 40 ASN 309 B TYR 310 n 41 TYR 310 B PRO 311 n 42 PRO 311 B GLU 312 n 43 GLU 312 B ASN 313 n 44 ASN 313 B GLY 314 n 45 GLY 314 B TRP 315 n 46 TRP 315 B THR 316 n 47 THR 316 B PRO 317 n 48 PRO 317 B GLY 318 n 49 GLY 318 B GLU 319 n 50 GLU 319 B ASP 320 n 51 ASP 320 B SER 321 n 52 SER 321 B TYR 322 n 53 TYR 322 B ARG 323 n 54 ARG 323 B GLU 324 n 55 GLU 324 B TRP 325 n 56 TRP 325 B ILE 326 n 57 ILE 326 B GLN 327 n 58 GLN 327 B VAL 328 n 59 VAL 328 B ASP 329 n 60 ASP 329 B LEU 330 n 61 LEU 330 B GLY 331 n 62 GLY 331 B LEU 332 n 63 LEU 332 B LEU 333 n 64 LEU 333 B ARG 334 n 65 ARG 334 B PHE 335 n 66 PHE 335 B VAL 336 n 67 VAL 336 B THR 337 n 68 THR 337 B ALA 338 n 69 ALA 338 B VAL 339 n 70 VAL 339 B GLY 340 n 71 GLY 340 B THR 341 n 72 THR 341 B GLN 342 n 73 GLN 342 B GLY 343 n 74 GLY 343 B ALA 344 n 75 ALA 344 B ILE 345 n 76 ILE 345 B SER 346 n 77 SER 346 B LYS 347 n 78 LYS 347 B GLU 348 n 79 GLU 348 B THR 349 n 80 THR 349 B LYS 350 n 81 LYS 350 B LYS 351 n 82 LYS 351 B LYS 352 n 83 LYS 352 B TYR 353 n 84 TYR 353 B TYR 354 n 85 TYR 354 B VAL 355 n 86 VAL 355 B LYS 356 n 87 LYS 356 B THR 357 n 88 THR 357 B TYR 358 n 89 TYR 358 B LYS 359 n 90 LYS 359 B ILE 360 n 91 ILE 360 B ASP 361 n 92 ASP 361 B VAL 362 n 93 VAL 362 B SER 363 n 94 SER 363 B SER 364 n 95 SER 364 B ASN 365 n 96 ASN 365 B GLY 366 n 97 GLY 366 B GLU 367 n 98 GLU 367 B ASP 368 n 99 ASP 368 B TRP 369 n 100 TRP 369 B ILE 370 n 101 ILE 370 B THR 371 n 102 THR 371 B ILE 372 n 103 ILE 372 B LYS 373 n 104 LYS 373 B GLU 374 n 105 GLU 374 B GLY 375 n 106 GLY 375 B ASN 376 n 107 ASN 376 B LYS 377 n 108 LYS 377 B PRO 378 n 109 PRO 378 B VAL 379 n 110 VAL 379 B LEU 380 n 111 LEU 380 B PHE 381 n 112 PHE 381 B GLN 382 n 113 GLN 382 B GLY 383 n 114 GLY 383 B ASN 384 n 115 ASN 384 B THR 385 n 116 THR 385 B ASN 386 n 117 ASN 386 B PRO 387 n 118 PRO 387 B THR 388 n 119 THR 388 B ASP 389 n 120 ASP 389 B VAL 390 n 121 VAL 390 B VAL 391 n 122 VAL 391 B VAL 392 n 123 VAL 392 B ALA 393 n 124 ALA 393 B VAL 394 n 125 VAL 394 B PHE 395 n 126 PHE 395 B PRO 396 n 127 PRO 396 B LYS 397 n 128 LYS 397 B PRO 398 n 129 PRO 398 B LEU 399 n 130 LEU 399 B ILE 400 n 131 ILE 400 B THR 401 n 132 THR 401 B ARG 402 n 133 ARG 402 B PHE 403 n 134 PHE 403 B VAL 404 n 135 VAL 404 B ARG 405 n 136 ARG 405 B ILE 406 n 137 ILE 406 B LYS 407 n 138 LYS 407 B PRO 408 n 139 PRO 408 B ALA 409 n 140 ALA 409 B THR 410 n 141 THR 410 B TRP 411 n 142 TRP 411 B GLU 412 n 143 GLU 412 B THR 413 n 144 THR 413 B GLY 414 n 145 GLY 414 B ILE 415 n 146 ILE 415 B SER 416 n 147 SER 416 B MET 417 n 148 MET 417 B ARG 418 n 149 ARG 418 B PHE 419 n 150 PHE 419 B GLU 420 n 151 GLU 420 B VAL 421 n 152 VAL 421 B TYR 422 n 153 TYR 422 B GLY 423 n 154 GLY 423 B CYS 424 n 155 CYS 424 B LYS 425 n 156 LYS 425 B ILE 426 n 157 ILE 426 B THR 427 n 158 THR 427 B 0.6099 -0.8612 0.1639 1.2641 -0.3222 0.3457 0.1009 0.0173 -0.0211 -0.1735 -0.0497 0.0216 0.0659 -0.0290 -0.0512 0.0614 -0.0103 0.0052 0.0563 0.0033 0.0547 refined 34.8066 -21.6850 42.8396 X-RAY DIFFRACTION 0.7924 0.0997 -0.2357 1.0062 0.4852 0.5408 -0.0866 0.0018 0.0437 -0.0817 0.0287 0.1467 -0.0054 0.0092 0.0579 0.0162 0.0003 -0.0252 0.0512 -0.0093 0.0883 refined 54.6002 0.9342 56.9944 X-RAY DIFFRACTION A 274 A 427 X-RAY DIFFRACTION 1 B 270 B 427 X-RAY DIFFRACTION 2 author_defined_assembly 1 monomeric author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A GLY 270 A GLY 1 1 Y 1 A HIS 271 A HIS 2 1 Y 1 A MET 272 A MET 3 1 Y 1 A PHE 273 A PHE 4 1 Y 1 B B OE2 O GLU HOH 277 501 2.12 1 5.48 0.90 118.30 123.78 B B B CB CG OD1 ASP ASP ASP 289 289 289 N 1 A CYS 275 -151.29 68.89 1 A MET 276 -144.32 42.43 1 A ASN 313 64.56 -136.86 1 A THR 413 78.77 -55.89 1 B CYS 275 -150.68 71.99 1 B MET 276 -140.03 37.30 1 B ASN 313 62.81 -140.49 1 B GLU 367 -126.23 -55.05 1 B ASP 368 -61.21 94.92 1 B THR 413 79.43 -44.58 24.723 -0.08 0.00 -0.78 -0.16 0.00 0.45 0.964 0.944 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.21509 0.16728 0.16957 1.80 45.39 1303 25765 4.8 99.87 5.915 0.090 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.131 0.128 0.80 0.80 1.20 1kex MAXIMUM LIKELIHOOD MASK 1.80 45.39 206 2719 24 0 2489 0.016 0.020 2580 0.001 0.020 2414 1.731 1.941 3499 0.884 2.988 5573 7.274 5.000 312 36.260 24.107 112 13.262 15.000 444 20.801 15.000 14 0.118 0.200 378 0.009 0.021 2909 0.001 0.020 594 1.328 1.626 1249 1.329 1.625 1247 2.091 2.427 1557 2.090 2.427 1558 1.819 1.907 1331 1.818 1.909 1332 2.963 2.760 1942 5.236 14.243 2959 5.083 13.930 2901 0.324 0.269 1.847 118 1898 20 99.80 1.63 40.54 5JHK 36381 0.999 0.064 1 18.9 6.7 99.8 1.393 1.63 1.67 1.2 1 6.8 99.7 refinement REFMAC 5.8.0135 data reduction xia2 data scaling Aimless phasing PHASER N X-ray structure of neuropilin-1 b1 domain complexed with Arg-6 ligand. 1 N N 1 N N 2 N N 3 N N 3 N N A HIS 287 A HIS 18 HELX_P A ASP 289 A ASP 20 5 AA1 3 A SER 298 A SER 29 HELX_P A ARG 307 A ARG 38 5 AA2 10 B HIS 287 B HIS 18 HELX_P B ASP 289 B ASP 20 5 AA3 3 B SER 298 B SER 29 HELX_P B ARG 307 B ARG 38 5 AA4 10 disulf 2.034 A CYS 275 A SG CYS 6 1_555 A CYS 424 A SG CYS 155 1_555 disulf 2.080 B CYS 275 B SG CYS 6 1_555 B CYS 424 B SG CYS 155 1_555 SIGNALING PROTEIN SIGNALING PROTEIN, Neuropilin-1, Angiogenesis NRP1_HUMAN UNP 1 273 O14786 FKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKK YYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT 273 427 5JHK 273 427 O14786 A 1 4 158 273 427 5JHK 273 427 O14786 B 1 4 158 1 expression tag GLY 270 5JHK A O14786 UNP 1 1 expression tag HIS 271 5JHK A O14786 UNP 2 1 expression tag MET 272 5JHK A O14786 UNP 3 2 expression tag GLY 270 5JHK B O14786 UNP 1 2 expression tag HIS 271 5JHK B O14786 UNP 2 2 expression tag MET 272 5JHK B O14786 UNP 3 4 3 2 2 4 3 2 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ILE 291 A ILE 22 A ALA 293 A ALA 24 A ILE 326 A ILE 57 A ASP 329 A ASP 60 A PHE 403 A PHE 134 A PRO 408 A PRO 139 A TYR 358 A TYR 89 A SER 363 A SER 94 A LEU 399 A LEU 130 A THR 401 A THR 132 A ARG 334 A ARG 65 A GLN 342 A GLN 73 A ARG 418 A ARG 149 A CYS 424 A CYS 155 A ALA 338 A ALA 69 A THR 341 A THR 72 A VAL 391 A VAL 122 A VAL 394 A VAL 125 A TYR 354 A TYR 85 A THR 357 A THR 88 A THR 410 A THR 141 A GLU 412 A GLU 143 B ILE 291 B ILE 22 B ALA 293 B ALA 24 B ILE 326 B ILE 57 B ASP 329 B ASP 60 B PHE 403 B PHE 134 B PRO 408 B PRO 139 B TYR 358 B TYR 89 B SER 363 B SER 94 B LEU 399 B LEU 130 B THR 401 B THR 132 B ARG 334 B ARG 65 B GLN 342 B GLN 73 B ARG 418 B ARG 149 B CYS 424 B CYS 155 B ALA 338 B ALA 69 B THR 341 B THR 72 B VAL 391 B VAL 122 B VAL 394 B VAL 125 B TYR 354 B TYR 85 B THR 357 B THR 88 B THR 410 B THR 141 B GLU 412 B GLU 143 binding site for residue 6K8 A 501 A 6K8 501 Software 14 A TYR 297 A TYR 28 14 1_555 A TRP 301 A TRP 32 14 1_555 A THR 316 A THR 47 14 1_555 A ASP 320 A ASP 51 14 1_555 A SER 346 A SER 77 14 1_555 A THR 349 A THR 80 14 1_555 A TYR 353 A TYR 84 14 1_555 A GLY 414 A GLY 145 14 1_555 A ILE 415 A ILE 146 14 1_555 A HOH 606 D HOH 14 1_555 A HOH 632 D HOH 14 1_555 A HOH 677 D HOH 14 1_555 B MET 276 B MET 7 14 1_454 B TYR 422 B TYR 153 14 1_454 4 P 1 21 1