0.028415 0.000000 0.000000 0.000000 0.028415 0.000000 0.000000 0.000000 0.004870 0.000000 0.000000 0.000000 Kumar, P.R. Bonanno, J. Ahmed, M. Banu, R. Bhosle, R. Calarese, D. Celikigil, A. Chamala, S. Chan, M.K. Chowdhury, S. Fiser, A. Garforth, S. Glenn, A.S. Hillerich, B. Khafizov, K. Love, J. Patel, H. Seidel, R. Stead, M. Toro, R. Nathenson, S.G. Almo, S.C. New York Structural Genomics Research Consortium (NYSGRC) Atoms-to-Animals: The Immune Function Network (IFN) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 35.193 35.193 205.331 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 C2 H6 O2 62.068 1,2-ETHANEDIOL ETHYLENE GLYCOL non-polymer 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 LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE 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 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O 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 N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H 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 N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N C N 89 N O N 90 N C N 91 N O N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N N N 99 S C N 100 N C N 101 N O N 102 N C N 103 N C N 104 N C N 105 N O N 106 N N N 107 N O N 108 N H N 109 N H N 110 N H N 111 N H 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 N N 119 S C N 120 N C N 121 N O N 122 N C N 123 N C N 124 N C N 125 N O N 126 N O N 127 N O N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N N N 138 N C N 139 N C N 140 N O N 141 N O N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N N N 148 S C N 149 N C N 150 N O N 151 N C Y 152 N C Y 153 N N Y 154 N C Y 155 N C Y 156 N N N 157 N O N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N O N 169 N H N 170 N H N 171 N N N 172 S C N 173 N C N 174 N O N 175 N C N 176 N C N 177 N C N 178 N C N 179 N O N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N N N 194 S C N 195 N C N 196 N O N 197 N C N 198 N C N 199 N C N 200 N C N 201 N N N 202 N O N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N N N 219 S C N 220 N C N 221 N O N 222 N C Y 223 N C Y 224 N C Y 225 N C Y 226 N C Y 227 N C Y 228 N C N 229 N O N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N N N 242 S C N 243 N C N 244 N O N 245 N C N 246 N C N 247 N C N 248 N O N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N N N 259 S C N 260 N C N 261 N O N 262 N C N 263 N O N 264 N O 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 N N 273 S C N 274 N C N 275 N O N 276 R C N 277 N O N 278 N C N 279 N O N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N N N 290 S C N 291 N C N 292 N O N 293 N C Y 294 N C Y 295 N C Y 296 N C Y 297 N N Y 298 N C Y 299 N C Y 300 N C Y 301 N C Y 302 N C N 303 N O N 304 N H N 305 N H N 306 N H 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 N N 317 S C N 318 N C N 319 N O N 320 N C Y 321 N C Y 322 N C Y 323 N C Y 324 N C Y 325 N C Y 326 N C N 327 N O N 328 N O 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 H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N N N 341 S C N 342 N C N 343 N O N 344 N C N 345 N C N 346 N C N 347 N O N 348 N H N 349 N H N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N H N 358 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing 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 doub 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 doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing 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 doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub 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 doub N 77 N sing N 78 N sing 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 sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N doub 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 sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N doub N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N doub 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 sing N 135 N doub 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 sing N 143 N sing N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N sing Y 149 N sing Y 150 N doub Y 151 N doub N 152 N sing Y 153 N sing N 154 N sing Y 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 sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N doub N 168 N sing N 169 N sing N 170 N sing N 171 N sing 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 sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N doub N 189 N sing N 190 N sing N 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 sing 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 doub N 213 N sing N 214 N sing N 215 N sing N 216 N sing Y 217 N doub Y 218 N sing Y 219 N sing N 220 N sing Y 221 N doub N 222 N sing Y 223 N doub N 224 N sing Y 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 doub 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 sing 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 doub 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 doub N 266 N sing N 267 N sing N 268 N sing N 269 N sing 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 doub N 282 N sing N 283 N sing N 284 N sing N 285 N sing Y 286 N doub Y 287 N sing Y 288 N sing N 289 N sing Y 290 N doub Y 291 N sing Y 292 N sing N 293 N sing Y 294 N sing Y 295 N doub N 296 N sing Y 297 N doub N 298 N sing Y 299 N sing N 300 N sing N 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 doub N 310 N sing N 311 N sing N 312 N sing N 313 N sing Y 314 N doub Y 315 N sing Y 316 N sing N 317 N sing Y 318 N doub N 319 N sing Y 320 N doub N 321 N sing Y 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 sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N doub 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 sing N 342 N sing N 343 N sing N 344 N sing to be published 0353 Crystal structure of the D1 domain of human Nectin-4 extracellular fragment [NYSGRC-005624] 10.2210/pdb4jjh/pdb pdb_00004jjh 100 1 MIRRORS CCD 2013-02-07 ADSC QUANTUM 315 GRAPHITE SINGLE WAVELENGTH M x-ray 1 1.0750 1.0 X29A NSLS 1.0750 SYNCHROTRON NSLS BEAMLINE X29A 14439.062 Poliovirus receptor-related protein 4 D1 domain (UNP residues 32-153) 2 man polymer 62.068 1,2-ETHANEDIOL 1 syn non-polymer 18.015 water 1 nat water Ig superfamily receptor LNIR, Nectin-4, Processed poliovirus receptor-related protein 4 no no QDYGGGELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRN PLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLAENLYF QDYGGGELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRN PLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLAENLYF A,B NYSGRC-005624 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 human sample LNIR, Nectin-4, PRR4, PVRL4 9606 Homo sapiens 7111 Trichoplusia ni Hi5 Plasmid pIEX 1 2.20 44.13 VAPOR DIFFUSION, SITTING DROP 7.0 Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Sodium Chloride, 0.1M Bis-Tris:HCl, pH 6.5); Cryoprotection (Reservoir + final concentration of 20%(v/v) Ethylene glycol), Vapor Diffusion, Sitting Drop, temperature 298K 298 New York Structural Genomics Research Consortium NYSGRC PSI:Biology Atoms-to-Animals: The Immune Function Network IFN PSI:Biology software chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_ref_seq_dif struct_site repository Initial release Structure summary Refinement description Data collection Database references Derived calculations Refinement description 1 0 2013-03-27 1 1 2013-11-27 1 2 2017-11-15 1 3 2023-09-20 _software.classification _software.contact_author _software.contact_author_email _software.date _software.language _software.location _software.name _software.type _software.version _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y RCSB Y RCSB 2013-03-07 REL REL EDO 1,2-ETHANEDIOL HOH water 4FRW PDB experimental model EDO 1 2 EDO EDO 201 A HOH 1 3 HOH HOH 201 B n 1 27 A n 2 28 A n 3 29 A n 4 30 A n 5 31 A n 6 32 A n 7 33 A n 8 34 A n 9 35 A THR 36 n 10 THR 36 A SER 37 n 11 SER 37 A ASP 38 n 12 ASP 38 A VAL 39 n 13 VAL 39 A VAL 40 n 14 VAL 40 A THR 41 n 15 THR 41 A VAL 42 n 16 VAL 42 A VAL 43 n 17 VAL 43 A LEU 44 n 18 LEU 44 A GLY 45 n 19 GLY 45 A GLN 46 n 20 GLN 46 A ASP 47 n 21 ASP 47 A ALA 48 n 22 ALA 48 A LYS 49 n 23 LYS 49 A LEU 50 n 24 LEU 50 A PRO 51 n 25 PRO 51 A CYS 52 n 26 CYS 52 A PHE 53 n 27 PHE 53 A TYR 54 n 28 TYR 54 A ARG 55 n 29 ARG 55 A GLY 56 n 30 GLY 56 A ASP 57 n 31 ASP 57 A n 32 58 A n 33 59 A GLU 60 n 34 GLU 60 A GLN 61 n 35 GLN 61 A VAL 62 n 36 VAL 62 A GLY 63 n 37 GLY 63 A GLN 64 n 38 GLN 64 A VAL 65 n 39 VAL 65 A ALA 66 n 40 ALA 66 A TRP 67 n 41 TRP 67 A ALA 68 n 42 ALA 68 A ARG 69 n 43 ARG 69 A VAL 70 n 44 VAL 70 A n 45 71 A n 46 72 A n 47 73 A n 48 74 A n 49 75 A ALA 76 n 50 ALA 76 A GLN 77 n 51 GLN 77 A GLU 78 n 52 GLU 78 A LEU 79 n 53 LEU 79 A ALA 80 n 54 ALA 80 A LEU 81 n 55 LEU 81 A LEU 82 n 56 LEU 82 A HIS 83 n 57 HIS 83 A SER 84 n 58 SER 84 A LYS 85 n 59 LYS 85 A TYR 86 n 60 TYR 86 A GLY 87 n 61 GLY 87 A LEU 88 n 62 LEU 88 A HIS 89 n 63 HIS 89 A VAL 90 n 64 VAL 90 A SER 91 n 65 SER 91 A PRO 92 n 66 PRO 92 A ALA 93 n 67 ALA 93 A TYR 94 n 68 TYR 94 A GLU 95 n 69 GLU 95 A GLY 96 n 70 GLY 96 A ARG 97 n 71 ARG 97 A VAL 98 n 72 VAL 98 A GLU 99 n 73 GLU 99 A GLN 100 n 74 GLN 100 A PRO 101 n 75 PRO 101 A PRO 102 n 76 PRO 102 A PRO 103 n 77 PRO 103 A PRO 104 n 78 PRO 104 A ARG 105 n 79 ARG 105 A ASN 106 n 80 ASN 106 A PRO 107 n 81 PRO 107 A LEU 108 n 82 LEU 108 A ASP 109 n 83 ASP 109 A GLY 110 n 84 GLY 110 A SER 111 n 85 SER 111 A VAL 112 n 86 VAL 112 A LEU 113 n 87 LEU 113 A LEU 114 n 88 LEU 114 A ARG 115 n 89 ARG 115 A ASN 116 n 90 ASN 116 A ALA 117 n 91 ALA 117 A VAL 118 n 92 VAL 118 A GLN 119 n 93 GLN 119 A ALA 120 n 94 ALA 120 A ASP 121 n 95 ASP 121 A GLU 122 n 96 GLU 122 A GLY 123 n 97 GLY 123 A GLU 124 n 98 GLU 124 A TYR 125 n 99 TYR 125 A GLU 126 n 100 GLU 126 A CYS 127 n 101 CYS 127 A ARG 128 n 102 ARG 128 A VAL 129 n 103 VAL 129 A SER 130 n 104 SER 130 A THR 131 n 105 THR 131 A PHE 132 n 106 PHE 132 A PRO 133 n 107 PRO 133 A ALA 134 n 108 ALA 134 A GLY 135 n 109 GLY 135 A SER 136 n 110 SER 136 A PHE 137 n 111 PHE 137 A GLN 138 n 112 GLN 138 A ALA 139 n 113 ALA 139 A ARG 140 n 114 ARG 140 A LEU 141 n 115 LEU 141 A ARG 142 n 116 ARG 142 A LEU 143 n 117 LEU 143 A ARG 144 n 118 ARG 144 A VAL 145 n 119 VAL 145 A LEU 146 n 120 LEU 146 A VAL 147 n 121 VAL 147 A PRO 148 n 122 PRO 148 A PRO 149 n 123 PRO 149 A LEU 150 n 124 LEU 150 A PRO 151 n 125 PRO 151 A SER 152 n 126 SER 152 A LEU 153 n 127 LEU 153 A n 128 154 A n 129 155 A n 130 156 A n 131 157 A n 132 158 A n 133 159 A n 1 27 B n 2 28 B n 3 29 B n 4 30 B n 5 31 B n 6 32 B n 7 33 B n 8 34 B n 9 35 B THR 36 n 10 THR 36 B SER 37 n 11 SER 37 B ASP 38 n 12 ASP 38 B VAL 39 n 13 VAL 39 B VAL 40 n 14 VAL 40 B THR 41 n 15 THR 41 B VAL 42 n 16 VAL 42 B VAL 43 n 17 VAL 43 B LEU 44 n 18 LEU 44 B GLY 45 n 19 GLY 45 B GLN 46 n 20 GLN 46 B ASP 47 n 21 ASP 47 B ALA 48 n 22 ALA 48 B LYS 49 n 23 LYS 49 B LEU 50 n 24 LEU 50 B PRO 51 n 25 PRO 51 B CYS 52 n 26 CYS 52 B PHE 53 n 27 PHE 53 B TYR 54 n 28 TYR 54 B ARG 55 n 29 ARG 55 B n 30 56 B ASP 57 n 31 ASP 57 B SER 58 n 32 SER 58 B GLY 59 n 33 GLY 59 B GLU 60 n 34 GLU 60 B GLN 61 n 35 GLN 61 B VAL 62 n 36 VAL 62 B GLY 63 n 37 GLY 63 B GLN 64 n 38 GLN 64 B VAL 65 n 39 VAL 65 B ALA 66 n 40 ALA 66 B TRP 67 n 41 TRP 67 B ALA 68 n 42 ALA 68 B ARG 69 n 43 ARG 69 B VAL 70 n 44 VAL 70 B n 45 71 B n 46 72 B n 47 73 B n 48 74 B n 49 75 B ALA 76 n 50 ALA 76 B GLN 77 n 51 GLN 77 B GLU 78 n 52 GLU 78 B LEU 79 n 53 LEU 79 B ALA 80 n 54 ALA 80 B LEU 81 n 55 LEU 81 B LEU 82 n 56 LEU 82 B HIS 83 n 57 HIS 83 B SER 84 n 58 SER 84 B LYS 85 n 59 LYS 85 B TYR 86 n 60 TYR 86 B GLY 87 n 61 GLY 87 B LEU 88 n 62 LEU 88 B HIS 89 n 63 HIS 89 B VAL 90 n 64 VAL 90 B SER 91 n 65 SER 91 B PRO 92 n 66 PRO 92 B ALA 93 n 67 ALA 93 B TYR 94 n 68 TYR 94 B GLU 95 n 69 GLU 95 B GLY 96 n 70 GLY 96 B ARG 97 n 71 ARG 97 B VAL 98 n 72 VAL 98 B GLU 99 n 73 GLU 99 B GLN 100 n 74 GLN 100 B PRO 101 n 75 PRO 101 B PRO 102 n 76 PRO 102 B PRO 103 n 77 PRO 103 B PRO 104 n 78 PRO 104 B ARG 105 n 79 ARG 105 B ASN 106 n 80 ASN 106 B PRO 107 n 81 PRO 107 B LEU 108 n 82 LEU 108 B ASP 109 n 83 ASP 109 B GLY 110 n 84 GLY 110 B SER 111 n 85 SER 111 B VAL 112 n 86 VAL 112 B LEU 113 n 87 LEU 113 B LEU 114 n 88 LEU 114 B ARG 115 n 89 ARG 115 B ASN 116 n 90 ASN 116 B ALA 117 n 91 ALA 117 B VAL 118 n 92 VAL 118 B GLN 119 n 93 GLN 119 B ALA 120 n 94 ALA 120 B ASP 121 n 95 ASP 121 B GLU 122 n 96 GLU 122 B GLY 123 n 97 GLY 123 B GLU 124 n 98 GLU 124 B TYR 125 n 99 TYR 125 B GLU 126 n 100 GLU 126 B CYS 127 n 101 CYS 127 B ARG 128 n 102 ARG 128 B VAL 129 n 103 VAL 129 B SER 130 n 104 SER 130 B THR 131 n 105 THR 131 B PHE 132 n 106 PHE 132 B PRO 133 n 107 PRO 133 B ALA 134 n 108 ALA 134 B GLY 135 n 109 GLY 135 B SER 136 n 110 SER 136 B PHE 137 n 111 PHE 137 B GLN 138 n 112 GLN 138 B ALA 139 n 113 ALA 139 B ARG 140 n 114 ARG 140 B LEU 141 n 115 LEU 141 B ARG 142 n 116 ARG 142 B LEU 143 n 117 LEU 143 B ARG 144 n 118 ARG 144 B VAL 145 n 119 VAL 145 B LEU 146 n 120 LEU 146 B VAL 147 n 121 VAL 147 B PRO 148 n 122 PRO 148 B PRO 149 n 123 PRO 149 B LEU 150 n 124 LEU 150 B PRO 151 n 125 PRO 151 B SER 152 n 126 SER 152 B LEU 153 n 127 LEU 153 B n 128 154 B n 129 155 B n 130 156 B n 131 157 B n 132 158 B n 133 159 B 1.6044 0.6878 -0.6024 0.3371 -0.4122 1.9620 0.1437 -0.0385 0.0170 -0.3051 -0.1328 -0.0295 0.1291 0.3278 -0.0947 0.3675 0.0593 0.0403 0.1034 -0.0093 0.1464 refined 10.8380 16.8543 8.8493 X-RAY DIFFRACTION 0.9495 0.3743 0.2047 2.4122 -0.4364 1.6564 0.1556 0.2011 0.3479 -0.4060 -0.0390 0.2041 -0.2627 -0.0859 -0.0956 0.2871 -0.0291 0.0608 0.1693 -0.0180 0.1382 refined 4.4242 30.1113 8.3973 X-RAY DIFFRACTION 2.0956 -0.3116 -0.5076 1.1282 -0.0857 2.2514 0.3350 -0.3084 0.2572 0.0141 -0.1546 -0.0131 -0.2177 0.3006 -0.0958 0.2018 -0.0395 0.0148 0.1120 -0.0127 0.1532 refined 9.1193 24.0951 15.6561 X-RAY DIFFRACTION 0.7936 -0.2934 0.0892 1.5272 -0.8917 1.5600 0.1292 0.0041 -0.0649 -0.5916 -0.0161 0.2213 0.0600 0.0442 0.3348 0.3315 0.0301 -0.0795 0.2189 0.0063 0.0338 refined 3.2954 15.8873 9.3497 X-RAY DIFFRACTION 0.9405 0.8592 1.3006 1.2080 0.8145 2.1200 -0.0312 -0.5123 0.0182 0.1830 0.1530 -0.1276 -0.3007 -0.0872 -0.0500 0.2751 0.0298 -0.0106 0.3067 -0.0786 0.1396 refined 16.7874 10.9231 34.0479 X-RAY DIFFRACTION 2.5470 -0.8312 -0.2359 0.8658 -0.3603 2.1579 0.0018 -0.2065 -0.5370 0.2632 0.1527 -0.1516 -0.1648 0.2274 -0.0915 0.1355 0.0218 0.0057 0.3006 -0.0070 0.1169 refined 29.7509 4.7662 33.9077 X-RAY DIFFRACTION 1.9353 0.3840 0.3894 1.3198 0.0855 1.5667 -0.4456 0.0550 0.0486 0.0358 0.4062 0.0562 -0.1809 0.4411 0.0672 0.1889 0.0298 -0.0055 0.2030 -0.0455 0.1351 refined 23.0507 9.6830 26.7705 X-RAY DIFFRACTION 0.9003 0.8132 0.6197 1.1678 0.5358 1.5080 -0.0081 -0.4351 -0.2405 0.0799 -0.1070 -0.0985 0.0228 -0.0946 0.1908 0.1961 -0.0193 0.0871 0.3584 0.0598 0.0975 refined 15.6869 3.7562 32.7558 X-RAY DIFFRACTION A 0 A 0 X-RAY DIFFRACTION 1 chain 'A' and (resid 36 through 60 ) A 0 A 0 X-RAY DIFFRACTION 2 chain 'A' and (resid 61 through 93) A 0 A 0 X-RAY DIFFRACTION 3 chain 'A' and (resid 94 through 120 ) A 0 A 0 X-RAY DIFFRACTION 4 chain 'A' and (resid 121 through 153 ) B 0 B 0 X-RAY DIFFRACTION 5 chain 'B' and (resid 36 through 60 ) B 0 B 0 X-RAY DIFFRACTION 6 chain 'B' and (resid 61 through 93 ) B 0 B 0 X-RAY DIFFRACTION 7 chain 'B' and (resid 94 through 120 ) B 0 B 0 X-RAY DIFFRACTION 8 chain 'B' and (resid 121 through 153 ) 1 0.500 author_defined_assembly 2 dimeric software_defined_assembly PISA 1 monomeric software_defined_assembly PISA 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 A N VAL 40 A N VAL 14 A O ARG 144 A O ARG 118 A O PHE 137 A O PHE 111 A N VAL 129 A N VAL 103 A O ARG 128 A O ARG 102 A N ALA 66 A N ALA 40 A N TRP 67 A N TRP 41 A O LEU 79 A O LEU 53 A N LEU 81 A N LEU 55 A O HIS 89 A O HIS 63 A N LEU 50 A N LEU 24 A O VAL 112 A O VAL 86 A O LEU 113 A O LEU 87 A N GLU 99 A N GLU 73 B N VAL 40 B N VAL 14 B O ARG 142 B O ARG 116 B O LEU 143 B O LEU 117 B N GLY 123 B N GLY 97 B O PHE 132 B O PHE 106 B N GLN 61 B N GLN 35 B N ARG 69 B N ARG 43 B O GLN 77 B O GLN 51 B N LEU 81 B N LEU 55 B O HIS 89 B O HIS 63 B N LEU 50 B N LEU 24 B O VAL 112 B O VAL 86 B O LEU 113 B O LEU 87 B N GLU 99 B N GLU 73 1 A GLN 27 A GLN 1 1 Y 1 A ASP 28 A ASP 2 1 Y 1 A TYR 29 A TYR 3 1 Y 1 A GLY 30 A GLY 4 1 Y 1 A GLY 31 A GLY 5 1 Y 1 A GLY 32 A GLY 6 1 Y 1 A GLU 33 A GLU 7 1 Y 1 A LEU 34 A LEU 8 1 Y 1 A GLU 35 A GLU 9 1 Y 1 A SER 58 A SER 32 1 Y 1 A GLY 59 A GLY 33 1 Y 1 A ASP 71 A ASP 45 1 Y 1 A ALA 72 A ALA 46 1 Y 1 A GLY 73 A GLY 47 1 Y 1 A GLU 74 A GLU 48 1 Y 1 A GLY 75 A GLY 49 1 Y 1 A ALA 154 A ALA 128 1 Y 1 A GLU 155 A GLU 129 1 Y 1 A ASN 156 A ASN 130 1 Y 1 A LEU 157 A LEU 131 1 Y 1 A TYR 158 A TYR 132 1 Y 1 A PHE 159 A PHE 133 1 Y 1 B GLN 27 B GLN 1 1 Y 1 B ASP 28 B ASP 2 1 Y 1 B TYR 29 B TYR 3 1 Y 1 B GLY 30 B GLY 4 1 Y 1 B GLY 31 B GLY 5 1 Y 1 B GLY 32 B GLY 6 1 Y 1 B GLU 33 B GLU 7 1 Y 1 B LEU 34 B LEU 8 1 Y 1 B GLU 35 B GLU 9 1 Y 1 B GLY 56 B GLY 30 1 Y 1 B ASP 71 B ASP 45 1 Y 1 B ALA 72 B ALA 46 1 Y 1 B GLY 73 B GLY 47 1 Y 1 B GLU 74 B GLU 48 1 Y 1 B GLY 75 B GLY 49 1 Y 1 B ALA 154 B ALA 128 1 Y 1 B GLU 155 B GLU 129 1 Y 1 B ASN 156 B ASN 130 1 Y 1 B LEU 157 B LEU 131 1 Y 1 B TYR 158 B TYR 132 1 Y 1 B PHE 159 B PHE 133 1 Y 1 A CYS 52 -151.49 79.43 1 A ASN 116 54.30 73.46 1 A ALA 134 -144.13 -2.69 1 B SER 58 69.33 -106.37 1 B ASN 116 59.22 74.65 1 B ALA 134 -145.55 -4.42 72.530 31.2146 9.260 0.2921 0.2222 0.2257 2.2500 35.1930 541 11454 4.7200 97.2400 1.000 1.000 0.7540 RANDOM 1 1.420 MOLECULAR REPLACEMENT 31.5600 0.9000 1.1100 4FRW TWIN_LSQ_F FLAT BULK SOLVENT MODEL 2.2500 35.1930 1 1727 4 0 1722 0.011 1765 1.488 2400 0.055 269 0.008 319 15.216 659 0.3010 0.2551 2.4788 125 2805 2930 4 96.0000 0.2878 0.2463 2.8356 147 2740 2887 4 95.0000 0.3208 0.2336 3.5657 140 2800 2940 4 94.0000 0.2766 0.1907 15.6931 128 2520 2648 4 86.0000 2.250 50.000 4JJH 11848 11529 0.069 1.038 1 8.3 9.000 97.300 0.262 2.250 2.290 585 0.842 1 9.500 100.000 0.273 2.290 2.330 600 0.854 1 10.000 100.000 0.262 2.330 2.380 594 0.833 1 9.900 100.000 0.241 2.380 2.420 554 0.905 1 10.000 100.000 0.203 2.420 2.480 625 0.912 1 10.000 100.000 0.182 2.480 2.530 600 0.997 1 9.900 100.000 0.166 2.530 2.600 561 1.033 1 9.900 100.000 0.154 2.600 2.670 581 1.019 1 9.900 100.000 0.130 2.670 2.750 609 1.133 1 9.700 100.000 0.109 2.750 2.830 556 1.172 1 9.400 100.000 0.098 2.830 2.940 642 1.200 1 9.400 100.000 0.082 2.940 3.050 547 1.205 1 9.100 99.800 0.079 3.050 3.190 617 1.238 1 9.000 100.000 0.067 3.190 3.360 574 1.231 1 8.400 99.800 0.061 3.360 3.570 579 1.158 1 7.900 96.300 0.058 3.570 3.850 560 1.114 1 7.800 94.800 0.054 3.850 4.230 514 1.071 1 6.800 88.000 0.053 4.230 4.850 471 1.011 1 6.400 78.100 0.051 4.850 6.100 566 0.950 1 7.700 94.300 0.053 6.100 50.000 594 0.984 1 8.300 96.300 data reduction Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ DENZO package data scaling Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ SCALEPACK package refinement Paul D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package 1.8.2_1309 data extraction PDB deposit@deposit.rcsb.org April 22, 2011 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.11 data collection CBASS data reduction HKL-2000 phasing PHENIX 1.8.2_1309 Crystal structure of the D1 domain from human Nectin-4 extracellular fragment [PSI-NYSGRC-005624] 1 N N 1 N N 2 N N 3 N N A PRO 92 A PRO 66 HELX_P A GLU 95 A GLU 69 5 1 4 A VAL 118 A VAL 92 HELX_P A GLU 122 A GLU 96 5 2 5 B PRO 92 B PRO 66 HELX_P B GLU 95 B GLU 69 5 3 4 B VAL 118 B VAL 92 HELX_P B GLU 122 B GLU 96 5 4 5 disulf 2.027 A CYS 52 A SG CYS 26 1_555 A CYS 127 A SG CYS 101 1_555 disulf 2.015 B CYS 52 B SG CYS 26 1_555 B CYS 127 B SG CYS 101 1_555 CELL ADHESION Nectin-4, Ig-like D1 domain, Ig superfamily, IMMUNE SYSTEM, Cell adhesion, Structural genomics, PSI-Biology, New York Structural Genomics Research Consortium, NYSGRC, Atoms-to-Animals: The Immune Function Network, IFN A PRO 103 A PRO 77 1 A PRO 104 A PRO 78 3.04 A PHE 132 A PHE 106 1 A PRO 133 A PRO 107 -6.27 B PRO 103 B PRO 77 1 B PRO 104 B PRO 78 -0.78 B PHE 132 B PHE 106 1 B PRO 133 B PRO 107 -8.61 PVRL4_HUMAN UNP 1 32 Q96NY8 GELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRNPLDGS VLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSL 32 153 4JJH 32 153 Q96NY8 A 1 6 127 32 153 4JJH 32 153 Q96NY8 B 1 6 127 1 expression tag GLN 27 4JJH A Q96NY8 UNP 1 1 expression tag ASP 28 4JJH A Q96NY8 UNP 2 1 expression tag TYR 29 4JJH A Q96NY8 UNP 3 1 expression tag GLY 30 4JJH A Q96NY8 UNP 4 1 expression tag GLY 31 4JJH A Q96NY8 UNP 5 1 expression tag ALA 154 4JJH A Q96NY8 UNP 128 1 expression tag GLU 155 4JJH A Q96NY8 UNP 129 1 expression tag ASN 156 4JJH A Q96NY8 UNP 130 1 expression tag LEU 157 4JJH A Q96NY8 UNP 131 1 expression tag TYR 158 4JJH A Q96NY8 UNP 132 1 expression tag PHE 159 4JJH A Q96NY8 UNP 133 2 expression tag GLN 27 4JJH B Q96NY8 UNP 1 2 expression tag ASP 28 4JJH B Q96NY8 UNP 2 2 expression tag TYR 29 4JJH B Q96NY8 UNP 3 2 expression tag GLY 30 4JJH B Q96NY8 UNP 4 2 expression tag GLY 31 4JJH B Q96NY8 UNP 5 2 expression tag ALA 154 4JJH B Q96NY8 UNP 128 2 expression tag GLU 155 4JJH B Q96NY8 UNP 129 2 expression tag ASN 156 4JJH B Q96NY8 UNP 130 2 expression tag LEU 157 4JJH B Q96NY8 UNP 131 2 expression tag TYR 158 4JJH B Q96NY8 UNP 132 2 expression tag PHE 159 4JJH B Q96NY8 UNP 133 6 3 6 3 parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A VAL 39 A VAL 13 A VAL 43 A VAL 17 A SER 136 A SER 110 A LEU 146 A LEU 120 A GLY 123 A GLY 97 A THR 131 A THR 105 A VAL 62 A VAL 36 A ARG 69 A ARG 43 A GLN 77 A GLN 51 A HIS 83 A HIS 57 A GLY 87 A GLY 61 A VAL 90 A VAL 64 A ALA 48 A ALA 22 A LEU 50 A LEU 24 A VAL 112 A VAL 86 A LEU 114 A LEU 88 A VAL 98 A VAL 72 A GLU 99 A GLU 73 B VAL 39 B VAL 13 B VAL 43 B VAL 17 B SER 136 B SER 110 B LEU 146 B LEU 120 B GLY 123 B GLY 97 B PHE 132 B PHE 106 B GLN 61 B GLN 35 B ARG 69 B ARG 43 B GLN 77 B GLN 51 B HIS 83 B HIS 57 B GLY 87 B GLY 61 B VAL 90 B VAL 64 B ALA 48 B ALA 22 B LEU 50 B LEU 24 B VAL 112 B VAL 86 B LEU 114 B LEU 88 B VAL 98 B VAL 72 B GLU 99 B GLU 73 BINDING SITE FOR RESIDUE EDO A 201 A EDO 201 Software 4 A VAL 90 A VAL 64 4 1_555 A GLU 95 A GLU 69 4 1_555 A GLY 96 A GLY 70 4 1_555 B VAL 147 B VAL 121 4 1_565 76 P 41