HEADER DE NOVO PROTEIN 15-MAY-26 35TL TITLE PD-L1 COMPLEXED WITH GERMINAL-DESIGNED ANTI-PD-L1 SCFV H5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PD-L1,PDCD1 LIGAND 1,PROGRAMMED DEATH LIGAND 1,HPD-L1,B7 COMPND 5 HOMOLOG 1,B7-H1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GERMINAL-DESIGNED ANTI-PD-L1 SCFV H5, V(H) DOMAIN; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: GERMINAL-DESIGNED ANTI-PD-L1 SCFV H5, V(L) DOMAIN; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SCFV, DESIGNED, BINDER, DE NOVO PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.L.ZHANG,B.RAO,L.FENG REVDAT 1 22-JUL-26 35TL 0 JRNL AUTH L.S.MILLE-FRAGOSO,C.L.DRISCOLL,J.N.WANG,H.DAI,T.WIDATALLA, JRNL AUTH 2 J.L.ZHANG,X.ZHANG,B.RAO,L.FENG,B.L.HIE,X.J.GAO JRNL TITL EFFICIENT GENERATION OF EPITOPE-TARGETED ANTIBODIES WITH JRNL TITL 2 GERMINAL. JRNL REF NAT.BIOTECHNOL. 2026 JRNL REFN ISSN 1087-0156 JRNL PMID 42337361 JRNL DOI 10.1038/S41587-026-03187-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.S.MILLE-FRAGOSO,C.L.DRISCOLL,J.N.WANG,H.DAI,T.WIDATALLA, REMARK 1 AUTH 2 J.L.ZHANG,X.ZHANG,B.RAO,L.FENG,B.L.HIE,X.J.GAO REMARK 1 TITL EFFICIENT GENERATION OF EPITOPE-TARGETED DE NOVO ANTIBODIES REMARK 1 TITL 2 WITH GERMINAL REMARK 1 REF BIORXIV 2025 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 41040335 REMARK 1 DOI 10.1093/BIOINFORMATICS/BTAD424 REMARK 2 REMARK 2 RESOLUTION. 3.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, TOPAZ, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.930 REMARK 3 NUMBER OF PARTICLES : 94644 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 35TL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1000308040. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : PD-L1 COMPLEXED WITH GERMINAL REMARK 245 -DESIGNED ANTI-PD-L1 SCFV H5 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -16 REMARK 465 ARG A -15 REMARK 465 ILE A -14 REMARK 465 PHE A -13 REMARK 465 ALA A -12 REMARK 465 VAL A -11 REMARK 465 PHE A -10 REMARK 465 ILE A -9 REMARK 465 PHE A -8 REMARK 465 MET A -7 REMARK 465 THR A -6 REMARK 465 TYR A -5 REMARK 465 TRP A -4 REMARK 465 HIS A -3 REMARK 465 LEU A -2 REMARK 465 LEU A -1 REMARK 465 ASN A 0 REMARK 465 ALA A 1 REMARK 465 PRO A 116 REMARK 465 TYR A 117 REMARK 465 ASN A 118 REMARK 465 LYS A 119 REMARK 465 ILE A 120 REMARK 465 ASN A 121 REMARK 465 GLN A 122 REMARK 465 ARG A 123 REMARK 465 ILE A 124 REMARK 465 LEU A 125 REMARK 465 VAL A 126 REMARK 465 VAL A 127 REMARK 465 ASP A 128 REMARK 465 PRO A 129 REMARK 465 VAL A 130 REMARK 465 THR A 131 REMARK 465 SER A 132 REMARK 465 GLU A 133 REMARK 465 HIS A 134 REMARK 465 GLU A 135 REMARK 465 LEU A 136 REMARK 465 THR A 137 REMARK 465 CYS A 138 REMARK 465 GLN A 139 REMARK 465 ALA A 140 REMARK 465 GLU A 141 REMARK 465 GLY A 142 REMARK 465 TYR A 143 REMARK 465 PRO A 144 REMARK 465 LYS A 145 REMARK 465 ALA A 146 REMARK 465 GLU A 147 REMARK 465 VAL A 148 REMARK 465 ILE A 149 REMARK 465 TRP A 150 REMARK 465 THR A 151 REMARK 465 SER A 152 REMARK 465 SER A 153 REMARK 465 ASP A 154 REMARK 465 HIS A 155 REMARK 465 GLN A 156 REMARK 465 VAL A 157 REMARK 465 LEU A 158 REMARK 465 SER A 159 REMARK 465 GLY A 160 REMARK 465 LYS A 161 REMARK 465 THR A 162 REMARK 465 THR A 163 REMARK 465 THR A 164 REMARK 465 THR A 165 REMARK 465 ASN A 166 REMARK 465 SER A 167 REMARK 465 LYS A 168 REMARK 465 ARG A 169 REMARK 465 GLU A 170 REMARK 465 GLU A 171 REMARK 465 LYS A 172 REMARK 465 LEU A 173 REMARK 465 PHE A 174 REMARK 465 ASN A 175 REMARK 465 VAL A 176 REMARK 465 THR A 177 REMARK 465 SER A 178 REMARK 465 THR A 179 REMARK 465 LEU A 180 REMARK 465 ARG A 181 REMARK 465 ILE A 182 REMARK 465 ASN A 183 REMARK 465 THR A 184 REMARK 465 THR A 185 REMARK 465 THR A 186 REMARK 465 ASN A 187 REMARK 465 GLU A 188 REMARK 465 ILE A 189 REMARK 465 PHE A 190 REMARK 465 TYR A 191 REMARK 465 CYS A 192 REMARK 465 THR A 193 REMARK 465 PHE A 194 REMARK 465 ARG A 195 REMARK 465 ARG A 196 REMARK 465 LEU A 197 REMARK 465 ASP A 198 REMARK 465 PRO A 199 REMARK 465 GLU A 200 REMARK 465 GLU A 201 REMARK 465 ASN A 202 REMARK 465 HIS A 203 REMARK 465 THR A 204 REMARK 465 ALA A 205 REMARK 465 GLU A 206 REMARK 465 LEU A 207 REMARK 465 VAL A 208 REMARK 465 ILE A 209 REMARK 465 PRO A 210 REMARK 465 GLU A 211 REMARK 465 LEU A 212 REMARK 465 PRO A 213 REMARK 465 LEU A 214 REMARK 465 ALA A 215 REMARK 465 HIS A 216 REMARK 465 PRO A 217 REMARK 465 PRO A 218 REMARK 465 ASN A 219 REMARK 465 GLU A 220 REMARK 465 ARG A 221 REMARK 465 THR A 222 REMARK 465 HIS A 223 REMARK 465 LEU A 224 REMARK 465 VAL A 225 REMARK 465 ILE A 226 REMARK 465 LEU A 227 REMARK 465 GLY A 228 REMARK 465 ALA A 229 REMARK 465 ILE A 230 REMARK 465 LEU A 231 REMARK 465 LEU A 232 REMARK 465 CYS A 233 REMARK 465 LEU A 234 REMARK 465 GLY A 235 REMARK 465 VAL A 236 REMARK 465 ALA A 237 REMARK 465 LEU A 238 REMARK 465 THR A 239 REMARK 465 PHE A 240 REMARK 465 ILE A 241 REMARK 465 PHE A 242 REMARK 465 ARG A 243 REMARK 465 LEU A 244 REMARK 465 ARG A 245 REMARK 465 LYS A 246 REMARK 465 GLY A 247 REMARK 465 ARG A 248 REMARK 465 MET A 249 REMARK 465 MET A 250 REMARK 465 ASP A 251 REMARK 465 VAL A 252 REMARK 465 LYS A 253 REMARK 465 LYS A 254 REMARK 465 CYS A 255 REMARK 465 GLY A 256 REMARK 465 ILE A 257 REMARK 465 GLN A 258 REMARK 465 ASP A 259 REMARK 465 THR A 260 REMARK 465 ASN A 261 REMARK 465 SER A 262 REMARK 465 LYS A 263 REMARK 465 LYS A 264 REMARK 465 GLN A 265 REMARK 465 SER A 266 REMARK 465 ASP A 267 REMARK 465 THR A 268 REMARK 465 HIS A 269 REMARK 465 LEU A 270 REMARK 465 GLU A 271 REMARK 465 GLU A 272 REMARK 465 THR A 273 REMARK 465 GLU B 1 REMARK 465 VAL B 2 REMARK 465 VAL B 118 REMARK 465 SER B 119 REMARK 465 SER B 120 REMARK 465 ALA B 121 REMARK 465 SER B 122 REMARK 465 THR B 123 REMARK 465 LYS B 124 REMARK 465 GLY B 125 REMARK 465 PRO B 126 REMARK 465 SER B 127 REMARK 465 VAL B 128 REMARK 465 PHE B 129 REMARK 465 PRO B 130 REMARK 465 LEU B 131 REMARK 465 ALA B 132 REMARK 465 PRO B 133 REMARK 465 SER B 134 REMARK 465 SER B 135 REMARK 465 LYS B 136 REMARK 465 SER B 137 REMARK 465 THR B 138 REMARK 465 SER B 139 REMARK 465 GLY B 140 REMARK 465 GLY B 141 REMARK 465 THR B 142 REMARK 465 ALA B 143 REMARK 465 ALA B 144 REMARK 465 LEU B 145 REMARK 465 GLY B 146 REMARK 465 CYS B 147 REMARK 465 LEU B 148 REMARK 465 VAL B 149 REMARK 465 LYS B 150 REMARK 465 ASP B 151 REMARK 465 TYR B 152 REMARK 465 PHE B 153 REMARK 465 PRO B 154 REMARK 465 GLU B 155 REMARK 465 PRO B 156 REMARK 465 VAL B 157 REMARK 465 THR B 158 REMARK 465 VAL B 159 REMARK 465 SER B 160 REMARK 465 TRP B 161 REMARK 465 ASN B 162 REMARK 465 SER B 163 REMARK 465 GLY B 164 REMARK 465 ALA B 165 REMARK 465 LEU B 166 REMARK 465 THR B 167 REMARK 465 SER B 168 REMARK 465 GLY B 169 REMARK 465 VAL B 170 REMARK 465 HIS B 171 REMARK 465 THR B 172 REMARK 465 PHE B 173 REMARK 465 PRO B 174 REMARK 465 ALA B 175 REMARK 465 VAL B 176 REMARK 465 LEU B 177 REMARK 465 GLN B 178 REMARK 465 SER B 179 REMARK 465 SER B 180 REMARK 465 GLY B 181 REMARK 465 LEU B 182 REMARK 465 TYR B 183 REMARK 465 SER B 184 REMARK 465 LEU B 185 REMARK 465 SER B 186 REMARK 465 SER B 187 REMARK 465 VAL B 188 REMARK 465 VAL B 189 REMARK 465 THR B 190 REMARK 465 VAL B 191 REMARK 465 PRO B 192 REMARK 465 SER B 193 REMARK 465 SER B 194 REMARK 465 SER B 195 REMARK 465 LEU B 196 REMARK 465 GLY B 197 REMARK 465 THR B 198 REMARK 465 GLN B 199 REMARK 465 THR B 200 REMARK 465 TYR B 201 REMARK 465 ILE B 202 REMARK 465 CYS B 203 REMARK 465 ASN B 204 REMARK 465 VAL B 205 REMARK 465 ASN B 206 REMARK 465 HIS B 207 REMARK 465 LYS B 208 REMARK 465 PRO B 209 REMARK 465 SER B 210 REMARK 465 ASN B 211 REMARK 465 THR B 212 REMARK 465 LYS B 213 REMARK 465 VAL B 214 REMARK 465 ASP B 215 REMARK 465 LYS B 216 REMARK 465 LYS B 217 REMARK 465 VAL B 218 REMARK 465 GLU B 219 REMARK 465 PRO B 220 REMARK 465 LYS B 221 REMARK 465 SER B 222 REMARK 465 CYS B 223 REMARK 465 ASP C 1 REMARK 465 ILE C 2 REMARK 465 ARG C 108 REMARK 465 THR C 109 REMARK 465 VAL C 110 REMARK 465 ALA C 111 REMARK 465 ALA C 112 REMARK 465 PRO C 113 REMARK 465 SER C 114 REMARK 465 VAL C 115 REMARK 465 PHE C 116 REMARK 465 ILE C 117 REMARK 465 PHE C 118 REMARK 465 PRO C 119 REMARK 465 PRO C 120 REMARK 465 SER C 121 REMARK 465 ASP C 122 REMARK 465 GLU C 123 REMARK 465 GLN C 124 REMARK 465 LEU C 125 REMARK 465 LYS C 126 REMARK 465 SER C 127 REMARK 465 GLY C 128 REMARK 465 THR C 129 REMARK 465 ALA C 130 REMARK 465 SER C 131 REMARK 465 VAL C 132 REMARK 465 VAL C 133 REMARK 465 CYS C 134 REMARK 465 LEU C 135 REMARK 465 LEU C 136 REMARK 465 ASN C 137 REMARK 465 ASN C 138 REMARK 465 PHE C 139 REMARK 465 TYR C 140 REMARK 465 PRO C 141 REMARK 465 ARG C 142 REMARK 465 GLU C 143 REMARK 465 ALA C 144 REMARK 465 LYS C 145 REMARK 465 VAL C 146 REMARK 465 GLN C 147 REMARK 465 TRP C 148 REMARK 465 LYS C 149 REMARK 465 VAL C 150 REMARK 465 ASP C 151 REMARK 465 ASN C 152 REMARK 465 ALA C 153 REMARK 465 LEU C 154 REMARK 465 GLN C 155 REMARK 465 SER C 156 REMARK 465 GLY C 157 REMARK 465 ASN C 158 REMARK 465 SER C 159 REMARK 465 GLN C 160 REMARK 465 GLU C 161 REMARK 465 SER C 162 REMARK 465 VAL C 163 REMARK 465 THR C 164 REMARK 465 GLU C 165 REMARK 465 GLN C 166 REMARK 465 ASP C 167 REMARK 465 SER C 168 REMARK 465 LYS C 169 REMARK 465 ASP C 170 REMARK 465 SER C 171 REMARK 465 THR C 172 REMARK 465 TYR C 173 REMARK 465 SER C 174 REMARK 465 LEU C 175 REMARK 465 SER C 176 REMARK 465 SER C 177 REMARK 465 THR C 178 REMARK 465 LEU C 179 REMARK 465 THR C 180 REMARK 465 LEU C 181 REMARK 465 SER C 182 REMARK 465 LYS C 183 REMARK 465 ALA C 184 REMARK 465 ASP C 185 REMARK 465 TYR C 186 REMARK 465 GLU C 187 REMARK 465 LYS C 188 REMARK 465 HIS C 189 REMARK 465 LYS C 190 REMARK 465 VAL C 191 REMARK 465 TYR C 192 REMARK 465 ALA C 193 REMARK 465 CYS C 194 REMARK 465 GLU C 195 REMARK 465 VAL C 196 REMARK 465 THR C 197 REMARK 465 HIS C 198 REMARK 465 GLN C 199 REMARK 465 GLY C 200 REMARK 465 LEU C 201 REMARK 465 SER C 202 REMARK 465 SER C 203 REMARK 465 PRO C 204 REMARK 465 VAL C 205 REMARK 465 THR C 206 REMARK 465 LYS C 207 REMARK 465 SER C 208 REMARK 465 PHE C 209 REMARK 465 ASN C 210 REMARK 465 ARG C 211 REMARK 465 GLY C 212 REMARK 465 GLU C 213 REMARK 465 CYS C 214 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP B 28 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 3 68.90 36.40 REMARK 500 LYS A 29 -125.44 49.18 REMARK 500 ILE A 47 -64.44 -101.36 REMARK 500 TYR A 64 71.51 -114.32 REMARK 500 LEU A 70 151.97 81.67 REMARK 500 LEU A 82 74.93 -113.09 REMARK 500 LYS A 88 -158.89 -94.10 REMARK 500 ALA B 92 -168.76 -165.46 REMARK 500 TRP B 97 81.62 -157.72 REMARK 500 GLN C 27 -169.91 -129.66 REMARK 500 SER C 63 -151.49 -148.68 REMARK 500 SER C 67 74.16 -102.70 REMARK 500 PHE C 98 -137.16 -104.80 REMARK 500 GLN C 100 -133.68 -85.46 REMARK 500 GLU C 105 -154.97 -110.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-77181 RELATED DB: EMDB REMARK 900 PD-L1 COMPLEXED WITH GERMINAL-DESIGNED ANTI-PD-L1 SCFV H5 DBREF 35TL A -16 273 UNP Q9NZQ7 PD1L1_HUMAN 1 290 DBREF 35TL B 1 223 PDB 35TL 35TL 1 223 DBREF 35TL C 1 214 PDB 35TL 35TL 1 214 SEQRES 1 A 290 MET ARG ILE PHE ALA VAL PHE ILE PHE MET THR TYR TRP SEQRES 2 A 290 HIS LEU LEU ASN ALA PHE THR VAL THR VAL PRO LYS ASP SEQRES 3 A 290 LEU TYR VAL VAL GLU TYR GLY SER ASN MET THR ILE GLU SEQRES 4 A 290 CYS LYS PHE PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA SEQRES 5 A 290 LEU ILE VAL TYR TRP GLU MET GLU ASP LYS ASN ILE ILE SEQRES 6 A 290 GLN PHE VAL HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SEQRES 7 A 290 SER SER TYR ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN SEQRES 8 A 290 LEU SER LEU GLY ASN ALA ALA LEU GLN ILE THR ASP VAL SEQRES 9 A 290 LYS LEU GLN ASP ALA GLY VAL TYR ARG CYS MET ILE SER SEQRES 10 A 290 TYR GLY GLY ALA ASP TYR LYS ARG ILE THR VAL LYS VAL SEQRES 11 A 290 ASN ALA PRO TYR ASN LYS ILE ASN GLN ARG ILE LEU VAL SEQRES 12 A 290 VAL ASP PRO VAL THR SER GLU HIS GLU LEU THR CYS GLN SEQRES 13 A 290 ALA GLU GLY TYR PRO LYS ALA GLU VAL ILE TRP THR SER SEQRES 14 A 290 SER ASP HIS GLN VAL LEU SER GLY LYS THR THR THR THR SEQRES 15 A 290 ASN SER LYS ARG GLU GLU LYS LEU PHE ASN VAL THR SER SEQRES 16 A 290 THR LEU ARG ILE ASN THR THR THR ASN GLU ILE PHE TYR SEQRES 17 A 290 CYS THR PHE ARG ARG LEU ASP PRO GLU GLU ASN HIS THR SEQRES 18 A 290 ALA GLU LEU VAL ILE PRO GLU LEU PRO LEU ALA HIS PRO SEQRES 19 A 290 PRO ASN GLU ARG THR HIS LEU VAL ILE LEU GLY ALA ILE SEQRES 20 A 290 LEU LEU CYS LEU GLY VAL ALA LEU THR PHE ILE PHE ARG SEQRES 21 A 290 LEU ARG LYS GLY ARG MET MET ASP VAL LYS LYS CYS GLY SEQRES 22 A 290 ILE GLN ASP THR ASN SER LYS LYS GLN SER ASP THR HIS SEQRES 23 A 290 LEU GLU GLU THR SEQRES 1 B 223 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 223 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER SER SEQRES 3 B 223 ILE ASP LEU GLU MET TYR LYS ILE HIS TRP VAL ARG GLN SEQRES 4 B 223 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA ARG ILE ASN SEQRES 5 B 223 VAL GLY PHE ASP VAL THR ARG TYR ALA ASP SER VAL LYS SEQRES 6 B 223 GLY ARG PHE THR ILE SER ALA ASP THR SER LYS ASN THR SEQRES 7 B 223 ALA TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 B 223 ALA VAL TYR TYR CYS TRP PRO TYR SER ILE VAL MET LEU SEQRES 9 B 223 PRO PHE HIS GLY TYR TRP GLY GLN GLY THR LEU VAL THR SEQRES 10 B 223 VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO SEQRES 11 B 223 LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA SEQRES 12 B 223 ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO SEQRES 13 B 223 VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY SEQRES 14 B 223 VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU SEQRES 15 B 223 TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SER SEQRES 16 B 223 LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS SEQRES 17 B 223 PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SEQRES 18 B 223 SER CYS SEQRES 1 C 214 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 C 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 C 214 GLN ASP VAL GLY LYS ASP VAL ALA TRP TYR GLN GLN LYS SEQRES 4 C 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR TYR TYR LYS SEQRES 5 C 214 PHE LEU TYR SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 C 214 ARG SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 C 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS LEU ASN ALA SEQRES 8 C 214 ASN THR GLY GLY ILE THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 C 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 C 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 C 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 C 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 C 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 C 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 C 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 C 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 C 214 PHE ASN ARG GLY GLU CYS HELIX 1 AA1 HIS A 61 ARG A 65 5 5 HELIX 2 AA2 ASP B 28 MET B 31 5 4 HELIX 3 AA3 SER B 100 HIS B 107 5 8 HELIX 4 AA4 GLN C 79 PHE C 83 5 5 SHEET 1 AA1 6 TYR A 11 VAL A 12 0 SHEET 2 AA1 6 LYS A 107 LYS A 112 1 O LYS A 112 N TYR A 11 SHEET 3 AA1 6 VAL A 94 SER A 100 -1 N TYR A 95 O ILE A 109 SHEET 4 AA1 6 ILE A 37 MET A 42 -1 N TYR A 39 O MET A 98 SHEET 5 AA1 6 LYS A 45 VAL A 51 -1 O ILE A 47 N TRP A 40 SHEET 6 AA1 6 GLU A 54 ASP A 56 -1 O GLU A 54 N VAL A 51 SHEET 1 AA2 4 GLU B 6 SER B 7 0 SHEET 2 AA2 4 SER B 17 CYS B 22 -1 O SER B 21 N SER B 7 SHEET 3 AA2 4 THR B 78 ASN B 84 -1 O MET B 83 N LEU B 18 SHEET 4 AA2 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA3 6 GLY B 10 LEU B 11 0 SHEET 2 AA3 6 THR B 114 THR B 117 1 O THR B 117 N GLY B 10 SHEET 3 AA3 6 ALA B 92 TYR B 99 -1 N ALA B 92 O VAL B 116 SHEET 4 AA3 6 LYS B 33 GLN B 39 -1 N VAL B 37 O TYR B 95 SHEET 5 AA3 6 GLU B 46 ASN B 52 -1 O GLU B 46 N ARG B 38 SHEET 6 AA3 6 VAL B 57 TYR B 60 -1 O ARG B 59 N ARG B 50 SHEET 1 AA4 3 THR C 5 GLN C 6 0 SHEET 2 AA4 3 ARG C 18 ARG C 24 -1 O ARG C 24 N THR C 5 SHEET 3 AA4 3 ASP C 70 SER C 76 -1 O PHE C 71 N CYS C 23 SHEET 1 AA5 4 PRO C 44 ILE C 48 0 SHEET 2 AA5 4 VAL C 33 GLN C 38 -1 N GLN C 37 O LYS C 45 SHEET 3 AA5 4 THR C 85 ASN C 92 -1 O THR C 85 N GLN C 38 SHEET 4 AA5 4 GLY C 95 THR C 97 -1 O THR C 97 N ASN C 90 SHEET 1 AA6 4 PRO C 44 ILE C 48 0 SHEET 2 AA6 4 VAL C 33 GLN C 38 -1 N GLN C 37 O LYS C 45 SHEET 3 AA6 4 THR C 85 ASN C 92 -1 O THR C 85 N GLN C 38 SHEET 4 AA6 4 THR C 102 LYS C 103 -1 O THR C 102 N TYR C 86 SSBOND 1 CYS A 23 CYS A 97 1555 1555 2.03 SSBOND 2 CYS B 22 CYS B 96 1555 1555 2.30 SSBOND 3 CYS C 23 CYS C 88 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 CONECT 174 778 CONECT 778 174 CONECT 1052 1639 CONECT 1639 1052 CONECT 1962 2486 CONECT 2486 1962 MASTER 560 0 0 4 27 0 0 6 2620 3 6 58 END