HEADER IMMUNE SYSTEM 28-FEB-25 9NK9 TITLE NANO-BODY PEPTIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SER-PHE-GLU-ASP-PHE-TRP-LYS-GLY-GLU-ASP; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: BACTERIAL EXPRESSION VECTOR PET-11A; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1944663; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630 KEYWDS ANTIBODY LIGAND COMPLEX, STRUCTURAL PROTEIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHAO,R.W.CHELOHA,C.A.BEWLEY REVDAT 1 28-MAY-25 9NK9 0 JRNL AUTH S.SACHDEV,S.ROY,S.J.SAHA,G.ZHAO,R.KUMARIYA,B.A.CREEMER, JRNL AUTH 2 R.YIN,B.G.PIERCE,C.A.BEWLEY,R.W.CHELOHA JRNL TITL EVALUATION OF ALPHAFOLD MODELING FOR ELUCIDATION OF JRNL TITL 2 NANOBODY-PEPTIDE EPITOPE INTERACTIONS JRNL REF J.BIOL.CHEM. 2025 JRNL REFN ESSN 1083-351X JRNL DOI 10.1016/J.JBC.2025.110268 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 7157 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 712 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.8800 - 3.5900 1.00 1374 143 0.1514 0.2045 REMARK 3 2 3.5800 - 2.8500 1.00 1295 144 0.1760 0.1979 REMARK 3 3 2.8500 - 2.4900 1.00 1266 143 0.1969 0.2316 REMARK 3 4 2.4900 - 2.2600 0.99 1247 142 0.1944 0.2406 REMARK 3 5 2.2600 - 2.1000 0.99 1263 140 0.1783 0.2303 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 1008 REMARK 3 ANGLE : 1.204 1357 REMARK 3 CHIRALITY : 0.063 141 REMARK 3 PLANARITY : 0.009 177 REMARK 3 DIHEDRAL : 6.456 139 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -5.2126 23.5345 45.0037 REMARK 3 T TENSOR REMARK 3 T11: 0.1172 T22: 0.1557 REMARK 3 T33: 0.1360 T12: 0.0218 REMARK 3 T13: -0.0082 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 0.7607 L22: 1.0249 REMARK 3 L33: 0.5169 L12: 0.6988 REMARK 3 L13: -0.1382 L23: -0.0394 REMARK 3 S TENSOR REMARK 3 S11: 0.0224 S12: 0.0050 S13: -0.0152 REMARK 3 S21: 0.0234 S22: 0.0414 S23: -0.0431 REMARK 3 S31: 0.0135 S32: 0.0051 S33: 0.0033 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9NK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1000293548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7180 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 51.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 14.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, PH8.5 2 M (NH4)2SO4, REMARK 280 EVAPORATION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.39467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.78933 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.78933 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.39467 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 119 REMARK 465 GLY A 120 REMARK 465 LEU A 121 REMARK 465 PRO A 122 REMARK 465 GLU A 123 REMARK 465 THR A 124 REMARK 465 GLY A 125 REMARK 465 GLY A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 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 ALA A 91 157.12 179.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 9NK9 A 1 132 PDB 9NK9 9NK9 1 132 DBREF 9NK9 B 1 10 PDB 9NK9 9NK9 1 10 SEQRES 1 A 132 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 132 ALA GLY GLU SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 132 SER THR PHE ASP PHE LYS VAL MET GLY TRP TYR ARG GLN SEQRES 4 A 132 PRO PRO GLY LYS GLN ARG GLU GLY VAL ALA ALA ILE ARG SEQRES 5 A 132 LEU SER GLY ASN MET HIS TYR ALA GLU SER VAL LYS GLY SEQRES 6 A 132 ARG PHE ALA ILE SER LYS ALA ASN ALA LYS ASN THR VAL SEQRES 7 A 132 TYR LEU GLN MET ASN SER LEU ARG PRO GLU ASP THR ALA SEQRES 8 A 132 VAL TYR TYR CYS LYS VAL ASN ILE ARG GLY GLN ASP TYR SEQRES 9 A 132 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER VAL SER SEQRES 10 A 132 SER GLY GLY LEU PRO GLU THR GLY GLY HIS HIS HIS HIS SEQRES 11 A 132 HIS HIS SEQRES 1 B 10 SER PHE GLU ASP PHE TRP LYS GLY GLU ASP FORMUL 3 HOH *65(H2 O) HELIX 1 AA1 ARG A 86 THR A 90 5 5 HELIX 2 AA2 PHE B 2 GLY B 8 1 7 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 21 N SER A 7 SHEET 3 AA1 4 THR A 77 MET A 82 -1 O MET A 82 N LEU A 18 SHEET 4 AA1 4 PHE A 67 LYS A 71 -1 N ALA A 68 O GLN A 81 SHEET 1 AA2 6 GLY A 10 GLN A 13 0 SHEET 2 AA2 6 THR A 109 SER A 114 1 O THR A 112 N VAL A 12 SHEET 3 AA2 6 ALA A 91 ILE A 99 -1 N TYR A 93 O THR A 109 SHEET 4 AA2 6 VAL A 33 GLN A 39 -1 N GLY A 35 O LYS A 96 SHEET 5 AA2 6 GLU A 46 ARG A 52 -1 O GLU A 46 N ARG A 38 SHEET 6 AA2 6 MET A 57 TYR A 59 -1 O HIS A 58 N ALA A 50 SHEET 1 AA3 4 GLY A 10 GLN A 13 0 SHEET 2 AA3 4 THR A 109 SER A 114 1 O THR A 112 N VAL A 12 SHEET 3 AA3 4 ALA A 91 ILE A 99 -1 N TYR A 93 O THR A 109 SHEET 4 AA3 4 GLN A 102 TRP A 105 -1 O TYR A 104 N VAL A 97 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.03 CRYST1 46.876 46.876 91.184 90.00 90.00 120.00 P 31 2 1 6 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 0.021333 0.012317 0.000000 0.00000 SCALE2 0.000000 0.024633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010967 0.00000