HEADER IMMUNE SYSTEM 14-FEB-24 8W0Q TITLE PEMBROLIZUMAB CDR-H3 LOOP MIMIC COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEMBROLIZUMAB CDR-H3 LOOP MIMIC; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS CDR-H3 LOOP, ANTIBODY, BULGED HAIRPIN, CONFORMATIONAL ENSEMBLE, BETA- KEYWDS 2 HAIRPIN, PEPTIDE MIMIC, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.FEIG,S.P.ROCHE REVDAT 3 31-JUL-24 8W0Q 1 JRNL REVDAT 2 10-JUL-24 8W0Q 1 JRNL REVDAT 1 03-JUL-24 8W0Q 0 JRNL AUTH G.ZHAO,A.D.RICHAUD,R.T.WILLIAMSON,M.FEIG,S.P.ROCHE JRNL TITL DE NOVO SYNTHESIS AND STRUCTURAL ELUCIDATION OF CDR-H3 LOOP JRNL TITL 2 MIMICS. JRNL REF ACS CHEM.BIOL. V. 19 1583 2024 JRNL REFN ESSN 1554-8937 JRNL PMID 38916527 JRNL DOI 10.1021/ACSCHEMBIO.4C00236 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CHARMM C42A2 REMARK 3 AUTHORS : B. R. BROOKS, C. L. BROOKS III, A. D. MACKERELL REMARK 3 JR., L. NILSSON, R. J. PETRELLA, B. ROUX, Y. WON, REMARK 3 G. ARCHONTIS, C. BARTELS, S. BORESCH, A. CAFLISCH, REMARK 3 L. CAVES, Q. CUI, A. R. DINNER, M. FEIG, S. REMARK 3 FISCHER, J. GAO, M. HODOSCEK, W. IM, K. KUCZERA, REMARK 3 T. LAZARIDIS, J. MA, V. OVCHINNIKOV, E. PACI, R. REMARK 3 W. PASTOR, C. B. POST, J. Z. PU, M. SCHAEFER, B. REMARK 3 TIDOR, R. M. VENABLE, H. L. WOODCOCK, X. WU, W. REMARK 3 YANG, D. M. YORK, M. KARPLUS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FROM MD SNAPSHOTS A FIXED NUMBER OF REMARK 3 CONFOMERS WERE SELECTED AND WEIGHTED TO MAXIMIZE REPRODUCTION OF REMARK 3 ENSEMBLE-AVERAGED NMR OBSERVABLES REMARK 4 REMARK 4 8W0Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281590. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 291 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NA REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 5.0 MM HAIRPIN, 90% H2O/10% DMSO REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-13C HSQC; 2D DQF-COSY; 2D REMARK 210 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN MERCURY500; BRUKER NEO REMARK 210 NMR; BRUKER AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ 4.2, TOPSPIN 3.2, CHARMM REMARK 210 C42A2, MESTRELAB (MNOVA / REMARK 210 MESTRENOVA / MESTREC) 15.0.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 5379 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 1 ASP A 15 -71.72 -109.59 REMARK 500 3 TYR A 8 32.07 82.47 REMARK 500 3 ASP A 15 -14.47 -159.46 REMARK 500 4 TYR A 8 29.74 82.02 REMARK 500 4 ARG A 9 -135.45 -104.33 REMARK 500 4 MET A 12 17.32 54.65 REMARK 500 5 ASP A 7 30.45 -89.41 REMARK 500 5 PHE A 14 118.40 -30.18 REMARK 500 5 TYR A 16 48.79 94.39 REMARK 500 7 TYR A 8 33.63 74.86 REMARK 500 8 ASP A 11 -14.77 66.77 REMARK 500 8 TYR A 16 38.64 77.31 REMARK 500 9 ASP A 7 14.17 -69.02 REMARK 500 9 TYR A 16 54.98 80.02 REMARK 500 10 ASP A 15 -63.41 -104.76 REMARK 500 11 ARG A 6 -21.61 -144.71 REMARK 500 11 ASP A 7 -170.40 56.53 REMARK 500 12 PHE A 14 146.38 -29.50 REMARK 500 12 ASP A 15 -155.98 -101.89 REMARK 500 12 TYR A 16 38.15 89.56 REMARK 500 13 ARG A 6 -97.31 -117.68 REMARK 500 13 ASP A 7 78.47 18.95 REMARK 500 13 TYR A 8 44.64 -86.02 REMARK 500 14 PHE A 14 161.15 81.46 REMARK 500 14 TYR A 16 40.11 71.99 REMARK 500 15 ASP A 7 6.28 -163.72 REMARK 500 15 TYR A 8 34.17 71.66 REMARK 500 15 ARG A 9 -50.29 -179.14 REMARK 500 15 ASP A 11 37.86 71.59 REMARK 500 15 TYR A 16 46.38 79.63 REMARK 500 16 ARG A 5 -151.18 -113.17 REMARK 500 16 ARG A 9 103.04 -168.49 REMARK 500 16 MET A 12 -142.12 -128.04 REMARK 500 16 ASP A 15 -63.26 -99.48 REMARK 500 17 TYR A 8 31.29 73.07 REMARK 500 18 TYR A 16 101.23 92.80 REMARK 500 19 TYR A 8 68.97 -103.56 REMARK 500 19 PHE A 14 -64.17 -159.02 REMARK 500 19 ASP A 15 -28.15 98.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31146 RELATED DB: BMRB REMARK 900 PEMBROLIZUMAB CDR-H3 LOOP MIMIC DBREF 8W0Q A 1 20 PDB 8W0Q 8W0Q 1 20 SEQRES 1 A 20 ARG TRP VAL ALA ARG ARG ASP TYR ARG GLY ASP MET GLY SEQRES 2 A 20 PHE ASP TYR TRP VAL TRP GLU SHEET 1 AA1 2 TRP A 2 ALA A 4 0 SHEET 2 AA1 2 TRP A 17 TRP A 19 -1 O VAL A 18 N VAL A 3 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1