HEADER PROTEIN BINDING 25-JUN-25 9RPU TITLE PIN1 WW DOMAIN BINDING MODE WITH SPY-TIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PIN1,PPIASE PIN1, COMPND 5 ROTAMASE PIN1; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SPY-TIDE SPYPSPFPE; COMPND 10 CHAIN: B; COMPND 11 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: PIN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS WW DOMAIN, PIN1, PHOSPHOSERINE, EPISTATIC, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR M.JIANG,M.SUN,H.MOTT,P.CREIXELL REVDAT 1 09-SEP-26 9RPU 0 JRNL AUTH M.JIANG,M.SUN,C.NUO,M.ORD,T.L.AUGUSTIN,A.LI,N.H.SHAH, JRNL AUTH 2 J.RINEHART,H.MOTT,P.CREIXELL JRNL TITL IDENTIFYING MOLECULAR DETERMINANTS OF EPISTASIS AND JRNL TITL 2 ENGINEERING PROTEIN SUPERBINDERS WITH COMBINATORIAL DEEP JRNL TITL 3 MUTATIONAL SCANNING LIBRARIES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9RPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1292148856. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 200 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1000 UM PEPTIDYL-PROLYL CIS REMARK 210 -TRANS ISOMERASE NIMA- REMARK 210 INTERACTING 1 (PIN1) WW DOMAIN REMARK 210 BOUND TO EPISTATIC SPY-TIDE, REMARK 210 2000 UM SPY-TIDE SPYPSPFPE, 100 REMARK 210 MM SODIUM CHLORIDE, 50 MM SODIUM REMARK 210 PHOSPHATE, 10 % [U-99% 2H] D2O, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D DQF-COSY; 2D REMARK 210 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 3.2.10, TOPSPIN REMARK 210 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 1 SER A 19 111.44 78.17 REMARK 500 1 THR A 29 19.28 -144.51 REMARK 500 1 ASN A 30 75.91 60.71 REMARK 500 1 SER B 82 167.68 62.68 REMARK 500 1 TYR B 84 -81.46 -111.08 REMARK 500 1 PRO B 86 -162.45 -77.51 REMARK 500 1 PHE B 87 98.41 -51.92 REMARK 500 2 SER A 19 122.04 71.01 REMARK 500 2 ASN A 30 65.97 64.21 REMARK 500 2 SER B 82 165.88 63.10 REMARK 500 2 TYR B 84 -71.56 -109.18 REMARK 500 2 PHE B 87 99.03 -53.09 REMARK 500 3 SER A 19 129.59 69.80 REMARK 500 3 ASN A 30 75.27 62.80 REMARK 500 3 SER A 38 37.54 -87.13 REMARK 500 3 TYR B 84 -79.42 -103.71 REMARK 500 3 PHE B 87 98.63 -54.52 REMARK 500 4 SER A 19 104.56 68.48 REMARK 500 4 ASN A 30 73.60 60.11 REMARK 500 4 ASN A 40 -84.93 -152.82 REMARK 500 4 SER B 82 166.13 61.61 REMARK 500 4 TYR B 84 -81.49 -94.15 REMARK 500 4 PRO B 86 -167.30 -76.71 REMARK 500 4 PHE B 87 99.83 -51.90 REMARK 500 5 SER A 19 119.23 70.82 REMARK 500 5 ASN A 30 73.66 62.08 REMARK 500 5 ASN A 40 -62.04 -144.31 REMARK 500 5 TYR B 84 -78.45 -102.33 REMARK 500 5 PHE B 87 97.98 -53.04 REMARK 500 5 GLU B 89 -77.41 -80.57 REMARK 500 6 SER A 19 124.55 76.94 REMARK 500 6 ASN A 30 70.53 61.76 REMARK 500 6 ASN A 40 111.26 70.55 REMARK 500 6 TYR B 84 -68.59 -101.39 REMARK 500 6 PRO B 86 -162.47 -76.93 REMARK 500 6 PHE B 87 98.45 -51.82 REMARK 500 7 SER A 19 114.25 72.76 REMARK 500 7 THR A 29 15.53 -141.35 REMARK 500 7 ASN A 30 80.06 60.86 REMARK 500 7 TYR B 84 -77.42 -105.44 REMARK 500 7 PHE B 87 99.71 -53.87 REMARK 500 8 SER A 19 124.52 74.91 REMARK 500 8 THR A 29 13.22 -144.75 REMARK 500 8 ASN A 30 74.95 68.61 REMARK 500 8 SER B 82 158.56 64.74 REMARK 500 8 TYR B 84 -68.06 -104.34 REMARK 500 8 PRO B 86 -166.46 -74.98 REMARK 500 8 PHE B 87 99.55 -56.86 REMARK 500 9 SER A 19 113.71 75.20 REMARK 500 9 TYR B 84 -74.81 -94.53 REMARK 500 REMARK 500 THIS ENTRY HAS 148 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9RPN RELATED DB: PDB REMARK 900 RELATED ID: 35005 RELATED DB: BMRB REMARK 900 PIN1 WW DOMAIN BINDING MODE WITH SPY-TIDE DBREF 9RPU A 5 41 UNP Q13526 PIN1_HUMAN 5 41 DBREF 9RPU B 80 91 PDB 9RPU 9RPU 80 91 SEQRES 1 A 37 GLU LYS LEU PRO PRO GLY TRP GLU LYS ARG MET SER ARG SEQRES 2 A 37 SER SER GLY ARG VAL TYR TYR PHE ASN HIS ILE THR ASN SEQRES 3 A 37 ALA SER GLN TRP GLU ARG PRO SER GLY ASN SER SEQRES 1 B 12 ACE GLY SER PRO TYR SEP PRO PHE PRO GLU GLY NH2 HET ACE B 80 6 HET SEP B 85 14 HET NH2 B 91 3 HETNAM ACE ACETYL GROUP HETNAM SEP PHOSPHOSERINE HETNAM NH2 AMINO GROUP HETSYN SEP PHOSPHONOSERINE FORMUL 2 ACE C2 H4 O FORMUL 2 SEP C3 H8 N O6 P FORMUL 2 NH2 H2 N SHEET 1 AA1 3 TRP A 11 MET A 15 0 SHEET 2 AA1 3 VAL A 22 ASN A 26 -1 O PHE A 25 N GLU A 12 SHEET 3 AA1 3 ALA A 31 GLN A 33 -1 O GLN A 33 N TYR A 24 LINK C ACE B 80 N GLY B 81 1555 1555 1.33 LINK C TYR B 84 N SEP B 85 1555 1555 1.33 LINK C SEP B 85 N PRO B 86 1555 1555 1.34 LINK C GLY B 90 N NH2 B 91 1555 1555 1.33 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MODEL 21 ENDMDL MODEL 22 ENDMDL MODEL 23 ENDMDL MODEL 24 ENDMDL MODEL 25 ENDMDL CONECT 601 602 603 607 CONECT 602 601 CONECT 603 601 604 605 606 CONECT 604 603 CONECT 605 603 CONECT 606 603 CONECT 607 601 CONECT 641 660 CONECT 660 641 661 670 CONECT 661 660 662 664 671 CONECT 662 661 663 672 673 CONECT 663 662 666 CONECT 664 661 665 674 CONECT 665 664 CONECT 666 663 667 668 669 CONECT 667 666 CONECT 668 666 CONECT 669 666 CONECT 670 660 CONECT 671 661 CONECT 672 662 CONECT 673 662 CONECT 674 664 CONECT 739 744 CONECT 744 739 745 746 CONECT 745 744 CONECT 746 744 MASTER 159 0 3 0 3 0 0 6 389 2 27 4 END