PDB Short entry for 2LB3 HEADER SIGNALING PROTEIN/TRANSCRIPTION 22-MAR-11 2LB3 TITLE STRUCTURE OF THE WW DOMAIN OF PIN1 IN COMPLEX WITH A HUMAN TITLE 2 PHOSPHORYLATED SMAD3 DERIVED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 6-41; COMPND 5 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PIN1, PPIASE PIN1, COMPND 6 ROTAMASE PIN1; COMPND 7 EC: 5.2.1.8; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 2; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 176-183; COMPND 13 SYNONYM: MAD HOMOLOG 2, MOTHERS AGAINST DPP HOMOLOG 2, JV18-1, MAD- COMPND 14 RELATED PROTEIN 2, HMAD-2, SMAD FAMILY MEMBER 2, SMAD 2, SMAD2, COMPND 15 HSMAD2; COMPND 16 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 EXPRESSION_SYSTEM_VECTOR: PETM11; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS PIN1, SMAD, CDK, SIGNAL TRANSDUCTION, SIGNALING PROTEIN-TRANSCRIPTION KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.J.MACIAS,E.ARAGON,N.GOERNER,A.ZAROMYTIDOU,Q.XI,A.ESCOBEDO, AUTHOR 2 J.MASSAGUE REVDAT 1 06-JUL-11 2LB3 0 JRNL AUTH E.ARAGON,N.GOERNER,A.I.ZAROMYTIDOU,Q.XI,A.ESCOBEDO, JRNL AUTH 2 J.MASSAGUE,M.J.MACIAS JRNL TITL A SMAD ACTION TURNOVER SWITCH OPERATED BY WW DOMAIN READERS JRNL TITL 2 OF A PHOSPHOSERINE CODE. JRNL REF GENES DEV. V. 25 1275 2011 JRNL REFN ISSN 0890-9369 JRNL PMID 21685363 JRNL DOI 10.1101/GAD.2060811 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LB3 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-11. REMARK 100 THE RCSB ID CODE IS RCSB102179. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 285 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.420 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM NEDD4LWW3, 3 MM SMAD3, 20 REMARK 210 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 2 MM SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 15N] NEDD4LWW3, 3 MM SMAD3, REMARK 210 20 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 2 MM SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 13C; U-100% 15N] NEDD4LWW3, REMARK 210 3 MM SMAD3, 20 MM SODIUM REMARK 210 PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 2 MM SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 2D 1H- REMARK 210 15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.3, XEASY, TOPSPIN, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY 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 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 HH2 TRP A 38 HA PRO B 181 1.34 REMARK 500 HD2 ARG A 18 H MET A 19 1.38 REMARK 500 HG3 ARG A 18 HE2 TYR A 27 1.42 REMARK 500 HH TYR A 27 O PRO B 177 1.47 REMARK 500 HA3 GLY A 14 HD13 ILE A 32 1.51 REMARK 500 HG2 GLU A 16 HG2 PRO B 177 1.60 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 PRO A 13 -3.53 -58.90 REMARK 500 1 SER A 22 -89.79 -73.04 REMARK 500 1 ASN A 34 83.50 69.50 REMARK 500 1 TRP A 38 -7.95 -49.48 REMARK 500 1 TPO B 179 72.47 62.44 REMARK 500 2 LEU A 11 177.74 63.14 REMARK 500 2 PRO A 13 0.20 -68.49 REMARK 500 2 SER A 22 -84.54 -73.18 REMARK 500 2 ASN A 34 77.71 68.84 REMARK 500 2 ASN A 44 6.69 -154.02 REMARK 500 2 TPO B 179 72.54 63.90 REMARK 500 2 PRO B 181 142.72 -39.08 REMARK 500 3 PRO A 13 30.07 -56.23 REMARK 500 3 SER A 22 -78.88 -79.82 REMARK 500 3 ASN A 34 78.12 68.00 REMARK 500 3 PRO A 41 -70.18 -76.47 REMARK 500 3 SER A 42 -66.36 -130.07 REMARK 500 3 TPO B 179 72.90 70.25 REMARK 500 4 SER A 22 -78.43 -66.49 REMARK 500 4 ASN A 34 73.92 62.62 REMARK 500 4 TPO B 179 72.62 62.80 REMARK 500 4 PRO B 181 133.72 -35.22 REMARK 500 5 SER A 22 -89.67 -70.94 REMARK 500 5 ASN A 34 71.11 66.61 REMARK 500 5 TRP A 38 -7.96 -39.39 REMARK 500 5 TPO B 179 73.14 85.86 REMARK 500 6 LEU A 11 175.97 65.30 REMARK 500 6 SER A 22 -73.82 -67.35 REMARK 500 6 ASN A 34 75.34 71.31 REMARK 500 6 TPO B 179 72.79 65.02 REMARK 500 7 PRO A 13 0.77 -67.94 REMARK 500 7 SER A 22 -86.98 -88.07 REMARK 500 7 ASN A 34 64.24 63.84 REMARK 500 7 TRP A 38 -8.31 -46.62 REMARK 500 7 TPO B 179 73.01 75.08 REMARK 500 8 ASN A 34 77.21 64.21 REMARK 500 8 TPO B 179 72.25 73.17 REMARK 500 8 PRO B 182 -88.26 -75.32 REMARK 500 9 ASN A 34 77.31 66.15 REMARK 500 9 TRP A 38 -8.32 -59.75 REMARK 500 9 ASN A 44 -34.22 -165.69 REMARK 500 9 TPO B 179 72.11 60.94 REMARK 500 9 PRO B 182 108.93 -25.17 REMARK 500 10 SER A 22 -78.18 -69.66 REMARK 500 10 ASN A 34 73.52 69.33 REMARK 500 10 TRP A 38 -7.90 -40.32 REMARK 500 10 TPO B 179 72.83 62.29 REMARK 500 11 ASN A 34 82.08 62.45 REMARK 500 11 ASN A 44 17.72 -147.18 REMARK 500 11 TPO B 179 72.51 62.49 REMARK 500 REMARK 500 THIS ENTRY HAS 84 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 38 GLU A 39 1 -147.53 REMARK 500 PRO B 180 PRO B 181 1 -148.90 REMARK 500 TRP A 38 GLU A 39 2 -147.91 REMARK 500 PRO B 180 PRO B 181 2 -149.21 REMARK 500 TRP A 38 GLU A 39 3 -148.56 REMARK 500 PRO B 180 PRO B 181 4 -148.17 REMARK 500 PRO B 180 PRO B 181 5 -148.63 REMARK 500 TRP A 38 GLU A 39 7 -147.60 REMARK 500 PRO B 180 PRO B 181 9 -149.62 REMARK 500 TRP A 38 GLU A 39 11 -149.55 REMARK 500 TRP A 38 GLU A 39 12 -149.95 REMARK 500 PRO B 180 PRO B 181 12 -149.55 REMARK 500 PRO B 180 PRO B 181 13 -150.00 REMARK 500 PRO B 177 GLU B 178 15 149.76 REMARK 500 TRP A 38 GLU A 39 16 -149.96 REMARK 500 PRO B 180 PRO B 181 16 -148.65 REMARK 500 TRP A 38 GLU A 39 17 -146.57 REMARK 500 TRP A 38 GLU A 39 18 -149.71 REMARK 500 TRP A 38 GLU A 39 19 -146.92 REMARK 500 PRO B 177 GLU B 178 19 148.53 REMARK 500 PRO B 180 PRO B 181 19 -149.81 REMARK 500 PRO B 180 PRO B 181 20 -148.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 4 GLU A 39 11.31 REMARK 500 9 GLU A 39 10.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 4 TPO B 179 25.0 L L OUTSIDE RANGE REMARK 500 5 TPO B 179 21.3 L L OUTSIDE RANGE REMARK 500 7 TPO B 179 23.9 L L OUTSIDE RANGE REMARK 500 10 TPO B 179 24.8 L L OUTSIDE RANGE REMARK 500 12 TPO B 179 24.8 L L OUTSIDE RANGE REMARK 500 13 TPO B 179 24.4 L L OUTSIDE RANGE REMARK 500 15 TPO B 179 24.8 L L OUTSIDE RANGE REMARK 500 18 TPO B 179 24.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17545 RELATED DB: BMRB REMARK 900 RELATED ID: 2LAW RELATED DB: PDB REMARK 900 RELATED ID: 2LAX RELATED DB: PDB REMARK 900 RELATED ID: 2LAY RELATED DB: PDB REMARK 900 RELATED ID: 2LAZ RELATED DB: PDB REMARK 900 RELATED ID: 2LB0 RELATED DB: PDB REMARK 900 RELATED ID: 2LB1 RELATED DB: PDB REMARK 900 RELATED ID: 2LB2 RELATED DB: PDB DBREF 2LB3 A 10 45 UNP Q13526 PIN1_HUMAN 6 41 DBREF 2LB3 B 176 183 UNP Q15796 SMAD2_HUMAN 217 224 SEQRES 1 A 36 LYS LEU PRO PRO GLY TRP GLU LYS ARG MET SER ARG SER SEQRES 2 A 36 SER GLY ARG VAL TYR TYR PHE ASN HIS ILE THR ASN ALA SEQRES 3 A 36 SER GLN TRP GLU ARG PRO SER GLY ASN SER SEQRES 1 B 8 ILE PRO GLU TPO PRO PRO PRO GLY MODRES 2LB3 TPO B 179 THR PHOSPHOTHREONINE HET TPO B 179 17 HETNAM TPO PHOSPHOTHREONINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 2 TPO C4 H10 N O6 P SHEET 1 A 3 LYS A 17 SER A 20 0 SHEET 2 A 3 ARG A 25 ASN A 30 -1 O ARG A 25 N SER A 20 SHEET 3 A 3 ALA A 35 GLN A 37 -1 O ALA A 35 N ASN A 30 LINK C GLU B 178 N TPO B 179 1555 1555 1.34 LINK C TPO B 179 N PRO B 180 1555 1555 1.36 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