PDB Short entry for 6GBE HEADER PROTEIN BINDING 13-APR-18 6GBE TITLE MURINE PROTEIN TYROSINE PHOSPHATASE PTPN13 PDZ3 DOMAIN-PRK2 PEPTIDE TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 13; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PTP36,PROTEIN TYROSINE PHOSPHATASE DPZPTP,PROTEIN TYROSINE COMPND 5 PHOSPHATASE PTP-BL,PROTEIN-TYROSINE PHOSPHATASE RIP; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SERINE/THREONINE-PROTEIN KINASE N2; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: PKN GAMMA,PROTEIN KINASE C-LIKE 2,PROTEIN-KINASE C-RELATED COMPND 12 KINASE 2; COMPND 13 EC: 2.7.11.13; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PTPN13, PTP14; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS PTPN13, PDZ3, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.KOCK,R.STOLL REVDAT 3 29-JAN-20 6GBE 1 REMARK REVDAT 2 08-MAY-19 6GBE 1 REMARK REVDAT 1 05-DEC-18 6GBE 0 JRNL AUTH G.KOCK,M.DICKS,K.T.YIP,B.KOHL,S.PUTZ,R.HEUMANN,K.S.ERDMANN, JRNL AUTH 2 R.STOLL JRNL TITL MOLECULAR BASIS OF CLASS III LIGAND RECOGNITION BY PDZ3 IN JRNL TITL 2 MURINE PROTEIN TYROSINE PHOSPHATASE PTPN13. JRNL REF J. MOL. BIOL. V. 430 4275 2018 JRNL REFN ESSN 1089-8638 JRNL PMID 30189200 JRNL DOI 10.1016/J.JMB.2018.08.023 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6GBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009673. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : PBS REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-99% 13C; U-99% 15N] REMARK 210 PDZ3/PRK2, 90% H2O/10% D2O; 0.5 REMARK 210 MM [U-99% 15N] PDZ3/PRK2, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HCCH-TOCSY; 2D 1H-1H REMARK 210 NOESY; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 TOTAL BURIED SURFACE AREA: 820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 HG1 THR A 11 H ASP A 13 1.29 REMARK 500 HG1 THR A 11 H GLU A 12 1.33 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 2 104.09 -52.66 REMARK 500 1 THR A 11 -162.53 -119.33 REMARK 500 1 SER A 25 161.89 58.16 REMARK 500 1 LEU A 27 104.03 57.85 REMARK 500 1 ASN A 36 4.41 -173.26 REMARK 500 1 PRO A 39 20.08 -72.32 REMARK 500 1 ILE A 42 173.16 -50.88 REMARK 500 1 ASN A 43 72.56 45.27 REMARK 500 1 SER A 45 -174.34 -53.96 REMARK 500 1 LEU A 52 131.68 -170.91 REMARK 500 1 SER A 61 -29.82 -33.37 REMARK 500 1 VAL A 66 95.65 -67.51 REMARK 500 1 ASP A 68 155.72 -36.47 REMARK 500 1 ASN A 74 18.22 56.02 REMARK 500 1 LEU A 78 38.89 -74.11 REMARK 500 1 ALA A 94 157.60 -41.29 REMARK 500 1 PRO A 104 -172.18 -51.32 REMARK 500 1 PRO A 115 168.11 -41.12 REMARK 500 1 ASP B 123 -157.10 -153.18 REMARK 500 1 PHE B 124 -54.12 -134.46 REMARK 500 1 ALA B 128 35.78 -169.59 REMARK 500 2 THR A 11 -164.46 -111.19 REMARK 500 2 SER A 24 101.54 61.06 REMARK 500 2 SER A 25 -179.21 57.30 REMARK 500 2 PRO A 39 21.03 -74.45 REMARK 500 2 GLN A 41 82.35 -155.46 REMARK 500 2 ASN A 43 74.83 178.50 REMARK 500 2 SER A 61 -38.10 -33.02 REMARK 500 2 VAL A 66 94.58 -49.68 REMARK 500 2 ASP A 68 146.16 -36.95 REMARK 500 2 ASN A 74 11.83 49.42 REMARK 500 2 PRO A 106 172.79 -40.93 REMARK 500 2 PRO A 110 152.83 -49.02 REMARK 500 2 SER A 118 -138.87 -104.07 REMARK 500 2 ARG B 122 79.13 56.51 REMARK 500 2 ASP B 123 -102.53 -84.13 REMARK 500 2 TYR B 126 -88.23 49.33 REMARK 500 2 ALA B 128 49.32 -150.14 REMARK 500 3 PRO A 2 -13.64 -48.62 REMARK 500 3 THR A 11 -167.24 -122.56 REMARK 500 3 ASN A 36 -2.52 -149.50 REMARK 500 3 ASN A 43 86.69 -160.35 REMARK 500 3 SER A 45 134.30 -37.72 REMARK 500 3 SER A 61 -26.64 -37.90 REMARK 500 3 ASP A 68 151.80 -43.23 REMARK 500 3 PRO A 104 172.06 -51.02 REMARK 500 3 TYR B 126 122.43 57.15 REMARK 500 3 ALA B 128 48.59 -165.44 REMARK 500 4 PHE A 16 82.33 -170.96 REMARK 500 4 SER A 24 -166.85 -57.51 REMARK 500 REMARK 500 THIS ENTRY HAS 385 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16879 RELATED DB: BMRB DBREF 6GBE A 1 114 UNP Q64512 PTN13_MOUSE 1475 1588 DBREF 6GBE B 120 131 UNP Q16513 PKN2_HUMAN 973 984 SEQADV 6GBE PRO A 115 UNP Q64512 EXPRESSION TAG SEQADV 6GBE GLY A 116 UNP Q64512 EXPRESSION TAG SEQADV 6GBE ASN A 117 UNP Q64512 EXPRESSION TAG SEQADV 6GBE SER A 118 UNP Q64512 EXPRESSION TAG SEQADV 6GBE SER A 119 UNP Q64512 EXPRESSION TAG SEQRES 1 A 119 THR PRO HIS VAL LYS ASP TYR SER PHE VAL THR GLU ASP SEQRES 2 A 119 ASN THR PHE GLU VAL LYS LEU PHE LYS ASN SER SER GLY SEQRES 3 A 119 LEU GLY PHE SER PHE SER ARG GLU ASP ASN LEU ILE PRO SEQRES 4 A 119 GLU GLN ILE ASN GLY SER ILE VAL ARG VAL LYS LYS LEU SEQRES 5 A 119 PHE PRO GLY GLN PRO ALA ALA GLU SER GLY LYS ILE ASP SEQRES 6 A 119 VAL GLY ASP VAL ILE LEU LYS VAL ASN GLY ALA PRO LEU SEQRES 7 A 119 LYS GLY LEU SER GLN GLN ASP VAL ILE SER ALA LEU ARG SEQRES 8 A 119 GLY THR ALA PRO GLU VAL SER LEU LEU LEU CYS ARG PRO SEQRES 9 A 119 ALA PRO GLY VAL LEU PRO GLU ILE ASP THR PRO GLY ASN SEQRES 10 A 119 SER SER SEQRES 1 B 12 MET PHE ARG ASP PHE ASP TYR ILE ALA ASP TRP CYS HELIX 1 AA1 GLN A 56 SER A 61 1 6 HELIX 2 AA2 GLN A 84 ARG A 91 1 8 SHEET 1 AA1 3 THR A 15 LEU A 20 0 SHEET 2 AA1 3 VAL A 97 CYS A 102 -1 O LEU A 99 N VAL A 18 SHEET 3 AA1 3 VAL A 69 VAL A 73 -1 N VAL A 69 O CYS A 102 SHEET 1 AA2 3 ARG A 48 LYS A 51 0 SHEET 2 AA2 3 PHE A 29 SER A 32 -1 N SER A 32 O ARG A 48 SHEET 3 AA2 3 TRP B 130 CYS B 131 -1 O CYS B 131 N PHE A 29 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