PDB Short entry for 2DDI HEADER PROTEIN BINDING 30-JAN-06 2DDI TITLE NMR STRUCTURE OF THE SECOND KUNITZ DOMAIN OF HUMAN WFIKKN1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: WAP, FOLLISTATIN/KAZAL, IMMUNOGLOBULIN, KUNITZ AND NETRIN COMPND 3 DOMAIN CONTAINING 1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: SECOND KUNITZ DOMAIN; COMPND 6 SYNONYM: WFIKKN1, TRYPSIN INHIBITOR; COMPND 7 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: WFIKKN1; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: GS115 (HIS4); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZALFAA KEYWDS KUNITZ DOMAIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.LIEPINSH,G.OTTING REVDAT 3 09-MAR-22 2DDI 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DDI 1 VERSN REVDAT 1 19-DEC-06 2DDI 0 JRNL AUTH E.LIEPINSH,A.NAGY,M.TREXLER,L.PATTHY,G.OTTING JRNL TITL SECOND KUNITZ-TYPE PROTEASE INHIBITOR DOMAIN OF THE HUMAN JRNL TITL 2 WFIKKN1 PROTEIN JRNL REF J.BIOMOL.NMR V. 35 73 2006 JRNL REFN ISSN 0925-2738 JRNL PMID 16791741 JRNL DOI 10.1007/S10858-006-9013-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, OPAL 2.6 REMARK 3 AUTHORS : GUENTERT (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DDI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000025287. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 10 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1 MM KUNITZ DOMAIN; 90% H2O, REMARK 210 10% D2O; 1.1 MM KUNITZ DOMAIN; REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 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: 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 HG SER A 52 OE1 GLU A 54 1.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 3 VAL A 62 CA - CB - CG1 ANGL. DEV. = 9.5 DEGREES REMARK 500 4 HIS A 70 C - N - CA ANGL. DEV. = 20.3 DEGREES REMARK 500 8 VAL A 62 C - N - CA ANGL. DEV. = 16.7 DEGREES REMARK 500 10 ARG A 53 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 12 TYR A 40 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 12 VAL A 62 C - N - CA ANGL. DEV. = 16.0 DEGREES REMARK 500 19 ARG A 53 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES 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 ALA A 2 178.15 -57.41 REMARK 500 1 GLU A 44 133.60 -33.62 REMARK 500 1 HIS A 67 93.90 -51.35 REMARK 500 2 GLU A 3 -71.34 -138.21 REMARK 500 2 THR A 7 115.55 -171.65 REMARK 500 2 GLU A 44 133.64 -33.30 REMARK 500 2 HIS A 66 94.77 172.93 REMARK 500 2 HIS A 67 99.90 -34.85 REMARK 500 2 HIS A 68 44.88 -82.99 REMARK 500 3 ALA A 2 86.02 -67.33 REMARK 500 3 GLU A 5 -22.71 -37.75 REMARK 500 3 THR A 7 94.50 -68.38 REMARK 500 3 PRO A 13 154.22 -49.76 REMARK 500 3 GLU A 44 134.20 -34.41 REMARK 500 3 VAL A 62 -157.40 -93.17 REMARK 500 3 ASP A 64 113.86 -33.65 REMARK 500 3 HIS A 65 -63.87 -95.25 REMARK 500 3 HIS A 67 90.90 -33.72 REMARK 500 4 GLU A 5 -78.81 -117.09 REMARK 500 4 PRO A 13 153.62 -49.88 REMARK 500 4 GLU A 44 133.86 -33.62 REMARK 500 4 VAL A 62 -153.45 -131.43 REMARK 500 4 HIS A 66 56.44 173.05 REMARK 500 5 THR A 7 93.77 173.48 REMARK 500 5 GLU A 44 133.54 -33.37 REMARK 500 5 HIS A 66 -57.79 -148.47 REMARK 500 5 HIS A 69 -85.85 -138.39 REMARK 500 6 ALA A 2 20.99 -148.89 REMARK 500 6 THR A 7 110.11 -161.27 REMARK 500 6 CYS A 43 -173.39 -69.05 REMARK 500 6 GLU A 44 133.57 -34.77 REMARK 500 6 CYS A 60 75.64 -116.41 REMARK 500 6 HIS A 67 109.99 -33.67 REMARK 500 6 HIS A 68 30.30 -73.05 REMARK 500 7 ALA A 2 -55.53 -159.77 REMARK 500 7 PRO A 13 154.71 -49.91 REMARK 500 7 GLU A 44 133.94 -33.99 REMARK 500 7 PRO A 61 -163.17 -78.37 REMARK 500 7 HIS A 66 83.01 -33.02 REMARK 500 7 HIS A 68 87.75 -62.76 REMARK 500 7 HIS A 69 -168.05 173.71 REMARK 500 8 THR A 7 137.26 173.54 REMARK 500 8 GLU A 44 133.52 -33.26 REMARK 500 8 VAL A 62 -152.75 -105.16 REMARK 500 8 HIS A 66 -85.29 -140.30 REMARK 500 8 HIS A 67 37.89 173.17 REMARK 500 9 PHE A 6 94.39 -64.74 REMARK 500 9 GLN A 33 16.85 55.65 REMARK 500 9 GLU A 44 134.04 -34.14 REMARK 500 9 HIS A 67 89.31 -56.78 REMARK 500 REMARK 500 THIS ENTRY HAS 113 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 GLU A 1 ALA A 2 9 149.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 HIS A 51 0.08 SIDE CHAIN REMARK 500 2 ARG A 53 0.20 SIDE CHAIN REMARK 500 3 HIS A 51 0.12 SIDE CHAIN REMARK 500 3 HIS A 66 0.08 SIDE CHAIN REMARK 500 3 HIS A 67 0.08 SIDE CHAIN REMARK 500 4 GLU A 23 0.08 SIDE CHAIN REMARK 500 7 GLU A 1 0.07 SIDE CHAIN REMARK 500 8 HIS A 51 0.10 SIDE CHAIN REMARK 500 8 ARG A 53 0.11 SIDE CHAIN REMARK 500 9 ARG A 53 0.14 SIDE CHAIN REMARK 500 10 ARG A 53 0.11 SIDE CHAIN REMARK 500 11 ARG A 53 0.09 SIDE CHAIN REMARK 500 12 TYR A 40 0.08 SIDE CHAIN REMARK 500 12 HIS A 68 0.10 SIDE CHAIN REMARK 500 13 ARG A 53 0.08 SIDE CHAIN REMARK 500 14 GLU A 1 0.07 SIDE CHAIN REMARK 500 14 HIS A 51 0.09 SIDE CHAIN REMARK 500 16 HIS A 67 0.12 SIDE CHAIN REMARK 500 18 ARG A 53 0.14 SIDE CHAIN REMARK 500 19 ARG A 53 0.10 SIDE CHAIN REMARK 500 20 GLU A 1 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DDJ RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH PRO 61 IN CIS CONFORMATION DBREF 2DDI A 8 62 GB 75517744 AAI01603 357 411 SEQADV 2DDI GLU A 1 GB 75517744 CLONING ARTIFACT SEQADV 2DDI ALA A 2 GB 75517744 CLONING ARTIFACT SEQADV 2DDI GLU A 3 GB 75517744 CLONING ARTIFACT SEQADV 2DDI ALA A 4 GB 75517744 CLONING ARTIFACT SEQADV 2DDI GLU A 5 GB 75517744 CLONING ARTIFACT SEQADV 2DDI PHE A 6 GB 75517744 CLONING ARTIFACT SEQADV 2DDI THR A 7 GB 75517744 CLONING ARTIFACT SEQADV 2DDI VAL A 63 GB 75517744 EXPRESSION TAG SEQADV 2DDI ASP A 64 GB 75517744 EXPRESSION TAG SEQADV 2DDI HIS A 65 GB 75517744 EXPRESSION TAG SEQADV 2DDI HIS A 66 GB 75517744 EXPRESSION TAG SEQADV 2DDI HIS A 67 GB 75517744 EXPRESSION TAG SEQADV 2DDI HIS A 68 GB 75517744 EXPRESSION TAG SEQADV 2DDI HIS A 69 GB 75517744 EXPRESSION TAG SEQADV 2DDI HIS A 70 GB 75517744 EXPRESSION TAG SEQRES 1 A 70 GLU ALA GLU ALA GLU PHE THR ASP ALA CYS VAL LEU PRO SEQRES 2 A 70 ALA VAL GLN GLY PRO CYS ARG GLY TRP GLU PRO ARG TRP SEQRES 3 A 70 ALA TYR SER PRO LEU LEU GLN GLN CYS HIS PRO PHE VAL SEQRES 4 A 70 TYR GLY GLY CYS GLU GLY ASN GLY ASN ASN PHE HIS SER SEQRES 5 A 70 ARG GLU SER CYS GLU ASP ALA CYS PRO VAL VAL ASP HIS SEQRES 6 A 70 HIS HIS HIS HIS HIS HELIX 1 1 ASP A 8 LEU A 12 5 5 HELIX 2 2 PRO A 30 GLN A 33 5 4 HELIX 3 3 SER A 52 CYS A 60 1 9 SHEET 1 A 2 GLU A 23 SER A 29 0 SHEET 2 A 2 GLN A 34 TYR A 40 -1 O HIS A 36 N ALA A 27 SSBOND 1 CYS A 10 CYS A 60 1555 1555 2.04 SSBOND 2 CYS A 19 CYS A 43 1555 1555 2.02 SSBOND 3 CYS A 35 CYS A 56 1555 1555 2.03 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