10 20 30 40 50 60 70 80 1PDC - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER COLLAGEN-BINDING TYPE II DOMAIN 10-OCT-91 1PDC
TITLE REFINED SOLUTION STRUCTURE AND LIGAND-BINDING PROPERTIES OF TITLE 2 PDC-109 DOMAIN B. A COLLAGEN-BINDING TYPE II DOMAIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEMINAL FLUID PROTEIN PDC-109; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913
KEYWDS COLLAGEN-BINDING TYPE II DOMAIN
EXPDTA SOLUTION NMR
AUTHOR M.LLINAS,K.L.CONSTANTINE,L.PATTHY
REVDAT 2 24-FEB-09 1PDC 1 VERSN REVDAT 1 31-JAN-94 1PDC 0
JRNL AUTH K.L.CONSTANTINE,M.MADRID,L.BANYAI,M.TREXLER, JRNL AUTH 2 L.PATTHY,M.LLINAS JRNL TITL REFINED SOLUTION STRUCTURE AND LIGAND-BINDING JRNL TITL 2 PROPERTIES OF PDC-109 DOMAIN B. A COLLAGEN-BINDING JRNL TITL 3 TYPE II DOMAIN. JRNL REF J.MOL.BIOL. V. 223 281 1992 JRNL REFN ISSN 0022-2836 JRNL PMID 1731074 JRNL DOI 10.1016/0022-2836(92)90731-X
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.L.CONSTANTINE,V.RAMESH,L.BANYAI,M.TREXLER, REMARK 1 AUTH 2 L.PATTHY,M.LLINAS REMARK 1 TITL SEQUENCE-SPECIFIC 1H NMR ASSIGNMENTS AND REMARK 1 TITL 2 STRUCTURAL CHARACTERIZATION OF BOVINE SEMINAL REMARK 1 TITL 3 FLUID PROTEIN PDC-109 DOMAIN B REMARK 1 REF BIOCHEMISTRY V. 30 1663 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.BANYAI,M.TREXLER,S.KONCZ,M.GYENES,G.SIPOS, REMARK 1 AUTH 2 L.PATTHY REMARK 1 TITL THE COLLAGEN-BINDING SITE OF TYPE-II UNITS OF REMARK 1 TITL 2 BOVINE SEMINAL FLUID PROTEIN PDC-109 AND REMARK 1 TITL 3 FIBRONECTIN REMARK 1 REF EUR.J.BIOCHEM. V. 193 801 1990 REMARK 1 REFN ISSN 0014-2956
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DIANA, MIDGE, X-PLOR REMARK 3 AUTHORS : GUENTERT,BRAUN,WUTHRICH (DIANA), MADRID (MIDGE) REMARK 3 , BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1PDC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP A 23 CG TRP A 23 CD2 -0.110 REMARK 500 TRP A 26 CG TRP A 26 CD2 -0.132 REMARK 500 TRP A 39 CG TRP A 39 CD2 -0.121 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 TRP A 23 CG - CD1 - NE1 ANGL. DEV. = -6.5 DEGREES REMARK 500 TRP A 23 CD1 - NE1 - CE2 ANGL. DEV. = 5.4 DEGREES REMARK 500 TRP A 23 NE1 - CE2 - CZ2 ANGL. DEV. = 9.2 DEGREES REMARK 500 TRP A 23 NE1 - CE2 - CD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 TRP A 26 CD1 - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 TRP A 26 CG - CD1 - NE1 ANGL. DEV. = -7.5 DEGREES REMARK 500 TRP A 26 CD1 - NE1 - CE2 ANGL. DEV. = 5.4 DEGREES REMARK 500 TRP A 26 NE1 - CE2 - CZ2 ANGL. DEV. = 10.3 DEGREES REMARK 500 TRP A 26 NE1 - CE2 - CD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 TRP A 26 CG - CD2 - CE3 ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP A 39 CD1 - CG - CD2 ANGL. DEV. = 4.9 DEGREES REMARK 500 TRP A 39 CG - CD1 - NE1 ANGL. DEV. = -7.0 DEGREES REMARK 500 TRP A 39 NE1 - CE2 - CZ2 ANGL. DEV. = 9.9 DEGREES REMARK 500 TRP A 39 NE1 - CE2 - CD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 TRP A 39 CG - CD2 - CE3 ANGL. DEV. = -5.6 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 LYS A -1 -49.70 -137.95 REMARK 500 CYS A 1 115.93 -169.92 REMARK 500 VAL A 2 -79.30 -93.86 REMARK 500 PHE A 3 140.52 72.94 REMARK 500 LYS A 11 127.15 71.84 REMARK 500 GLU A 13 -83.56 -119.03 REMARK 500 CYS A 15 177.33 -59.24 REMARK 500 ILE A 18 40.60 38.91 REMARK 500 SER A 20 -136.20 -80.36 REMARK 500 TRP A 23 37.05 35.94 REMARK 500 MET A 24 -136.21 -160.01 REMARK 500 SER A 25 -178.13 172.48 REMARK 500 TYR A 33 -72.61 -94.15 REMARK 500 ASP A 34 7.86 47.66 REMARK 500 LYS A 35 1.98 91.36 REMARK 500 ARG A 37 35.01 32.98 REMARK 500 ALA A 38 30.22 -84.75 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 ARG A 37 0.30 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: B1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL
DBREF 1PDC A -4 42 UNP P02784 SFP1_BOVIN 90 134
SEQRES 1 A 45 ASP TYR ALA LYS CYS VAL PHE PRO PHE ILE TYR GLY GLY SEQRES 2 A 45 LYS LYS TYR GLU THR CYS THR LYS ILE GLY SER MET TRP SEQRES 3 A 45 MET SER TRP CYS SER LEU SER PRO ASN TYR ASP LYS ASP SEQRES 4 A 45 ARG ALA TRP LYS TYR CYS
HELIX 1 1 TYR A 7 LYS A 10 5 4
SHEET 1 A1 2 PHE A 5 TYR A 7 0 SHEET 2 A1 2 LYS A 10 TYR A 12 -1 O TYR A 12 N PHE A 5 SHEET 1 A2 2 SER A 25 SER A 28 0 SHEET 2 A2 2 TRP A 39 CYS A 42 -1 O LYS A 40 N CYS A 27
SSBOND 1 CYS A 1 CYS A 27 1555 1555 2.02 SSBOND 2 CYS A 15 CYS A 42 1555 1555 2.03
CISPEP 1 PHE A 3 PRO A 4 0 -1.70
SITE 1 B1 5 TYR A 7 TRP A 26 TYR A 33 ASP A 34 SITE 2 B1 5 TRP A 39
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