HEADER DE NOVO PROTEIN 25-JAN-02 1KVF TITLE EMP-18 ERYTHROPOIETIN RECEPTOR AGONIST PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN: EMP-18 RECEPTOR AGONIST; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. IT IS A NOVEL SOURCE 4 SEQUENCE DERIVED FROM PHAGE-DISPLAY SELECTION. KEYWDS BETA HAIRPIN PEPTIDE, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.J.SKELTON,S.RUSSELL,F.DE SAUVAGE,A.G.COCHRAN REVDAT 3 23-FEB-22 1KVF 1 REMARK LINK REVDAT 2 24-FEB-09 1KVF 1 VERSN REVDAT 1 06-MAR-02 1KVF 0 JRNL AUTH N.J.SKELTON,S.RUSSELL,F.DE SAUVAGE,A.G.COCHRAN JRNL TITL AMINO ACID DETERMINANTS OF BETA-HAIRPIN CONFORMATION IN JRNL TITL 2 ERYTHROPOEITIN RECEPTOR AGONIST PEPTIDES DERIVED FROM A JRNL TITL 3 PHAGE DISPLAY LIBRARY JRNL REF J.MOL.BIOL. V. 316 1111 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 11884148 JRNL DOI 10.1006/JMBI.2002.5410 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.L.JOHNSON,F.X.FARRELL,F.P.BARBONE,F.J.MCMAHON,J.TULLAI, REMARK 1 AUTH 2 K.HOEY,O.LIVNAH,N.C.WRIGHTON,S.A.MIDDLETON,D.A.LOUGHNEY, REMARK 1 AUTH 3 W.J.DOWER,L.S.MULCAHY,I.A.WILSON,L.K.JOLLIFFE REMARK 1 TITL IDENTIFICATION OF A 13 AMINO ACID PEPTIDE MIMETIC OF REMARK 1 TITL 2 ERYTHROPOIETIN AND DESCRIPTION OF AMINO ACIDS CRITICAL FOR REMARK 1 TITL 3 THE MIMETIC ACTIVITY OF EMP1 REMARK 1 REF BIOCHEMISTRY V. 37 3699 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI971956Y REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DGII 98.0, DISCOVER 3.1 REMARK 3 AUTHORS : TIMOTHY HAVEL (DGII), ACCELRYS (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON 52 NOE DISTANCE RESTRAINTS, 11 PHI AND REMARK 3 4 CHI-1 DIHEDRAL ANGLE RESTRAINTS. REMARK 3 NO HYDROGEN BOND RESTRAINTS WERE EMPLOYED. REMARK 3 THE MEAN BACKBONE ATOM RMSD TO THE MEAN STRUCTURE WITHIN THE REMARK 3 DISULFIDE CYCLE IS 0.43 +/- 0.12 ANGSTOMS. REMARK 4 REMARK 4 1KVF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015380. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 303 REMARK 210 PH : 5.1; 5.1 REMARK 210 IONIC STRENGTH : 0; 0 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 3 MM PEPTIDE; 3 MM PEPTIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D-ROESY; 2D-NOESY; DQF-COSY; REMARK 210 COSY-35 REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY AND RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 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: REMARK 210 THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR REMARK 210 TECHNIQUES. REMARK 210 THE SAMPLE CONTAINS A MIXTURE OF CIS AND TRANS ISOMERS ABOUT THE REMARK 210 GLY7-PRO8 PEPTIDE BOND. REMARK 210 BOTH SETS OF RESONANCES WERE ASSIGNED. REMARK 210 THE TRANS ISOFORM IS NOT WELL ORDERED IN SOLUTION. REMARK 210 THE CIS ISOFORM IS STRUCTURED, ESPECIALLY WITHIN THE DISULFIDE REMARK 210 CYCLE. REMARK 210 STRUCTURES WERE CALCULATED ON THE BASIS OF RESTRAINTS GENERATED REMARK 210 ONLY FROM THE CIS ISOFORM. 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: 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 LEU A 9 -60.23 -99.96 REMARK 500 2 LEU A 9 -55.17 -121.72 REMARK 500 3 LEU A 9 -55.96 -123.72 REMARK 500 5 LEU A 9 -52.66 -139.97 REMARK 500 7 TYR A 2 47.81 -82.27 REMARK 500 7 LEU A 9 36.08 -140.46 REMARK 500 10 LEU A 9 -54.63 -140.05 REMARK 500 11 LEU A 9 33.58 -140.90 REMARK 500 12 LEU A 9 -64.84 -102.18 REMARK 500 12 LYS A 14 75.76 -118.92 REMARK 500 13 LEU A 9 25.41 -140.22 REMARK 500 16 SER A 3 74.57 -113.25 REMARK 500 18 LEU A 9 26.54 -140.17 REMARK 500 19 TYR A 2 45.86 -76.90 REMARK 500 19 LEU A 9 -54.87 -140.08 REMARK 500 19 PRO A 15 107.87 -51.13 REMARK 500 20 TYR A 2 21.14 -145.29 REMARK 500 20 LEU A 9 -64.73 -103.06 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 5 TYR A 2 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 17 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GJE RELATED DB: PDB REMARK 900 PEPTIDE ANTAGONIST OF IGFBP-1, MINIMIZED AVERAGE STRUCTURE REMARK 900 RELATED ID: 1KVG RELATED DB: PDB REMARK 900 EPO-3 BETA HAIRPIN PEPTIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 AN APPROPRIATE DATABASE MATCH WAS REMARK 999 NOT AVAILABLE AT THE TIME OF PROCESSING. DBREF 1KVF A 1 17 PDB 1KVF 1KVF 1 17 SEQRES 1 A 17 THR TYR SER CYS HIS PHE GLY PRO LEU THR TRP VAL CYS SEQRES 2 A 17 LYS PRO GLN NH2 HET NH2 A 17 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N SHEET 1 A 2 SER A 3 PHE A 6 0 SHEET 2 A 2 TRP A 11 LYS A 14 -1 O LYS A 14 N SER A 3 SSBOND 1 CYS A 4 CYS A 13 1555 1555 2.05 LINK C GLN A 16 N NH2 A 17 1555 1555 1.33 CISPEP 1 GLY A 7 PRO A 8 1 4.83 CISPEP 2 GLY A 7 PRO A 8 2 -0.49 CISPEP 3 GLY A 7 PRO A 8 3 1.02 CISPEP 4 GLY A 7 PRO A 8 4 -0.34 CISPEP 5 GLY A 7 PRO A 8 5 1.02 CISPEP 6 GLY A 7 PRO A 8 6 3.75 CISPEP 7 GLY A 7 PRO A 8 7 -5.54 CISPEP 8 GLY A 7 PRO A 8 8 2.09 CISPEP 9 GLY A 7 PRO A 8 9 1.27 CISPEP 10 GLY A 7 PRO A 8 10 3.35 CISPEP 11 GLY A 7 PRO A 8 11 -0.29 CISPEP 12 GLY A 7 PRO A 8 12 5.24 CISPEP 13 GLY A 7 PRO A 8 13 1.59 CISPEP 14 GLY A 7 PRO A 8 14 3.73 CISPEP 15 GLY A 7 PRO A 8 15 4.93 CISPEP 16 GLY A 7 PRO A 8 16 2.47 CISPEP 17 GLY A 7 PRO A 8 17 1.45 CISPEP 18 GLY A 7 PRO A 8 18 -1.19 CISPEP 19 GLY A 7 PRO A 8 19 2.78 CISPEP 20 GLY A 7 PRO A 8 20 4.67 SITE 1 AC1 1 GLN A 16 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