PDB Short entry for 1MPV HEADER PROTEIN BINDING 12-SEP-02 1MPV TITLE STRUCTURE OF BHPBR3, THE BAFF-BINDING LOOP OF BR3 EMBEDDED IN A BETA- TITLE 2 HAIRPIN PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BLYS RECEPTOR 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BR3 LOOP (RESIDUES 26-31); COMPND 5 SYNONYM: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 13C, B COMPND 6 CELL-ACTIVATING FACTOR RECEPTOR, BAFF RECEPTOR, BAFF-R, BLYS RECEPTOR COMPND 7 3; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: THE RECEPTOR LOOP IS EMBEDDED WITHIN A BETA-HAIRPIN COMPND 10 (BHP) SCAFFOLD SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS SYNTHESIZED CHEMICALLY WITH SOURCE 4 ACETYLATED N-TERMINUS AND AMIDATED C-TERMINUS KEYWDS BETA-HAIRPIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.KAYAGAKI,M.YAN,D.SESHASAYEE,H.WANG,W.LEE,D.M.FRENCH,I.S.GREWAL, AUTHOR 2 A.G.COCHRAN,N.C.GORDON,J.YIN,M.A.STAROVASNIK,V.M.DIXIT REVDAT 4 23-FEB-22 1MPV 1 REMARK LINK REVDAT 3 24-FEB-09 1MPV 1 VERSN REVDAT 2 01-APR-03 1MPV 1 JRNL REVDAT 1 30-OCT-02 1MPV 0 JRNL AUTH N.KAYAGAKI,M.YAN,D.SESHASAYEE,H.WANG,W.LEE,D.M.FRENCH, JRNL AUTH 2 I.S.GREWAL,A.G.COCHRAN,N.C.GORDON,J.YIN,M.A.STAROVASNIK, JRNL AUTH 3 V.M.DIXIT JRNL TITL BAFF/BLYS RECEPTOR 3 BINDS THE B CELL SURVIVAL FACTOR BAFF JRNL TITL 2 LIGAND THROUGH A DISCRETE SURFACE LOOP AND PROMOTES JRNL TITL 3 PROCESSING OF NF-KAPPAB2. JRNL REF IMMUNITY V. 17 515 2002 JRNL REFN ISSN 1074-7613 JRNL PMID 12387744 JRNL DOI 10.1016/S1074-7613(02)00425-9 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 1.37.4.2, DISCOVER 98.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), ACCELRYS (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 COMPLETE 1H RESONANCE ASSIGNMENTS WERE OBTAINED USING STANDARD 2D REMARK 3 HOMONUCLEAR NMR METHODS. DISTANCE RESTRAINTS WERE DERIVED FROM REMARK 3 ANALYSIS OF A 2D NOESY SPECTRUM (250MS MIXING TIME); HN-HA REMARK 3 COUPLING CONSTANTS WERE OBTAINED FROM ANALYSIS OF A DQF-COSY REMARK 3 SPECTRUM ACQUIRED IN WATER; AND HAHB VALUES WERE OBTAINED FROM REMARK 3 ANALYSIS OF A COSY-35 SPECTRUM ACQUIRED IN D2O. REMARK 3 STRUCTURES WERE CALCULATED FROM A TOTAL OF 119 NOE-DERIVED REMARK 3 (INCLUDING 46 LONG-RANGE) DISTANCE RESTRAINTS AND 16 DIHEDRAL REMARK 3 ANGLE RESTRAINTS. STRUCTURES SATISFY THE EXPERIMENTAL DATA VERY REMARK 3 WELL WITH NO DISTANCE OR DIHEDRAL ANGLE VIOLATIONS GREATER THAN REMARK 3 0.1 ANGSTROM OR 1 DEGREE, RESPECTIVELY. REMARK 4 REMARK 4 1MPV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017081. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : NO ADDED SALT REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.9 MM BHPBR3 PEPTIDE; 2.9 MM REMARK 210 BHPBR3 PEPTIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 COSY-35 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 : FELIX 98.0, DGII 98.0 REMARK 210 METHOD USED : HYBRID DISTANCE REMARK 210 GEOMETRY/SIMULATED ANNEALING REMARK 210 FOLLOWED BY RESTRAINED MOLECULAR REMARK 210 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: 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: 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 ARG A 30 58.17 85.86 REMARK 500 2 ARG A 30 60.69 74.13 REMARK 500 3 ARG A 30 58.92 75.75 REMARK 500 4 ARG A 30 56.28 87.63 REMARK 500 5 ARG A 30 59.91 70.80 REMARK 500 6 ARG A 30 59.43 71.05 REMARK 500 7 ARG A 30 60.23 73.48 REMARK 500 8 ARG A 30 51.71 90.63 REMARK 500 9 ARG A 30 62.74 68.58 REMARK 500 10 ARG A 30 60.57 74.03 REMARK 500 11 ARG A 30 58.08 73.92 REMARK 500 12 ARG A 30 60.15 74.03 REMARK 500 13 ARG A 30 59.79 75.10 REMARK 500 14 ARG A 30 52.46 83.37 REMARK 500 15 ARG A 30 52.40 103.41 REMARK 500 16 ARG A 30 55.93 84.88 REMARK 500 17 ARG A 30 60.16 73.51 REMARK 500 18 ARG A 30 60.80 65.95 REMARK 500 19 ARG A 30 52.08 106.57 REMARK 500 20 ARG A 30 60.45 74.72 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 ACE A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 35 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS IS PART OF AN OPTIMIZED BETA-HAIRPIN REMARK 999 SCAFFOLD, (SEE RUSSELL, BLANDL, SKELTON, & REMARK 999 COCHRAN, "STABILITY OF CYCLIC BETA-HAIRPINS: REMARK 999 ASYMMETRIC CONTRIBUTIONS FROM SIDE CHAINS OF REMARK 999 A HYDROGEN-BONDED CROSS-STRAND RESIDUE PAIR", REMARK 999 J. AMER. CHEM. SOC., IN PRESS.) DBREF 1MPV A 26 31 UNP Q96RJ3 TR13C_HUMAN 26 31 SEQADV 1MPV CYS A 23 UNP Q96RJ3 SEE REMARK 999 SEQADV 1MPV HIS A 24 UNP Q96RJ3 SEE REMARK 999 SEQADV 1MPV TRP A 25 UNP Q96RJ3 SEE REMARK 999 SEQADV 1MPV TRP A 32 UNP Q96RJ3 SEE REMARK 999 SEQADV 1MPV VAL A 33 UNP Q96RJ3 SEE REMARK 999 SEQADV 1MPV CYS A 34 UNP Q96RJ3 SEE REMARK 999 SEQRES 1 A 14 ACE CYS HIS TRP ASP LEU LEU VAL ARG HIS TRP VAL CYS SEQRES 2 A 14 NH2 HET ACE A 22 6 HET NH2 A 35 3 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N SHEET 1 A 2 HIS A 24 ASP A 26 0 SHEET 2 A 2 HIS A 31 VAL A 33 -1 O VAL A 33 N HIS A 24 SSBOND 1 CYS A 23 CYS A 34 1555 1555 2.06 LINK C ACE A 22 N CYS A 23 1555 1555 1.34 LINK C CYS A 34 N NH2 A 35 1555 1555 1.34 SITE 1 AC1 2 HIS A 24 VAL A 33 SITE 1 AC2 1 CYS A 34 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