10 20 30 40 50 60 70 80 1MDI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER COMPLEX (ELECTRON TRANSPORT/PEPTIDE) 27-FEB-95 1MDI
TITLE HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE TITLE 2 INTERMEDIATE BETWEEN MUTANT HUMAN THIOREDOXIN AND A 13 TITLE 3 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TARGET SITE IN HUMAN NFKB; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2
KEYWDS COMPLEX (ELECTRON TRANSPORT/PEPTIDE)
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,J.QIN,A.M.GRONENBORN
REVDAT 3 24-FEB-09 1MDI 1 VERSN REVDAT 2 01-APR-03 1MDI 1 JRNL REVDAT 1 03-JUN-95 1MDI 0
JRNL AUTH J.QIN,G.M.CLORE,W.M.KENNEDY,J.R.HUTH,A.M.GRONENBORN JRNL TITL SOLUTION STRUCTURE OF HUMAN THIOREDOXIN IN A MIXED JRNL TITL 2 DISULFIDE INTERMEDIATE COMPLEX WITH ITS TARGET JRNL TITL 3 PEPTIDE FROM THE TRANSCRIPTION FACTOR NF KAPPA B. JRNL REF STRUCTURE V. 3 289 1995 JRNL REFN ISSN 0969-2126 JRNL PMID 7788295 JRNL DOI 10.1016/S0969-2126(01)00159-9
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE 3D STRUCTURE OF THE HUMAN THIOREDOXIN-NFKB PEPTIDE REMARK 3 COMPLEX IN SOLUTION BY NMR IS BASED ON 3213 EXPERIMENTAL REMARK 3 RESTRAINTS COMPRISING: REMARK 3 2546 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS REMARK 3 36 RESTRAINTS FOR 18 BACKBONE H-BONDS REMARK 3 44 RESTRAINTS FOR 6 BOUND WATER MOLECULES REMARK 3 300 TORSION ANGLE RESTRAINTS (104 PHI, 76 PSI, 78 CHI1 REMARK 3 AND 31 CHI2 FOR HUMAN THIOREDOXIN, AND 7 CHI1 AND 4 REMARK 3 CHI2 RESTRAINTS FOR THE NFKB PEPTIDE) REMARK 3 88 HN-HALPHA THREE-BOND COUPLING CONSTANTS REMARK 3 102 13CALPHA AND 97 13CB CHEMICAL SHIFT RESTRAINTS. REMARK 3 REMARK 3 THE BREAKDOWN OF THE INTERPROTON DISTANCE RESTRAINTS IS AS REMARK 3 FOLLOWS: REMARK 3 INTRAMOLECULAR HTRX RESTRAINTS: REMARK 3 503 SEQUENTIAL REMARK 3 437 SHORT RANGE (1 < |I-J|<=5) REMARK 3 727 LONG RANGE (|I-J|>5) REMARK 3 690 INTRARESIDUE REMARK 3 INTRAMOLECULAR PEPTIDE RESTRAINTS: 115 REMARK 3 INTERMOLECULAR HTRX-NFKB: 74 REMARK 3 REMARK 3 THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC REMARK 3 MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING REMARK 3 METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & REMARK 3 GRONENBORN, A.M. (1988) FEBS LETT 229, 317 - 324. ALL REMARK 3 STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE. REMARK 3 REMARK 3 THE STRUCTURE FOUND IN PDB ENTRY 1MDI IS THE RESTRAINED REMARK 3 MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED REMARK 3 BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 60 REMARK 3 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO REMARK 3 RESIDUES 1 - 105 OF HTRX AND RESIDUES 57 - 67 OF THE REMARK 3 PEPTIDE AND SUBJECTING THE RESULTING COORDINATES TO REMARK 3 RESTRAINED MINIMIZATION. THE LAST NUMBER COLUMN IN THIS REMARK 3 SET OF COORDINATES (THE B-FACTOR COLUMN IN X-RAY REMARK 3 STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE REMARK 3 INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE REMARK 3 NUMBERS IN THE LAST COLUMN OF THE INDIVIDUAL STRUCTURES REMARK 3 HAVE NO MEANING.
REMARK 4 REMARK 4 1MDI 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: 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 PRO A 40 2.66 -66.83 REMARK 500 PHE A 41 -76.17 -118.48 REMARK 500 SER A 90 -168.12 -104.12 REMARK 500 ALA A 92 95.87 -57.57 REMARK 500 ARG B 4 -97.77 -136.44 REMARK 500 TYR B 5 -167.56 -117.31 REMARK 500 GLU B 8 43.23 -82.78 REMARK 500 PRO B 10 23.12 -66.74 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MDJ RELATED DB: PDB REMARK 900 RELATED ID: 1MDK RELATED DB: PDB
REMARK 999 REMARK 999 SEQUENCE REMARK 999 AT POSITION 74 THR WAS FOUND BY WOLMAN ET AL., JOURNAL OF REMARK 999 BIOCHEMISTRY 263, 15506 (1988).
DBREF 1MDI A 2 105 UNP P10599 THIO_HUMAN 1 104 DBREF 1MDI B 1 13 UNP P19838 NFKB1_HUMAN 53 65
SEQADV 1MDI ALA A 35 UNP P10599 CYS 34 CONFLICT SEQADV 1MDI ALA A 62 UNP P10599 CYS 61 CONFLICT SEQADV 1MDI ALA A 69 UNP P10599 CYS 68 CONFLICT SEQADV 1MDI ALA A 73 UNP P10599 CYS 72 CONFLICT SEQADV 1MDI THR A 74 UNP P10599 MET 73 CONFLICT
SEQRES 1 A 105 MET VAL LYS GLN ILE GLU SER LYS THR ALA PHE GLN GLU SEQRES 2 A 105 ALA LEU ASP ALA ALA GLY ASP LYS LEU VAL VAL VAL ASP SEQRES 3 A 105 PHE SER ALA THR TRP CYS GLY PRO ALA LYS MET ILE LYS SEQRES 4 A 105 PRO PHE PHE HIS SER LEU SER GLU LYS TYR SER ASN VAL SEQRES 5 A 105 ILE PHE LEU GLU VAL ASP VAL ASP ASP ALA GLN ASP VAL SEQRES 6 A 105 ALA SER GLU ALA GLU VAL LYS ALA THR PRO THR PHE GLN SEQRES 7 A 105 PHE PHE LYS LYS GLY GLN LYS VAL GLY GLU PHE SER GLY SEQRES 8 A 105 ALA ASN LYS GLU LYS LEU GLU ALA THR ILE ASN GLU LEU SEQRES 9 A 105 VAL SEQRES 1 B 13 PHE ARG PHE ARG TYR VAL CYS GLU GLY PRO SER HIS GLY
FORMUL 3 HOH *6(H2 O)
HELIX 1 1 LYS A 8 ALA A 17 1 10 HELIX 2 2 GLY A 33 PHE A 42 1 10 HELIX 3 3 SER A 44 LYS A 48 5 5 HELIX 4 4 GLN A 63 ALA A 69 1 7 HELIX 5 5 LYS A 94 LEU A 104 1 11
SHEET 1 A 5 VAL A 2 ILE A 5 0 SHEET 2 A 5 ILE A 53 VAL A 57 1 N PHE A 54 O LYS A 3 SHEET 3 A 5 VAL A 23 PHE A 27 1 N VAL A 24 O ILE A 53 SHEET 4 A 5 THR A 76 LYS A 81 -1 N PHE A 80 O VAL A 23 SHEET 5 A 5 GLN A 84 SER A 90 -1 N PHE A 89 O PHE A 77
SSBOND 1 CYS A 32 CYS B 7 1555 1555 2.02
CISPEP 1 THR A 74 PRO A 75 0 -1.61
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