Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB (RESIDUES 56-68 OF THE P50 SUBUNIT OF NFKB)
SOLUTION NMR
NMR Refinement
Method
Details
Software
THE 3D STRUCTURE OF THE HUMAN THIOREDOXIN-NFKB PEPTIDE
COMPLEX IN SOLUTION BY NMR IS BASED ON 3213 EXPERIMENTAL
RESTRAINTS COMPRISING:
2546 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS
36 RESTRAINTS FOR 18 BACKBONE H-BONDS
44 RESTRAINTS FOR 6 BOUND WATER MOLECULES
300 TORSION ANGLE RESTRAINTS (104 PHI, 76 PSI, 78 CHI1
AND 31 CHI2 FOR HUMAN THIOREDOXIN, AND 7 CHI1 AND 4
CHI2 RESTRAINTS FOR THE NFKB PEPTIDE)
88 HN-HALPHA THREE-BOND COUPLING CONSTANTS
102 13CALPHA AND 97 13CB CHEMICAL SHIFT RESTRAINTS.
THE BREAKDOWN OF THE INTERPROTON DISTANCE RESTRAINTS IS AS
FOLLOWS:
INTRAMOLECULAR HTRX RESTRAINTS:
503 SEQUENTIAL
437 SHORT RANGE (1 < |I-J|<=5)
727 LONG RANGE (|I-J|>5)
690 INTRARESIDUE
INTRAMOLECULAR PEPTIDE RESTRAINTS: 115
INTERMOLECULAR HTRX-NFKB: 74
THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC
MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. &
GRONENBORN, A.M. (1988) FEBS LETT 229, 317 - 324. ALL
STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE.
THE STRUCTURE FOUND IN PDB ENTRY 1MDI IS THE RESTRAINED
MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED
BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 60
DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO
RESIDUES 1 - 105 OF HTRX AND RESIDUES 57 - 67 OF THE
PEPTIDE AND SUBJECTING THE RESULTING COORDINATES TO
RESTRAINED MINIMIZATION. THE LAST NUMBER COLUMN IN THIS
SET OF COORDINATES (THE B-FACTOR COLUMN IN X-RAY
STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE
INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE
NUMBERS IN THE LAST COLUMN OF THE INDIVIDUAL STRUCTURES
HAVE NO MEANING.