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Table 2 Summary of conformational differences between PTS1-liganded and apo-Pex5p(C).

From: A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding

DynDomaparameters

Pex5p(C)/mSCP2bversus previous apo-Pex5p(C)c

Pex5p(C)/mSCP2bversus new apo-Pex5p(C)d

new apo-Pex5p(C)dversus previous apo-Pex5p(C)c

Whole protein residues

335–639

335–639

315–639

Whole protein RMSD (Ă… 2 )

3.06

3.26

2.20

Fixed domain residues

337–523

337–518

323–485

Fixed domain RMSD (Ă… 2 )

1.40

2.32

0.71

Rotation angle (°)

19.7

20.0

14.2

Translation along axis (Ă…)

-0.7

-0.1

0.1

Bending residues

495–500 (end of TPR5 helix A) 523–524 (start of TPR6 helix A) 533–537 (end of TPR6 helix A)

519–520 (loop connection TPRs 5 and 6) 530–531 (middle of TPR6 helix A) 535–536 (end of TPR6 helix A) 588–601 (entire 7C-loop)

485–489 (loop connecting TPRs 4 and 5) 496–499 (end of TPR5 helix A)

% Closure motion

92.0

83.8

1.7

  1. aAs described in [11] and [47]
  2. bAs described in [9], PDB indentifier 2C0L.
  3. cAs described in [9], PDB indentifier 2C0M.
  4. dAs described in this study, PDB identifier 2J9Q.