SMTL ID : 3b5g.1

Crystal Structure of the Unstable and Highly Fibrillogenic PRO7SER Mutant of the Recombinant Variable Domain 6AJL2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: Y.37, T.46, T.47 Chain B: V.100, V.101, F.102 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.37, B:F.102 Hydrogen bonds: A:T.47, A:T.47, A:T.47, B:F.102 ACT.2: 2 residues within 4Å: Chain A: R.55 Ligands: NA.8 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.55, A:R.55 Salt bridges: A:R.55

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: T.5, Q.6, H.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.6 Water bridges: A:S.9, A:S.9, A:S.9 GOL.4: 4 residues within 4Å: Chain A: R.40, S.43, S.44, T.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.40, A:S.43, A:S.44 Water bridges: A:Q.38 GOL.5: 5 residues within 4Å: Chain A: Y.33, E.51, D.52, N.53, Q.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.52, A:D.52, A:N.53, A:Q.54 GOL.6: 9 residues within 4Å: Chain A: S.9, D.88, Y.90, G.104, G.105, T.106 Chain B: G.42, S.43, S.44 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.43, A:S.9 Water bridges: A:Y.90 GOL.7: 7 residues within 4Å: Chain A: V.100, V.101, F.102 Chain B: Y.37, P.45, T.46, T.47 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.100, A:F.102, B:T.47, B:T.47 Water bridges: A:F.102, B:T.47 GOL.9: 4 residues within 4Å: Chain B: D.52, N.53, S.66, I.67 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.52, B:N.53, B:I.67 GOL.10: 5 residues within 4Å: Chain B: A.30, S.31, N.32, Y.33, D.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.31, B:D.52

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 6 residues within 4Å: Chain A: I.49, N.53, R.55, S.64, G.65 Ligands: ACT.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.55, A:G.65, A:G.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hernandez-Santoyo, A. et al., A single mutation at the sheet switch region results in conformational changes favoring lambda6 light-chain fibrillogenesis. J.Mol.Biol. (2010)

Release Date

2008-11-04

Peptides

AMYLOID LAMBDA 6 LIGHT CHAIN VARIABLE REGION PIP: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AMYLOID LAMBDA 6 LIGHT CHAIN VARIABLE REGION PIP

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