SMTL ID : 4ou1.1

Crystal structure of a computationally designed retro-aldolase covalently bound to folding probe 1 [(6-methoxynaphthalen-2-yl)(oxiran-2-yl)methanol]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x 2V7: (1S,2S)-1-(6-methoxynaphthalen-2-yl)propane-1,2-diol(Covalent)

2V7.1: 15 residues within 4Å: Chain A: K.53, D.56, P.57, S.58, F.89, Y.110, R.182, D.183, W.184, T.186, G.187, K.210, E.211 Ligands: BEZ.2, PO4.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.57, A:K.210 Hydrogen bonds: A:D.56, A:Y.110, A:E.211

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.2: 9 residues within 4Å: Chain A: Y.110, I.133, K.135, I.159, N.161, A.180, W.184, K.210 Ligands: 2V7.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.133, A:K.135, A:I.159, A:W.184 Hydrogen bonds: A:Y.110, A:Y.110 Salt bridges: A:K.210

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 9 residues within 4Å: Chain A: K.53, D.56, S.58, L.60, R.182, G.233, S.234 Ligands: 2V7.1, PO4.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.58, A:S.234 Water bridges: A:R.182, A:R.182 Salt bridges: A:K.53, A:R.182 PO4.4: 6 residues within 4Å: Chain A: R.182, I.189, E.211, G.212, I.213 Ligands: PO4.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.212, A:I.213 Water bridges: A:G.233, A:G.233, A:G.233 Salt bridges: A:R.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-03-05

Peptides

Retro-aldolase, design RA114: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Retro-aldolase, design RA114

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