SMTL ID : 4dxx.1

TGT K52M mutant crystallized at pH 8.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.318, C.320, C.323, H.349 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.318, A:C.320, A:C.323, A:H.349 ZN.6: 4 residues within 4Å: Chain B: C.318, C.320, C.323, H.349 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.318, B:C.320, B:C.323, B:H.349

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: A.305, S.308, H.332, R.336 Chain B: R.82 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.308, A:S.308, A:H.332, B:R.82, B:R.82 GOL.7: 5 residues within 4Å: Chain A: R.82 Chain B: A.305, S.308, H.332, R.336 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.308, B:S.308, B:H.332, A:R.82, A:R.82

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 5 residues within 4Å: Chain A: A.61, T.62, C.320, A.321, E.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.321, A:E.348 Salt bridges: A:E.348 DMS.4: 6 residues within 4Å: Chain A: R.38, T.62, G.63, Q.355, Q.356, Q.359 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.356 DMS.5: 7 residues within 4Å: Chain A: P.56, E.57, R.60, G.94, W.95, D.96, R.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.96 Salt bridges: A:D.96 DMS.8: 5 residues within 4Å: Chain B: A.61, T.62, C.320, A.321, E.348 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.321 Salt bridges: B:E.348 DMS.9: 6 residues within 4Å: Chain B: R.38, T.62, G.63, Q.355, Q.356, Q.359 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.356 DMS.10: 7 residues within 4Å: Chain B: P.56, E.57, R.60, G.94, W.95, D.96, R.97 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.96 Salt bridges: B:D.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jakobi, S. et al., Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme. Proteins (2014)

Release Date

2013-03-27

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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