SMTL ID : 3ty8.1

Crystal Structure of C. Thermocellum PNKP Ligase Domain Apo Form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: D.115, D.116, M.117, Q.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.115, A:M.117 GOL.2: 4 residues within 4Å: Chain A: A.282, T.283, N.284, H.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.283, A:H.285, A:H.285 Water bridges: A:M.266 GOL.5: 8 residues within 4Å: Chain B: E.72, Q.73, K.74, H.75, E.150, F.247, V.315, K.317 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.72, B:H.75, B:K.317

2 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.3: 3 residues within 4Å: Chain A: R.339, R.343, T.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.339 Salt bridges: A:R.339, A:R.343 TAR.4: 7 residues within 4Å: Chain A: S.23, R.24, R.111 Chain B: Y.166, R.174, T.216, E.220 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.23, A:R.111 Salt bridges: A:R.111, B:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, P. et al., The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-01-25

Peptides

Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase