SMTL ID : 3ty5.1

Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 13 residues within 4Å: Chain A: M.39, Q.73, K.74, G.77, S.78, R.79, R.108, E.150, F.247, V.315, K.317, K.335 Chain B: K.182 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.78, A:R.79, A:R.79, A:R.108, A:K.317 Water bridges: A:K.74, A:K.74, A:R.108, A:E.150, A:T.283, A:K.317, A:K.335, A:R.337, A:Y.341, A:Y.341, B:E.179, B:K.182, B:K.182 Salt bridges: A:K.74, A:R.108, A:R.108, A:K.335, B:K.182 pi-Stacking: A:F.247

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 14 residues within 4Å: Chain B: T.38, M.39, Q.73, K.74, H.75, R.79, R.108, E.150, F.247, V.315, K.317, K.335, K.367, L.413 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.38, B:T.38, B:M.39, B:H.75, B:R.79, B:K.317, B:L.413 Water bridges: B:R.108, B:R.108 Salt bridges: B:K.74, B:R.108, B:K.335, B:K.335, B:K.367 pi-Stacking: B:F.247

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 12 residues within 4Å: Chain B: Y.34, L.35, P.36, P.37, M.39, D.148, H.248, A.333, E.374, F.375, G.378, M.379 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.34, B:E.374, B:G.378 Water bridges: B:P.37, B:R.79

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