SMTL ID : 1ly1.1

Structure and Mechanism of T4 Polynucleotide Kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: C.10, P.11, G.12, S.13, G.14, K.15, S.16, R.126 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.12, A:S.13, A:G.14, A:K.15, A:S.16 Water bridges: A:G.14, A:K.15, A:T.17 Salt bridges: A:K.15, A:R.126 SO4.2: 6 residues within 4Å: Chain A: R.34, D.35, R.38, D.85, T.86, N.87 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.86, A:T.86, A:N.87 Water bridges: A:R.34, A:R.38, A:Y.52, A:Y.52, A:T.86, A:T.86 Salt bridges: A:R.38 SO4.3: 3 residues within 4Å: Chain A: V.107, E.108, H.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.109 SO4.4: 4 residues within 4Å: Chain A: R.93, E.97, H.109, Y.146 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.93, A:H.109 SO4.5: 8 residues within 4Å: Chain B: C.10, P.11, G.12, S.13, G.14, K.15, S.16, R.126 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.12, B:S.13, B:G.14, B:K.15, B:S.16 Water bridges: B:G.14, B:K.15, B:T.17 Salt bridges: B:K.15, B:R.126 SO4.6: 6 residues within 4Å: Chain B: R.34, D.35, R.38, D.85, T.86, N.87 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.86, B:T.86, B:T.86, B:N.87 Water bridges: B:R.34, B:R.38 Salt bridges: B:R.38 SO4.7: 3 residues within 4Å: Chain B: V.107, E.108, H.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.109 SO4.8: 4 residues within 4Å: Chain B: R.93, E.97, H.109, Y.146 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.93, B:H.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L.K. et al., Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme. EMBO J. (2002)

Release Date

2002-07-17

Peptides

polynucleotide kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

polynucleotide kinase