SMTL ID : 1yj5.1 (1 other biounit)

Molecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: F.233, P.234, G.235, A.236, G.237, K.238, S.239, R.324 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.235, A:A.236, A:G.237, A:K.238, A:S.239 Water bridges: A:R.324, A:R.324 Salt bridges: A:K.238, A:R.324 SO4.2: 4 residues within 4Å: Chain A: R.256, S.261, W.262, Q.263 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.262, A:Q.263 Water bridges: A:R.256 Salt bridges: A:R.256 SO4.3: 3 residues within 4Å: Chain A: N.78, M.80, R.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.78 Salt bridges: A:R.119 SO4.4: 8 residues within 4Å: Chain B: F.233, P.234, G.235, A.236, G.237, K.238, S.239, R.324 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.235, B:A.236, B:G.237, B:K.238, B:S.239 Water bridges: B:T.240, B:R.324 Salt bridges: B:K.238, B:R.324 SO4.5: 7 residues within 4Å: Chain A: A.236, G.237, F.241, I.361, P.362, F.363, R.364 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.236, A:P.362, A:R.364 SO4.6: 3 residues within 4Å: Chain B: R.256, S.261, W.262 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.262 Salt bridges: B:R.256 SO4.7: 6 residues within 4Å: Chain A: R.256, G.260 Chain B: A.193, A.194, R.195, F.196 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.260, B:A.193 Salt bridges: A:R.256 SO4.8: 6 residues within 4Å: Chain A: G.20, K.22, Q.24, Y.71, K.72, L.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.22, A:Q.24, A:L.73 SO4.9: 8 residues within 4Å: Chain B: G.20, V.21, K.22, Q.24, Y.71, K.72, L.73, P.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.22, B:L.73 SO4.10: 8 residues within 4Å: Chain A: P.199, F.201, P.203, H.319, R.322, F.380, S.381, E.382 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.381, A:E.382, A:E.382 Salt bridges: A:H.319, A:R.322 SO4.11: 7 residues within 4Å: Chain B: F.201, P.203, H.319, R.322, F.380, S.381, E.382 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.381, B:E.382, B:E.382 Salt bridges: B:H.319, B:R.322 SO4.12: 8 residues within 4Å: Chain B: A.236, G.237, F.241, F.310, I.361, P.362, F.363, R.364 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.364, B:R.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bernstein, N.K. et al., The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase. Mol.Cell (2005)

Release Date

2005-03-15

Peptides

5' polynucleotide kinase-3' phosphatase catalytic domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5' polynucleotide kinase-3' phosphatase catalytic domain