SMTL ID : 1rc8.1

T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

4 x DG- DT- DC: 5'-D(*GP*TP*CP*AP*C)-3'(Non-covalent)

DG-DT-DC.1: 14 residues within 4Å: Chain A: R.34, D.35, R.38, Y.52, G.58, T.61, D.85, T.86, N.87, N.89, R.92, V.131, P.132, V.135 Protein-ligand interaction information (PLIP) not available DG-DT-DC.5: 14 residues within 4Å: Chain B: R.34, D.35, R.38, Y.52, G.58, T.61, D.85, T.86, N.87, N.89, R.92, V.131, P.132, V.135 Protein-ligand interaction information (PLIP) not available DG-DT-DC.9: 14 residues within 4Å: Chain C: R.34, D.35, R.38, Y.52, G.58, T.61, D.85, T.86, N.87, N.89, R.92, V.131, P.132, V.135 Protein-ligand interaction information (PLIP) not available DG-DT-DC.13: 14 residues within 4Å: Chain D: R.34, D.35, R.38, Y.52, G.58, T.61, D.85, T.86, N.87, N.89, R.92, V.131, P.132, V.135 Protein-ligand interaction information (PLIP) not available

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: D.165, D.167, D.278 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.165, A:D.167, A:D.278, H2O.1, H2O.1 CA.6: 3 residues within 4Å: Chain B: D.165, D.167, D.278 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.165, B:D.167, B:D.278, H2O.4, H2O.4 CA.10: 3 residues within 4Å: Chain C: D.165, D.167, D.278 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.165, C:D.167, C:D.278, H2O.6, H2O.6 CA.14: 3 residues within 4Å: Chain D: D.165, D.167, D.278 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.165, D:D.167, D:D.278, H2O.8, H2O.8

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

DMS.3: 2 residues within 4Å: Chain A: E.108, H.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.109 DMS.7: 2 residues within 4Å: Chain B: E.108, H.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.109 DMS.11: 2 residues within 4Å: Chain C: E.108, H.109 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.109 DMS.15: 2 residues within 4Å: Chain D: E.108, H.109 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.109

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

ADP.4: 10 residues within 4Å: Chain A: P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.126, K.129 Chain D: E.45 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.12, A:S.13, A:G.14, A:G.14, A:S.16, A:S.16, A:T.17, A:T.17, A:K.129, A:K.129 Salt bridges: A:K.15, A:R.126 ADP.8: 10 residues within 4Å: Chain B: P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.126, K.129 Chain C: E.45 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.12, B:S.13, B:G.14, B:G.14, B:S.16, B:S.16, B:T.17, B:T.17, B:K.129, B:K.129 Salt bridges: B:K.15, B:R.126 ADP.12: 10 residues within 4Å: Chain B: E.45 Chain C: P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.126, K.129 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.12, C:S.13, C:G.14, C:G.14, C:S.16, C:S.16, C:T.17, C:K.129, C:K.129 Salt bridges: C:K.15, C:R.126 ADP.16: 10 residues within 4Å: Chain A: E.45 Chain D: P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.126, K.129 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.12, D:S.13, D:G.14, D:G.14, D:S.16, D:S.16, D:T.17, D:K.129, D:K.129 Salt bridges: D:K.15, D:R.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eastberg, J.H. et al., Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase. Nucleic Acids Res. (2004)

Release Date

2004-02-17

Peptides

Polynucleotide kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Polynucleotide kinase

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