SMTL ID : 1rrc.1

T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-GTC-3' SSDNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-tetramer

Ligands

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

DG-DT-DC.1: 15 residues within 4Å: Chain A: P.11, R.34, D.35, R.38, Y.50, Y.52, E.57, T.61, D.85, T.86, N.89, R.92, V.131, P.132, V.135 Protein-ligand interaction information (PLIP) not available DG-DT-DC.6: 15 residues within 4Å: Chain B: P.11, R.34, D.35, R.38, Y.50, Y.52, E.57, T.61, D.85, T.86, N.89, R.92, V.131, P.132, V.135 Protein-ligand interaction information (PLIP) not available DG-DT-DC.11: 15 residues within 4Å: Chain C: P.11, R.34, D.35, R.38, Y.50, Y.52, E.57, T.61, D.85, T.86, N.89, R.92, V.131, P.132, V.135 Protein-ligand interaction information (PLIP) not available DG-DT-DC.16: 15 residues within 4Å: Chain D: P.11, R.34, D.35, R.38, Y.50, Y.52, E.57, T.61, D.85, T.86, N.89, R.92, V.131, P.132, V.135 Protein-ligand interaction information (PLIP) not available

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.165, D.167, D.277, D.278 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.165, A:D.167, A:D.278 CA.3: 3 residues within 4Å: Chain A: W.116, Y.140, D.255 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.140 CA.7: 4 residues within 4Å: Chain B: D.165, D.167, D.277, D.278 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.165, B:D.167, B:D.278 CA.8: 3 residues within 4Å: Chain B: W.116, Y.140, D.255 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Y.140 CA.12: 4 residues within 4Å: Chain C: D.165, D.167, D.277, D.278 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.165, C:D.167, C:D.278 CA.13: 3 residues within 4Å: Chain C: W.116, Y.140, D.255 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:Y.140 CA.17: 4 residues within 4Å: Chain D: D.165, D.167, D.277, D.278 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.165, D:D.167, D:D.278 CA.18: 3 residues within 4Å: Chain D: W.116, Y.140, D.255 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:Y.140

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

DMS.4: 2 residues within 4Å: Chain A: E.108, H.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.109 Salt bridges: A:E.108 DMS.9: 2 residues within 4Å: Chain B: E.108, H.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.109 Salt bridges: B:E.108 DMS.14: 2 residues within 4Å: Chain C: E.108, H.109 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.109 Salt bridges: C:E.108 DMS.19: 2 residues within 4Å: Chain D: E.108, H.109 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.109 Salt bridges: D:E.108

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

ADP.5: 9 residues within 4Å: Chain A: P.11, G.12, G.14, K.15, S.16, T.17, R.122, R.126, K.129 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.12, A:G.14, A:K.15, A:S.16, A:S.16, A:S.16, A:T.17, A:R.126 Water bridges: A:N.33 Salt bridges: A:K.15, A:R.126, A:R.126, A:K.129, A:K.129 pi-Cation interactions: A:R.122, A:R.122 ADP.10: 9 residues within 4Å: Chain B: P.11, G.12, G.14, K.15, S.16, T.17, R.122, R.126, K.129 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.12, B:G.14, B:K.15, B:S.16, B:S.16, B:S.16, B:T.17, B:R.126 Water bridges: B:N.33 Salt bridges: B:K.15, B:R.126, B:R.126, B:K.129, B:K.129 pi-Cation interactions: B:R.122, B:R.122 ADP.15: 9 residues within 4Å: Chain C: P.11, G.12, G.14, K.15, S.16, T.17, R.122, R.126, K.129 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.12, C:G.14, C:K.15, C:S.16, C:S.16, C:S.16, C:T.17, C:T.17, C:R.126 Water bridges: C:N.33 Salt bridges: C:K.15, C:R.126, C:R.126, C:K.129, C:K.129 pi-Cation interactions: C:R.122, C:R.122 ADP.20: 9 residues within 4Å: Chain D: P.11, G.12, G.14, K.15, S.16, T.17, R.122, R.126, K.129 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:G.12, D:G.14, D:K.15, D:S.16, D:S.16, D:S.16, D:T.17, D:T.17, D:R.126 Water bridges: D:N.33 Salt bridges: D:K.15, D:R.126, D:R.126, D:K.129, D:K.129 pi-Cation interactions: D:R.122, D:R.122

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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