SMTL ID : 1rpz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

DT-DG-DC.1: 14 residues within 4Å: Chain A: P.11, R.34, D.35, R.38, Y.52, E.57, T.61, D.85, T.86, N.89, R.92, V.131, V.135, M.139 Protein-ligand interaction information (PLIP) not available DT-DG-DC.6: 14 residues within 4Å: Chain B: P.11, R.34, D.35, R.38, Y.52, E.57, T.61, D.85, T.86, N.89, R.92, V.131, V.135, M.139 Protein-ligand interaction information (PLIP) not available DT-DG-DC.11: 14 residues within 4Å: Chain C: P.11, R.34, D.35, R.38, Y.52, E.57, T.61, D.85, T.86, N.89, R.92, V.131, V.135, M.139 Protein-ligand interaction information (PLIP) not available DT-DG-DC.16: 14 residues within 4Å: Chain D: P.11, R.34, D.35, R.38, Y.52, E.57, T.61, D.85, T.86, N.89, R.92, V.131, V.135, M.139 Protein-ligand interaction information (PLIP) not available

4 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.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.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.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

8 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.4: 5 residues within 4Å: Chain A: E.97, A.100, W.105, K.106, V.107 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.97 DMS.8: 2 residues within 4Å: Chain B: E.108, H.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.109 DMS.9: 5 residues within 4Å: Chain B: E.97, A.100, W.105, K.106, V.107 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.97 DMS.13: 2 residues within 4Å: Chain C: E.108, H.109 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.109 DMS.14: 5 residues within 4Å: Chain C: E.97, A.100, W.105, K.106, V.107 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:E.97 DMS.18: 2 residues within 4Å: Chain D: E.108, H.109 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.109 DMS.19: 5 residues within 4Å: Chain D: E.97, A.100, W.105, K.106, V.107 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:E.97

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

ADP.5: 11 residues within 4Å: Chain A: C.10, P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.126, K.129 Chain D: E.45 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:C.10, A:G.12, A:S.13, A:G.14, A:G.14, A:K.15, A:S.16, A:T.17, A:T.17, A:R.126, A:K.129, D:E.45 Salt bridges: A:K.15, A:R.126, A:R.126 ADP.10: 11 residues within 4Å: Chain B: C.10, P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.126, K.129 Chain C: E.45 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:C.10, B:G.12, B:S.13, B:G.14, B:G.14, B:K.15, B:S.16, B:T.17, B:T.17, B:R.126, B:K.129, C:E.45 Salt bridges: B:K.15, B:R.126, B:R.126 ADP.15: 11 residues within 4Å: Chain B: E.45 Chain C: C.10, P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.126, K.129 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:C.10, C:G.12, C:S.13, C:G.14, C:G.14, C:K.15, C:S.16, C:T.17, C:R.126, C:K.129, B:E.45 Salt bridges: C:K.15, C:R.126, C:R.126 ADP.20: 11 residues within 4Å: Chain A: E.45 Chain D: C.10, P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.126, K.129 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:C.10, D:G.12, D:S.13, D:G.14, D:G.14, D:K.15, D:S.16, D:T.17, D:R.126, D:K.129, A:E.45 Salt bridges: D:K.15, D:R.126, 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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