SMTL ID : 1w4r.1 (1 other biounit)

Structure of a type II thymidine kinase with bound dTTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-tetramer

Ligands

4 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 23 residues within 4Å: Chain A: P.28, M.29, F.30, S.31, G.32, K.33, S.34, D.59, R.61, E.99, F.102, L.125, T.128, F.129, F.134, T.164, R.166, V.173, E.174, V.175, I.176, G.177, Y.182 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.125, A:T.164, A:Y.182, A:Y.182 Hydrogen bonds: A:F.30, A:S.31, A:G.32, A:K.33, A:S.34, A:D.59, A:R.61, A:E.99, A:Q.101, A:F.129, A:R.166, A:V.173, A:V.175, A:G.177, A:Y.182 Water bridges: A:S.34, A:S.34, A:T.35 Salt bridges: A:K.33, A:K.33, A:K.33, A:R.61, A:R.61 pi-Stacking: A:F.134, A:Y.182 TTP.3: 23 residues within 4Å: Chain B: P.28, M.29, F.30, S.31, G.32, K.33, S.34, D.59, R.61, E.99, F.102, L.125, T.128, F.129, F.134, T.164, R.166, V.173, E.174, V.175, I.176, G.177, Y.182 35 PLIP interactions: 35 interactions with chain B Hydrophobic interactions: B:L.125, B:T.164, B:Y.182, B:Y.182 Hydrogen bonds: B:P.28, B:F.30, B:S.31, B:G.32, B:K.33, B:S.34, B:S.34, B:D.59, B:R.61, B:Q.101, B:F.129, B:R.166, B:V.173, B:V.175, B:G.177, B:Y.182 Water bridges: B:S.34, B:S.34, B:S.34, B:S.34, B:T.35, B:R.61, B:R.61, B:S.63 Salt bridges: B:K.33, B:K.33, B:K.33, B:R.61, B:R.61 pi-Stacking: B:F.134, B:Y.182 TTP.5: 23 residues within 4Å: Chain C: P.28, M.29, F.30, S.31, G.32, K.33, S.34, D.59, R.61, E.99, F.102, L.125, T.128, F.129, F.134, T.164, R.166, V.173, E.174, V.175, I.176, G.177, Y.182 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:L.125, C:T.164, C:Y.182, C:Y.182 Hydrogen bonds: C:F.30, C:S.31, C:G.32, C:K.33, C:S.34, C:D.59, C:Q.101, C:F.129, C:R.166, C:V.173, C:V.175, C:G.177, C:Y.182 Water bridges: C:F.30, C:K.33, C:K.33, C:S.34, C:S.34, C:T.35 Salt bridges: C:K.33, C:K.33, C:K.33, C:R.61, C:R.61 pi-Stacking: C:F.134, C:Y.182 TTP.7: 24 residues within 4Å: Chain D: M.29, F.30, S.31, G.32, K.33, S.34, D.59, R.61, D.98, E.99, Q.101, F.102, L.125, T.128, F.129, F.134, T.164, R.166, V.173, E.174, V.175, I.176, G.177, Y.182 33 PLIP interactions: 33 interactions with chain D Hydrophobic interactions: D:L.125, D:T.164, D:Y.182, D:Y.182 Hydrogen bonds: D:F.30, D:S.31, D:G.32, D:K.33, D:S.34, D:S.34, D:S.34, D:S.34, D:D.59, D:E.99, D:Q.101, D:L.125, D:F.129, D:R.166, D:V.173, D:V.175, D:G.177, D:Y.182 Water bridges: D:K.33, D:K.33, D:R.61, D:R.61, D:E.99 Salt bridges: D:K.33, D:K.33, D:K.33, D:R.61 pi-Stacking: D:F.134, D:Y.182

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.154, C.157, C.186, C.189 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.154, A:C.157, A:C.186, A:C.189 ZN.4: 4 residues within 4Å: Chain B: C.154, C.157, C.186, C.189 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.154, B:C.157, B:C.186, B:C.189 ZN.6: 4 residues within 4Å: Chain C: C.154, C.157, C.186, C.189 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.154, C:C.157, C:C.186, C:C.189 ZN.8: 4 residues within 4Å: Chain D: C.154, C.157, C.186, C.189 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.154, D:C.157, D:C.186, D:C.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birringer, M.S. et al., Structure of a Type II Thymidine Kinase with Bound Dttp. FEBS Lett. (2005)

Release Date

2005-02-01

Peptides

THYMIDINE KINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

THYMIDINE KINASE

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