SMTL ID : 2j9r.1

Thymidine kinase from B. anthracis in complex with dT.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.165, C.168, C.203, C.206 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.165, A:C.168, A:C.203, A:C.206 ZN.4: 4 residues within 4Å: Chain B: C.165, C.168, C.203, C.206 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.165, B:C.168, B:C.203, B:C.206 ZN.7: 4 residues within 4Å: Chain C: C.165, C.168, C.203, C.206 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.165, C:C.168, C:C.203, C:C.206 ZN.10: 4 residues within 4Å: Chain D: C.165, C.168, C.203, C.206 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.165, D:C.168, D:C.203, D:C.206

4 x THM: THYMIDINE(Non-covalent)

THM.2: 15 residues within 4Å: Chain A: M.37, E.109, F.112, L.136, D.139, F.140, F.145, T.175, R.177, I.190, I.191, L.192, V.193, G.194, Y.199 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.175, A:Y.199, A:Y.199 Hydrogen bonds: A:F.140, A:R.177, A:I.190, A:L.192, A:G.194 pi-Stacking: A:F.145 THM.5: 15 residues within 4Å: Chain B: M.37, E.109, F.112, L.136, D.139, F.140, F.145, T.175, R.177, I.190, I.191, L.192, V.193, G.194, Y.199 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.175, B:Y.199, B:Y.199 Hydrogen bonds: B:F.140, B:R.177, B:I.190, B:L.192, B:G.194, B:Y.199 pi-Stacking: B:F.145 THM.8: 15 residues within 4Å: Chain C: M.37, E.109, F.112, L.136, D.139, F.140, F.145, T.175, R.177, I.190, I.191, L.192, V.193, G.194, Y.199 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:T.175, C:Y.199, C:Y.199 Hydrogen bonds: C:F.140, C:R.177, C:I.190, C:L.192, C:G.194, C:Y.199 pi-Stacking: C:F.145 THM.11: 15 residues within 4Å: Chain D: M.37, E.109, F.112, L.136, D.139, F.140, F.145, T.175, R.177, I.190, I.191, L.192, V.193, G.194, Y.199 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:T.175, D:Y.199, D:Y.199 Hydrogen bonds: D:F.140, D:R.177, D:I.190, D:L.192, D:G.194 pi-Stacking: D:F.145

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: S.36, M.37, F.38, S.39, G.40, K.41, S.42 Chain C: R.51 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:F.38, A:S.39, A:G.40, A:K.41, A:S.42, C:R.51 Water bridges: A:G.40, A:K.41, A:K.41, A:E.43 Salt bridges: A:K.41 PO4.6: 8 residues within 4Å: Chain B: S.36, M.37, F.38, S.39, G.40, K.41, S.42 Chain D: R.51 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:F.38, B:S.39, B:G.40, B:K.41, B:S.42, D:R.51 Water bridges: B:G.40, B:K.41, B:K.41, B:E.43 Salt bridges: B:K.41 PO4.9: 8 residues within 4Å: Chain A: R.51 Chain C: S.36, M.37, F.38, S.39, G.40, K.41, S.42 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:F.38, C:S.39, C:G.40, C:K.41, C:S.42, A:R.51 Water bridges: C:G.40, C:K.41, C:K.41, C:E.43 Salt bridges: C:K.41 PO4.12: 8 residues within 4Å: Chain B: R.51 Chain D: S.36, M.37, F.38, S.39, G.40, K.41, S.42 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:F.38, D:S.39, D:G.40, D:K.41, D:S.42, B:R.51 Water bridges: D:G.40, D:K.41, D:K.41, D:E.43 Salt bridges: D:K.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosinska, U. et al., Structural Studies of Thymidine Kinases from Bacillus Anthracis and Bacillus Cereus Provide Insights Into Quaternary Structure and Conformational Changes Upon Substrate Binding. FEBS J. (2007)

Release Date

2007-01-23

Peptides

THYMIDINE KINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

THYMIDINE KINASE