SMTL ID : 4uxj.3 (2 other biounits)

Leishmania major Thymidine Kinase in complex with dTTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.148, C.151, C.181, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.148, A:C.151, A:C.181, A:C.184 ZN.4: 4 residues within 4Å: Chain B: C.148, C.151, C.181, C.184 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.148, B:C.151, B:C.181, B:C.184 ZN.7: 4 residues within 4Å: Chain C: C.148, C.151, C.181, C.184 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.148, C:C.151, C:C.181, C:C.184 ZN.10: 4 residues within 4Å: Chain D: C.148, C.151, C.181, C.184 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.148, D:C.151, D:C.181, D:C.184

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

TTP.2: 22 residues within 4Å: Chain A: M.21, F.22, A.23, G.24, K.25, T.26, E.93, Q.95, F.96, L.119, D.122, Y.123, F.128, T.159, R.161, Q.168, E.169, L.170, I.171, G.172, Y.177 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.119, A:T.159, A:Y.177, A:Y.177 Hydrogen bonds: A:F.22, A:A.23, A:G.24, A:K.25, A:T.26, A:T.26, A:E.93, A:Q.95, A:Y.123, A:R.161, A:Q.168, A:L.170, A:G.172, A:Y.177 Salt bridges: A:K.25, A:K.25, A:K.25 TTP.5: 21 residues within 4Å: Chain B: M.21, F.22, A.23, G.24, K.25, T.26, E.93, Q.95, F.96, L.119, D.122, Y.123, F.128, T.159, Q.168, E.169, L.170, I.171, G.172, Y.177 Ligands: MG.6 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.119, B:T.159, B:Y.177, B:Y.177 Hydrogen bonds: B:F.22, B:A.23, B:G.24, B:K.25, B:T.26, B:T.26, B:T.26, B:Q.95, B:Y.123, B:Q.168, B:L.170, B:G.172, B:Y.177 Salt bridges: B:K.25, B:K.25, B:K.25 TTP.8: 22 residues within 4Å: Chain C: M.21, F.22, A.23, G.24, K.25, T.26, E.93, Q.95, F.96, L.119, D.122, Y.123, F.128, T.159, R.161, Q.168, E.169, L.170, I.171, G.172, Y.177 Ligands: MG.9 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:L.119, C:T.159, C:Y.177, C:Y.177 Hydrogen bonds: C:P.20, C:F.22, C:A.23, C:G.24, C:K.25, C:T.26, C:T.26, C:E.93, C:E.93, C:Q.95, C:Y.123, C:R.161, C:Q.168, C:L.170, C:G.172, C:Y.177 Salt bridges: C:K.25, C:K.25, C:K.25 TTP.11: 22 residues within 4Å: Chain D: M.21, F.22, A.23, G.24, K.25, T.26, E.93, Q.95, F.96, L.119, D.122, Y.123, F.128, T.159, R.161, Q.168, E.169, L.170, I.171, G.172, Y.177 Ligands: MG.12 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:L.119, D:T.159, D:Y.177, D:Y.177 Hydrogen bonds: D:F.22, D:A.23, D:G.24, D:K.25, D:T.26, D:T.26, D:Q.95, D:Y.123, D:R.161, D:Q.168, D:L.170, D:G.172, D:Y.177 Salt bridges: D:K.25, D:K.25, D:K.25 pi-Stacking: D:F.128, D:Y.177

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.26, E.93 Ligands: TTP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.26 MG.6: 2 residues within 4Å: Chain B: T.26 Ligands: TTP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.26 MG.9: 2 residues within 4Å: Chain C: T.26 Ligands: TTP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.26 MG.12: 2 residues within 4Å: Chain D: T.26 Ligands: TTP.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timm, J. et al., Structural and Kinetic Characterization of Thymidine Kinase from Leishmania Major. Plos Negl Trop Dis (2015)

Release Date

2015-05-27

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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