SMTL ID : 4uxh.1

Leishmania major Thymidine Kinase in complex with AP5dT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x T5A: P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE(Non-covalent)

T5A.1: 29 residues within 4Å: Chain A: M.14, F.15, A.16, G.17, K.18, T.19, T.20, M.23, K.40, D.44, R.46, Y.47, D.85, E.86, Q.88, F.89, L.112, D.115, Y.116, F.121, T.152, R.154, Q.161, E.162, L.163, I.164, G.165, Y.170 Chain D: H.31 41 PLIP interactions: 37 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.112, A:F.121, A:T.152, A:Y.170, A:Y.170 Hydrogen bonds: A:F.15, A:A.16, A:G.17, A:K.18, A:T.19, A:T.19, A:T.19, A:T.19, A:T.20, A:K.40, A:D.44, A:R.46, A:D.85, A:E.86, A:Q.88, A:L.112, A:Y.116, A:R.154, A:Q.161, A:L.163, A:G.165 Water bridges: A:K.18, A:K.18, A:T.20, A:R.46, A:R.46, A:Y.47, A:Y.47, D:H.31, D:H.31 Salt bridges: A:K.18, A:K.18, A:K.18, A:R.46, D:H.31, D:H.31 T5A.3: 27 residues within 4Å: Chain B: M.14, F.15, A.16, G.17, K.18, T.19, T.20, M.23, K.40, D.44, D.85, E.86, Q.88, F.89, L.112, D.115, Y.116, F.121, T.152, R.154, Q.161, E.162, L.163, I.164, G.165, Y.170 Chain C: H.31 31 PLIP interactions: 28 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.112, B:T.152, B:Y.170, B:Y.170 Hydrogen bonds: B:F.15, B:A.16, B:G.17, B:K.18, B:T.19, B:T.19, B:T.19, B:T.20, B:D.44, B:D.85, B:Q.88, B:L.112, B:Y.116, B:R.154, B:Q.161, B:L.163, B:G.165, B:Y.170 Water bridges: B:T.20, B:E.86, C:H.31 Salt bridges: B:K.18, B:K.18, B:K.18, C:H.31, C:H.31 pi-Stacking: B:F.121 T5A.5: 29 residues within 4Å: Chain B: H.31 Chain C: M.14, F.15, A.16, G.17, K.18, T.19, T.20, M.23, K.40, D.44, R.46, Y.47, D.85, E.86, Q.88, F.89, L.112, D.115, Y.116, F.121, T.152, R.154, Q.161, E.162, L.163, I.164, G.165, Y.170 38 PLIP interactions: 35 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.112, C:F.121, C:T.152, C:Y.170, C:Y.170 Hydrogen bonds: C:F.15, C:A.16, C:G.17, C:K.18, C:T.19, C:T.19, C:T.19, C:T.19, C:T.20, C:K.40, C:D.44, C:R.46, C:D.85, C:Q.88, C:L.112, C:Y.116, C:R.154, C:Q.161, C:L.163, C:G.165, C:Y.170 Water bridges: C:K.18, C:K.18, C:T.20, C:R.46, C:R.46, B:H.31 Salt bridges: C:K.18, C:K.18, C:K.18, C:R.46, B:H.31, B:H.31 T5A.7: 27 residues within 4Å: Chain A: H.31 Chain D: M.14, F.15, A.16, G.17, K.18, T.19, T.20, M.23, K.40, D.44, D.85, E.86, Q.88, F.89, L.112, D.115, Y.116, F.121, T.152, R.154, Q.161, E.162, L.163, I.164, G.165, Y.170 31 PLIP interactions: 28 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.112, D:T.152, D:Y.170, D:Y.170 Hydrogen bonds: D:F.15, D:A.16, D:G.17, D:K.18, D:T.19, D:T.19, D:T.19, D:D.44, D:D.85, D:E.86, D:Q.88, D:L.112, D:Y.116, D:R.154, D:Q.161, D:L.163, D:G.165 Water bridges: D:T.20, D:T.20, D:E.86, A:H.31 Salt bridges: D:K.18, D:K.18, D:K.18, A:H.31, A:H.31 pi-Stacking: D:F.121

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.141, C.144, C.174, C.177 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.141, A:C.144, A:C.174, A:C.177 ZN.4: 4 residues within 4Å: Chain B: C.141, C.144, C.174, C.177 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.141, B:C.144, B:C.174, B:C.177 ZN.6: 4 residues within 4Å: Chain C: C.141, C.144, C.174, C.177 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.141, C:C.144, C:C.174, C:C.177 ZN.8: 4 residues within 4Å: Chain D: C.141, C.144, C.174, C.177 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.141, D:C.144, D:C.174, D:C.177

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
A

D
B

THYMIDINE KINASE

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