SMTL ID : 5fuw.1

catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP or dThd

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

2 x QBT: [(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3-DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

QBT.1: 17 residues within 4Å: Chain A: M.12, K.16, E.84, Q.86, F.87, L.110, D.113, Y.114, T.150, R.152, R.159, K.160, L.161, V.162, G.163, Y.168 Ligands: PO4.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.110, A:T.150, A:Y.168, A:Y.168 Hydrogen bonds: A:E.84, A:Q.86, A:Y.114, A:R.152, A:R.159, A:L.161, A:G.163, A:Y.168 Water bridges: A:K.16, A:E.84, A:G.163 Salt bridges: A:K.16 QBT.8: 17 residues within 4Å: Chain C: M.12, K.16, E.84, Q.86, F.87, L.110, D.113, Y.114, T.150, R.152, R.159, K.160, L.161, V.162, G.163, Y.168 Ligands: PO4.9 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.110, C:T.150, C:Y.168, C:Y.168 Hydrogen bonds: C:E.84, C:Q.86, C:Y.114, C:R.152, C:R.159, C:L.161, C:G.163 Water bridges: C:K.16, C:T.17, C:T.17, C:G.163 Salt bridges: C:K.16

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

PO4.2: 8 residues within 4Å: Chain A: P.11, F.13, A.14, G.15, K.16, T.17 Ligands: QBT.1, PO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.13, A:A.14, A:G.15, A:K.16, A:T.17 Water bridges: A:K.16 Salt bridges: A:K.16 PO4.3: 5 residues within 4Å: Chain A: G.15, K.16, T.17, T.18 Ligands: PO4.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.17, A:T.18, A:T.18, A:T.18 Water bridges: A:F.13, A:F.13, A:A.14, A:G.15, A:G.15 PO4.5: 6 residues within 4Å: Chain B: P.11, F.13, A.14, G.15, K.16, T.17 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:F.13, B:A.14, B:G.15, B:K.16, B:T.17 Water bridges: B:F.13, B:G.15, B:K.16 Salt bridges: B:K.16 PO4.9: 8 residues within 4Å: Chain C: P.11, F.13, A.14, G.15, K.16, T.17 Ligands: QBT.8, PO4.10 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:F.13, C:A.14, C:G.15, C:K.16, C:T.17, C:T.17 Water bridges: C:K.16 Salt bridges: C:K.16 PO4.10: 5 residues within 4Å: Chain C: G.15, K.16, T.17, T.18 Ligands: PO4.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.17, C:T.17, C:T.18, C:T.18 Water bridges: C:F.13, C:F.13, C:A.14, C:G.15, C:G.15 PO4.12: 6 residues within 4Å: Chain D: P.11, F.13, A.14, G.15, K.16, T.17 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:F.13, D:A.14, D:G.15, D:K.16, D:T.17, D:T.17 Water bridges: D:F.13, D:G.15, D:K.16 Salt bridges: D:K.16

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.139, C.142, C.172, C.175 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.139, A:C.142, A:C.172, A:C.175 ZN.7: 4 residues within 4Å: Chain B: C.139, C.142, C.172, C.175 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.139, B:C.142, B:C.172, B:C.175 ZN.11: 4 residues within 4Å: Chain C: C.139, C.142, C.172, C.175 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.139, C:C.142, C:C.172, C:C.175 ZN.14: 4 residues within 4Å: Chain D: C.139, C.142, C.172, C.175 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.139, D:C.142, D:C.172, D:C.175

2 x THM: THYMIDINE(Non-covalent)

THM.6: 15 residues within 4Å: Chain B: M.12, E.84, Q.86, F.87, L.110, D.113, Y.114, T.150, R.152, R.159, K.160, L.161, V.162, G.163, Y.168 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.110, B:T.150, B:Y.168, B:Y.168 Hydrogen bonds: B:Q.86, B:Y.114, B:R.152, B:R.159, B:L.161, B:G.163, B:Y.168 Water bridges: B:K.16, B:K.16, B:E.84, B:E.84 THM.13: 15 residues within 4Å: Chain D: M.12, E.84, Q.86, F.87, L.110, D.113, Y.114, T.150, R.152, R.159, K.160, L.161, V.162, G.163, Y.168 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.110, D:T.150, D:Y.168, D:Y.168 Hydrogen bonds: D:Q.86, D:Y.114, D:R.152, D:R.159, D:L.161, D:G.163, D:Y.168 Water bridges: D:K.16, D:K.16, D:E.84, D:E.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valente, M. et al., Cell Cycle Regulation and Novel Structural Features of Thymidine Kinase, an Essential Enzyme in Trypanosoma Brucei. Mol.Microbiol. (2016)

Release Date

2016-07-27

Peptides

THYMDINE KINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

THYMDINE KINASE

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