SMTL ID : 3w34.1

Ternary complex of Thermus thermophilus HB8 uridine-cytidine kinase with substrates

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)

CTN.1: 15 residues within 4Å: Chain A: T.15, D.40, Y.43, Y.59, D.60, Y.88, F.90, Y.93, I.113, R.142, R.150, R.152, Q.160, V.165 Ligands: ACP.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.43, A:Y.59, A:Y.88 Hydrogen bonds: A:T.15, A:T.15, A:Y.43, A:Y.88, A:Y.88, A:R.142, A:R.142, A:R.150, A:R.152, A:R.152, A:Q.160 Water bridges: A:K.19, A:D.40, A:D.60, A:D.60, A:I.113, A:R.145, A:R.145 pi-Stacking: A:F.90 CTN.3: 14 residues within 4Å: Chain B: T.15, D.40, Y.43, Y.59, D.60, Y.88, F.90, Y.93, R.142, R.150, R.152, Q.160, V.165 Ligands: ACP.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.43, B:Y.59, B:Y.88 Hydrogen bonds: B:T.15, B:Y.88, B:R.142, B:R.142, B:R.150, B:R.152, B:R.152, B:Q.160 Water bridges: B:D.40, B:D.60, B:D.60, B:R.145, B:R.145 pi-Stacking: B:F.90

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 10 residues within 4Å: Chain A: T.15, A.16, S.17, G.18, K.19, T.20, T.21, I.113, R.145 Ligands: CTN.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.16, A:S.17, A:G.18, A:K.19, A:K.19, A:K.19, A:T.20, A:T.21, A:T.21, A:R.145, A:R.145 Water bridges: A:K.19, A:E.111, A:R.150, A:R.150 ACP.4: 11 residues within 4Å: Chain B: G.14, T.15, A.16, S.17, G.18, K.19, T.20, T.21, I.113, R.145 Ligands: CTN.3 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.15, B:T.15, B:A.16, B:S.17, B:G.18, B:K.19, B:K.19, B:T.20, B:T.20, B:T.20, B:T.21, B:R.145, B:R.145 Water bridges: B:D.40, B:R.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tomoike, F. et al., Structural and Biochemical Studies on the Reaction Mechanism of Uridine-Cytidine Kinase. Protein J. (2015)

Release Date

2013-12-11

Peptides

Uridine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uridine kinase

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