SMTL ID : 5xai.1

dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: D.9, G.10, S.11, G.12, K.13, T.14 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.10, A:S.11, A:G.12, A:K.13, A:T.14 Water bridges: A:R.90 Salt bridges: A:K.13 PO4.3: 6 residues within 4Å: Chain B: D.9, G.10, S.11, G.12, K.13, T.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.10, B:S.11, B:G.12, B:K.13, B:T.14, B:T.14 Salt bridges: B:K.13

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.2: 12 residues within 4Å: Chain A: D.9, K.13, E.36, P.37, R.47, F.64, R.68, R.90, S.94, T.95, Y.98, Q.99 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.36, A:R.90, A:Y.98 Hydrogen bonds: A:R.68, A:Q.99, A:Q.99 Water bridges: A:R.90, A:R.90 Salt bridges: A:K.13, A:R.47, A:R.90 pi-Stacking: A:F.64 TMP.4: 11 residues within 4Å: Chain B: D.9, K.13, E.36, P.37, R.47, F.64, R.68, R.90, T.95, Y.98, Q.99 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:E.36, B:F.64, B:Y.98 Hydrogen bonds: B:R.68, B:Q.99, B:Q.99 Salt bridges: B:K.13, B:R.47, B:R.90, B:R.145 pi-Stacking: B:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biswas, A. et al., Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate. FEBS J. (2017)

Release Date

2017-06-28

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Thymidylate kinase

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