SMTL ID : 5x99.1

T18V mutant of thermus thermophilus HB8 thymidylate kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 6 residues within 4Å: Chain A: L.11, G.13, S.14, G.15, K.16, R.139 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.13, A:S.14, A:G.15, A:K.16, A:R.139 Water bridges: A:G.15, A:T.17, A:T.17, A:R.91, A:R.139 FMT.6: 7 residues within 4Å: Chain B: L.11, D.12, G.13, S.14, G.15, K.16, T.17 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.13, B:S.14, B:G.15, B:T.17 Water bridges: B:T.17, B:V.18

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Y.102, R.157, E.160, G.161 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:R.157, H2O.4, H2O.5, H2O.6 MG.3: 3 residues within 4Å: Chain A: P.134, E.135, A.137 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:P.134, A:A.137 MG.4: 5 residues within 4Å: Chain A: T.7, E.9, Y.92, D.94, T.127 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.7, A:E.9, A:D.94, H2O.4 MG.5: 5 residues within 4Å: Chain A: Y.62, S.66, R.69, L.93, A.115 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.62, A:S.66 MG.7: 3 residues within 4Å: Chain B: P.109, R.112, E.113 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:P.109, H2O.9 MG.8: 5 residues within 4Å: Chain B: Y.62, S.66, R.69, L.93, A.115 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.62, B:S.66 MG.9: 5 residues within 4Å: Chain B: T.7, E.9, Y.92, D.94, T.127 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.7, B:E.9, B:D.94, H2O.7 MG.10: 4 residues within 4Å: Chain B: R.112, L.165, A.168, E.169 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:L.165, B:E.169, H2O.7, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaudhary, S.K. et al., Structural and functional roles of dynamically correlated residues in thymidylate kinase. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-03-14

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase