SMTL ID : 1n5k.1

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE (RESOLUTION 2.1 A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: G.10, A.11, G.12, K.13, R.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13 Salt bridges: A:K.13 ACT.2: 4 residues within 4Å: Chain A: R.122, I.123, R.127 Chain B: H.56 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.122, A:R.127, B:H.56 Water bridges: B:E.55 ACT.4: 6 residues within 4Å: Chain B: V.8, G.10, A.11, G.12, K.13, R.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.13 Hydrogen bonds: B:G.10, B:G.12, B:K.13, B:R.14 Salt bridges: B:K.13, B:R.14

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

TMP.3: 12 residues within 4Å: Chain A: D.9, F.36, P.37, Y.39, L.52, F.70, R.74, R.95, S.99, N.100, Y.103, Y.165 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.36, A:P.37, A:Y.103 Hydrogen bonds: A:R.74, A:R.74, A:N.100 Water bridges: A:D.9, A:D.163 Salt bridges: A:R.95 pi-Stacking: A:F.70 TMP.6: 12 residues within 4Å: Chain B: D.9, F.36, P.37, Y.39, L.52, F.70, R.74, R.95, N.100, Y.103, Y.165 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.36, B:P.37, B:Y.103 Hydrogen bonds: B:Y.39, B:R.74, B:R.74, B:N.100 Water bridges: B:D.9, B:R.95, B:R.95, B:D.163 Salt bridges: B:R.95 pi-Stacking: B:F.70

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain B: D.9 Ligands: TMP.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.9, H2O.8, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fioravanti, E. et al., Mycobacterium tuberculosis Thymidylate Kinase: Structural Studies of Intermediates along the Reaction Pathway. J.Mol.Biol. (2003)

Release Date

2003-04-15

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

THYMIDYLATE KINASE

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