SMTL ID : 1n5l.1

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE, AFTER CATALYSIS IN THE CRYSTAL (2.3 A RESOLUTION)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: R.122, I.123, R.127 Chain B: E.50, 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.2: 5 residues within 4Å: Chain A: G.10, A.11, G.12, K.13, R.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.14 Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13 Salt bridges: A:K.13

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

TMP.3: 10 residues within 4Å: Chain A: F.36, P.37, Y.39, F.70, R.74, R.95, S.99, N.100, Y.103, Y.165 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.37, A:F.70, A:Y.103 Hydrogen bonds: A:R.74, A:R.74, A:N.100 Water bridges: A:E.166 Salt bridges: A:R.95 pi-Stacking: A:F.70

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain B: D.9, E.166 Ligands: TYD.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.9, H2O.7, H2O.8

1 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.5: 14 residues within 4Å: Chain B: D.9, F.36, P.37, Y.39, L.52, F.70, R.74, R.95, S.99, N.100, Y.103, R.160, Y.165 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.36, B:P.37, B:Y.103 Hydrogen bonds: B:Y.39, B:Y.39, B:R.74, B:R.74, B:N.100, B:N.100 Water bridges: B:D.9, B:D.9, B:R.95, B:D.163 Salt bridges: B:R.95, B:R.160 pi-Stacking: B:F.70

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.6: 7 residues within 4Å: Chain B: V.8, G.10, A.11, G.12, K.13, R.14, T.15 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:R.14, B:T.15 Water bridges: B:D.9, B:K.13 Salt bridges: B:K.13, B:R.14, B:R.14

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

Related Entries With Identical Sequence