SMTL ID : 2pul.1 (1 other biounit)

Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: N.44, D.250, E.252 Ligands: ACP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.250, A:E.252, H2O.9 MG.4: 5 residues within 4Å: Chain B: N.44, K.61, D.250, E.252 Ligands: ACP.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.250, B:D.250, B:E.252

1 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.2: 5 residues within 4Å: Chain A: E.380, D.386, E.389, L.390, L.393 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.380, A:D.386, A:E.389, A:E.389, A:L.390, A:L.393 Hydrogen bonds: A:E.389

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

ACP.3: 17 residues within 4Å: Chain A: I.38, D.40, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, I.249, D.250, E.252 Ligands: MG.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.40, A:N.44, A:K.61, A:E.115, A:L.117, A:D.250 Water bridges: A:D.40, A:G.41, A:N.44, A:D.233, A:D.233, A:D.250 Salt bridges: A:K.61 pi-Stacking: A:F.240 ACP.5: 17 residues within 4Å: Chain B: I.38, D.40, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, I.249, D.250, E.252 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.44, B:K.61, B:E.115, B:D.116, B:L.117 Water bridges: B:N.44 Salt bridges: B:K.61 pi-Stacking: B:F.240, B:F.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ku, S.-Y. et al., Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding. J.Biol.Chem. (2007)

Release Date

2007-05-22

Peptides

Methylthioribose kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methylthioribose kinase

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