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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.250 Ligands: MG.2, ADP.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.250 MG.2: 4 residues within 4Å: Chain A: D.250, E.252 Ligands: MG.1, ADP.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.250, A:D.250, A:E.252, H2O.3247 MG.3: 3 residues within 4Å: Chain B: D.250 Ligands: MG.4, ADP.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.250, H2O.3248 MG.4: 4 residues within 4Å: Chain B: D.250, E.252 Ligands: MG.3, ADP.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.250, B:D.250, B:E.252, H2O.3249, H2O.3249 MG.8: 3 residues within 4Å: Chain C: D.250 Ligands: MG.9, ADP.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.250 MG.9: 4 residues within 4Å: Chain C: D.250, E.252 Ligands: MG.8, ADP.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.250, C:D.250, C:E.252, H2O.3334 MG.10: 3 residues within 4Å: Chain D: D.250 Ligands: MG.11, ADP.14 2 PLIP interactions: 1 Ligand-Water interactions, 1 interactions with chain D Metal complexes: H2O.3335, D:D.250 MG.11: 4 residues within 4Å: Chain D: D.250, E.252 Ligands: MG.10, ADP.14 5 PLIP interactions: 2 Ligand-Water interactions, 3 interactions with chain D Metal complexes: H2O.3336, H2O.3336, D:D.250, D:D.250, D:E.252

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

CPS.5: 10 residues within 4Å: Chain A: E.380, D.386, E.389, L.390, L.393 Chain D: K.377, E.380, L.390, L.393, L.394 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:E.380, A:D.386, A:E.389, A:L.390, A:L.393, D:L.390, D:L.393, D:L.394 Hydrogen bonds: A:E.389, D:E.380 Water bridges: A:E.380, D:R.365, D:R.365 CPS.12: 10 residues within 4Å: Chain C: E.380, D.386, E.389, L.390, L.393 Chain B: K.377, E.380, L.390, L.393, L.394 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:E.380, C:D.386, C:E.389, C:L.390, C:L.393, B:L.390, B:L.393, B:L.394 Hydrogen bonds: C:E.389, B:E.380 Water bridges: C:E.380, B:R.365, B:R.365

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 16 residues within 4Å: Chain A: I.38, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, D.250, E.252 Ligands: MG.1, MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.44, A:E.115, A:L.117 pi-Stacking: A:F.240 Salt bridges: A:K.61, A:K.61 Water bridges: A:G.41, A:N.44 ADP.7: 16 residues within 4Å: Chain B: I.38, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, D.250, E.252 Ligands: MG.3, MG.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.44, B:E.115, B:D.116, B:L.117 pi-Stacking: B:F.240 Salt bridges: B:K.61, B:K.61 Water bridges: B:G.237 ADP.13: 16 residues within 4Å: Chain C: I.38, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, D.250, E.252 Ligands: MG.8, MG.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.44, C:E.115, C:L.117 pi-Stacking: C:F.240 Salt bridges: C:K.61, C:K.61 Water bridges: C:G.41, C:N.44 ADP.14: 16 residues within 4Å: Chain D: I.38, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, D.250, E.252 Ligands: MG.10, MG.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.44, D:E.115, D:D.116, D:L.117 pi-Stacking: D:F.240 Salt bridges: D:K.61, D:K.61 Water bridges: D:G.237

Links

RCSB   PDBe   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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Methylthioribose kinase

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