SMTL ID : 2pyw.1

Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: H.240, N.274, K.362, R.366 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: H.240, N.274, K.362, R.365, R.366 Ligand excluded by PLIP

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: N.48, D.255, E.257 Ligands: MG.3, ADP.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.255, A:D.255, A:E.257, H2O.1, H2O.1 MG.3: 3 residues within 4Å: Chain A: D.255 Ligands: MG.2, ADP.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.255, H2O.1, H2O.1, H2O.1 MG.4: 1 residues within 4Å: Chain A: D.205 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.205, H2O.6, H2O.13, H2O.14 MG.9: 5 residues within 4Å: Chain B: N.48, D.255, E.257 Ligands: MG.10, ADP.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.255, B:D.255, B:E.257, H2O.17, H2O.17 MG.10: 3 residues within 4Å: Chain B: D.255 Ligands: MG.9, ADP.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.255, H2O.17, H2O.17, H2O.17

2 x SR1: 5-S-methyl-5-thio-alpha-D-ribofuranose(Non-covalent)

SR1.5: 9 residues within 4Å: Chain A: N.46, L.47, L.180, V.184, D.238, F.258, R.365, R.366, V.370 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.46, A:D.238, A:R.365, A:R.365, A:R.366 Water bridges: A:D.238, A:D.238, A:R.366 SR1.11: 9 residues within 4Å: Chain B: N.46, L.47, L.180, V.184, D.238, F.258, R.365, R.366, V.370 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.46, B:D.238, B:R.365, B:R.365, B:R.366 Water bridges: B:R.366

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

ADP.6: 19 residues within 4Å: Chain A: D.44, G.45, N.46, L.47, N.48, V.50, V.61, K.63, M.116, R.117, Y.118, L.119, I.125, M.245, I.254, D.255, E.257 Ligands: MG.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.46, A:L.47, A:N.48, A:N.48, A:R.117, A:L.119 Water bridges: A:D.44, A:G.45, A:G.45, A:D.255 Salt bridges: A:K.63, A:K.63 ADP.12: 19 residues within 4Å: Chain B: D.44, G.45, N.46, L.47, N.48, V.50, V.61, K.63, M.116, R.117, Y.118, L.119, I.125, M.245, I.254, D.255, E.257 Ligands: MG.9, MG.10 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.46, B:L.47, B:N.48, B:N.48, B:R.117, B:L.119, B:D.255, B:D.255 Water bridges: B:D.44, B:G.45 Salt bridges: B:K.63, B:K.63

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain A: N.196, R.197, W.198, S.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.198, A:W.198 Water bridges: A:N.196 EDO.13: 6 residues within 4Å: Chain B: R.230, Q.232, Y.347, N.350, L.351, D.354 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.230, B:R.230, B:Q.232, B:D.354 Water bridges: B:N.346, B:N.350 EDO.14: 6 residues within 4Å: Chain B: W.307, N.311, M.348, R.349, L.352, K.407 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.349, B:R.349 Water bridges: B:N.308, B:N.311, B:R.349 EDO.15: 8 residues within 4Å: Chain B: L.157, W.318, N.321, K.322, G.326, E.327, A.328, Y.329 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.322, B:Y.329 EDO.16: 3 residues within 4Å: Chain B: R.197, W.198, S.200 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.198, B:W.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ku, S.Y. et al., Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR reveals a more occluded active site than its bacterial homolog. Bmc Struct.Biol. (2007)

Release Date

2008-01-15

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uncharacterized protein