SMTL ID : 5bv3.2 (1 other biounit)

Yeast Scavenger Decapping Enzyme in complex with m7GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

1 x M7G: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE(Non-covalent)

M7G.1: 15 residues within 4Å: Chain A: K.121, W.156, E.166, P.188, D.189, M.190, K.191, H.254, P.257, S.258, Y.259, H.265 Chain B: N.86, Y.89, W.91 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.188, A:M.190, A:K.191, A:K.191, A:S.258, A:S.258, A:S.258, A:Y.259, A:H.265, B:N.86 Salt bridges: A:K.121, A:E.166, A:D.189, A:K.191, A:H.254, A:H.254, A:H.265, A:H.265

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: G.275, N.276, S.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.276, A:N.276, A:N.276 SO4.4: 4 residues within 4Å: Chain B: L.274, G.275, N.276, S.277 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.275, B:N.276, B:S.277, B:S.277 SO4.5: 7 residues within 4Å: Chain B: Q.125, F.127, Q.256, K.282, I.310, G.311, H.314 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.125, B:A.309, B:G.311 Salt bridges: B:K.282, B:H.314

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

CL.3: 1 residues within 4Å: Chain A: R.331 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: R.131, R.331 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: N.19, T.22, G.275 Chain B: P.272 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neu, A. et al., An excess of catalytically required motions inhibits the scavenger decapping enzyme. Nat.Chem.Biol. (2015)

Release Date

2015-08-12

Peptides

m7GpppX diphosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

m7GpppX diphosphatase

Related Entries With Identical Sequence