SMTL ID : 4ffs.1

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Helicobacter pylori with butyl-thio-DADMe-Immucillin-A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x BIG: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol(Non-covalent)

BIG.1: 20 residues within 4Å: Chain A: A.18, M.19, I.61, V.87, A.88, G.89, Q.161, F.162, V.163, V.181, E.182, M.183, E.184, S.206, D.207, A.209, F.217 Chain B: L.113, F.116, H.118 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.61, B:F.116 Hydrogen bonds: A:V.163, A:D.207, A:D.207 Water bridges: A:R.203, A:R.203 Salt bridges: A:E.22, A:E.184 BIG.3: 20 residues within 4Å: Chain A: L.113, F.116, H.118 Chain B: A.18, M.19, I.61, V.87, A.88, G.89, Q.161, F.162, V.163, V.181, E.182, M.183, E.184, S.206, D.207, A.209, F.217 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.61, A:F.116 Hydrogen bonds: B:V.163, B:D.207, B:D.207 Water bridges: B:R.203, B:R.203 Salt bridges: B:E.22, B:E.184

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

CL.2: 2 residues within 4Å: Chain A: V.32, D.33 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain B: V.32, D.33 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., A Picomolar Transition State Analogue Inhibitor of MTAN as a Specific Antibiotic for Helicobacter pylori. Biochemistry (2012)

Release Date

2012-09-26

Peptides

MTA/SAH nucleosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

MTA/SAH nucleosidase