SMTL ID : 4ynb.1

Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with pyrazinylthio-DADMe-Immucillin-A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

4EH.1: 21 residues within 4Å: Chain A: A.24, M.25, I.67, V.93, A.94, G.95, Q.167, F.168, V.169, V.187, E.188, M.189, E.190, S.212, D.213, A.215, F.223 Chain B: L.119, F.122, H.124, P.130 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.169, A:D.213, A:D.213 Water bridges: A:R.209, A:R.209 Salt bridges: A:E.28, A:E.190 pi-Stacking: A:F.168, B:F.122 4EH.5: 21 residues within 4Å: Chain A: L.119, F.122, H.124, P.130 Chain B: A.24, M.25, I.67, V.93, A.94, G.95, Q.167, F.168, V.169, V.187, E.188, M.189, E.190, S.212, D.213, A.215, F.223 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.169, B:D.213, B:D.213 Water bridges: B:R.209, B:R.209 Salt bridges: B:E.28, B:E.190 pi-Stacking: B:F.168, A:F.122

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: F.128, A.133, I.134, F.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.134, A:F.135 Water bridges: A:S.132 GOL.3: 5 residues within 4Å: Chain A: H.56, N.57, K.58, D.243, L.245 No protein-ligand interaction detected (PLIP) GOL.6: 4 residues within 4Å: Chain B: F.128, A.133, I.134, F.135 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.134, B:F.135 Water bridges: B:S.132 GOL.7: 5 residues within 4Å: Chain B: H.56, N.57, K.58, D.243, L.245 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: Q.167, R.174 Chain B: Q.167, R.174 Ligands: PEG.8 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.174, A:R.174 Water bridges: B:Q.167, B:R.174, A:Q.167, A:R.174 PEG.8: 5 residues within 4Å: Chain A: Q.167, R.174 Chain B: Q.167, R.174 Ligands: PEG.4 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.174, A:R.174 Water bridges: B:Q.167, B:R.174, A:Q.167, A:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., New Antibiotic Candidates against Helicobacter pylori. J.Am.Chem.Soc. (2015)

Release Date

2015-11-25

Peptides

Aminodeoxyfutalosine nucleosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aminodeoxyfutalosine nucleosidase

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