SMTL ID : 1n3i.1

Crystal Structure of Mycobacterium tuberculosis PNP with transition state analog DADMe-ImmH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 9 residues within 4Å: Chain A: G.35, S.36, H.68, R.88, H.90, N.119, A.120, S.208 Ligands: DIH.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.36, A:S.36, A:S.36, A:A.120, A:S.208, A:S.208 Water bridges: A:M.207 Salt bridges: A:H.68, A:R.88, A:H.90 PO4.3: 9 residues within 4Å: Chain B: G.35, S.36, H.68, R.88, H.90, N.119, A.120, S.208 Ligands: DIH.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.36, B:S.36, B:S.36, B:A.120, B:S.208, B:S.208 Water bridges: B:M.207 Salt bridges: B:H.68, B:R.88, B:H.90 PO4.5: 9 residues within 4Å: Chain C: G.35, S.36, H.68, R.88, H.90, N.119, A.120, S.208 Ligands: DIH.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.36, C:S.36, C:S.36, C:A.120, C:S.208, C:S.208 Water bridges: C:M.207 Salt bridges: C:H.68, C:R.88, C:H.90

3 x DIH: 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one(Non-covalent)

DIH.2: 18 residues within 4Å: Chain A: S.36, H.90, Y.92, A.120, A.121, G.122, Y.188, E.189, V.205, G.206, M.207, T.230, N.231, L.241, H.243, V.246 Chain B: F.153 Ligands: PO4.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.92, A:Y.92, A:Y.188, A:Y.188, A:E.189, A:T.230, A:N.231 Water bridges: A:M.207 pi-Stacking: A:Y.188 DIH.4: 18 residues within 4Å: Chain B: S.36, H.90, Y.92, A.120, A.121, G.122, Y.188, E.189, V.205, G.206, M.207, T.230, N.231, L.241, H.243, V.246 Chain C: F.153 Ligands: PO4.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.36, B:Y.92, B:Y.92, B:Y.188, B:Y.188, B:E.189, B:T.230, B:N.231 Water bridges: B:M.207 pi-Stacking: B:Y.188 DIH.6: 18 residues within 4Å: Chain A: F.153 Chain C: S.36, H.90, Y.92, A.120, A.121, G.122, Y.188, E.189, V.205, G.206, M.207, T.230, N.231, L.241, H.243, V.246 Ligands: PO4.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.36, C:Y.92, C:Y.92, C:Y.188, C:Y.188, C:E.189, C:T.230, C:N.231 Water bridges: C:M.207 pi-Stacking: C:Y.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewandowicz, A. et al., Over-The-Barrier Transition State Analogues Provide New Chemistries for Inhibitor Design: The Case of Purine Nucleoside Phosphorylase. BIOCHEMISTRY (2003)

Release Date

2003-09-30

Peptides

Purine Nucleoside Phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Purine Nucleoside Phosphorylase

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