SMTL ID : 8swq.1 (1 other biounit)

Structure of K. lactis PNP bound to transition state analog DADMe-IMMUCILLIN H and sulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-trimer

Ligands

2 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.1: 18 residues within 4Å: Chain A: S.43, H.99, Y.101, A.130, A.131, G.132, F.214, E.215, V.231, G.232, M.233, T.256, N.257, C.259, H.282, V.285 Chain C: F.173 Ligands: SO4.2 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.43, A:Y.101, A:E.215, A:N.257, A:N.257, A:H.282 Water bridges: A:E.215, A:E.215 pi-Stacking: A:F.214 Hydrophobic interactions: C:F.173 DIH.4: 18 residues within 4Å: Chain A: F.173 Chain B: S.43, H.99, Y.101, A.130, A.131, G.132, F.214, E.215, V.231, G.232, M.233, T.256, N.257, C.259, H.282, V.285 Ligands: SO4.5 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.101, B:E.215, B:N.257, B:N.257, B:H.282 Water bridges: B:E.215, B:E.215 pi-Stacking: B:F.214 Hydrophobic interactions: A:F.173

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

SO4.2: 8 residues within 4Å: Chain A: G.42, S.43, R.97, H.99, N.129, A.130, S.234 Ligands: DIH.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.43, A:S.43, A:A.130, A:S.234 Salt bridges: A:R.97, A:H.99 SO4.5: 8 residues within 4Å: Chain B: G.42, S.43, R.97, H.99, N.129, A.130, S.234 Ligands: DIH.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.43, B:A.130, B:S.234 Water bridges: B:H.99, B:S.234, B:S.234 Salt bridges: B:R.97, B:H.99 SO4.7: 5 residues within 4Å: Chain C: G.42, S.43, N.129, A.130, S.234 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.43, C:A.130, C:S.234 Water bridges: C:S.234

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: F.138, H.202, E.203 Chain B: H.268 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.202, A:E.203, B:H.268 Water bridges: A:N.135, A:N.135 GOL.6: 2 residues within 4Å: Chain B: H.202, E.203 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.202, B:E.203, B:E.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minnow, Y.V.T. et al., Phosphate Binding in PNP Alters Transition-State Analogue Affinity and Subunit Cooperativity. Biochemistry (2023)

Release Date

2023-10-18

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Purine nucleoside phosphorylase

Related Entries With Identical Sequence