SMTL ID : 4m1e.1 (2 other biounits)

Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: G.52, T.53, H.84, R.104, H.106, N.135, A.136, S.235 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.53, A:A.136, A:S.235 Salt bridges: A:H.84, A:R.104, A:H.106 SO4.4: 8 residues within 4Å: Chain B: G.52, T.53, H.84, R.104, H.106, N.135, A.136, S.235 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.53, B:T.53, B:A.136, B:S.235 Salt bridges: B:H.84, B:R.104, B:H.106 SO4.7: 8 residues within 4Å: Chain C: G.52, T.53, H.84, R.104, H.106, N.135, A.136, S.235 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.53, C:T.53, C:A.136, C:S.235, C:S.235 Salt bridges: C:H.84, C:R.104, C:H.106

3 x ADE: ADENINE(Non-covalent)

ADE.2: 12 residues within 4Å: Chain A: A.136, A.137, G.138, L.215, E.216, Y.221, V.232, G.233, M.234, T.257, D.258, C.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.136, A:Y.221, A:D.258 ADE.5: 12 residues within 4Å: Chain B: A.136, A.137, G.138, L.215, E.216, Y.221, V.232, G.233, M.234, T.257, D.258, C.260 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.136, B:G.138, B:Y.221, B:D.258 Water bridges: B:D.258 ADE.8: 12 residues within 4Å: Chain C: A.136, A.137, G.138, L.215, E.216, Y.221, V.232, G.233, M.234, T.257, D.258, C.260 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.136, C:D.258 Water bridges: C:D.258

3 x 6PC: PYRIDINE-2-CARBOXYLIC ACID(Non-covalent)

6PC.3: 3 residues within 4Å: Chain A: R.192, P.203, K.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.204 Salt bridges: A:R.192 6PC.6: 3 residues within 4Å: Chain B: R.192, P.203, K.204 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.204, B:K.204 Salt bridges: B:R.192, B:K.204 6PC.9: 5 residues within 4Å: Chain C: N.141, Q.143, L.144, H.201, P.203 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Q.143, C:L.144, C:P.203 Water bridges: C:H.201 Salt bridges: C:H.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malashkevich, V.N. et al., Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364. To be Published

Release Date

2013-08-21

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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