SMTL ID : 3o05.1

Crystal Structure of Yeast Pyridoxal 5-Phosphate Synthase Snz1 Complxed with Substrate PLP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 10 residues within 4Å: Chain A: I.77, E.98, W.105, H.108, K.123, E.127, R.130, R.131, K.142, R.184 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.77, A:E.98 Hydrogen bonds: A:K.123, A:K.142 Water bridges: A:E.127, A:R.130, A:R.184, A:R.184, A:R.184, A:R.184, A:R.184 Salt bridges: A:R.130, A:R.131, A:R.184 pi-Cation interactions: A:H.108 PLP.2: 11 residues within 4Å: Chain B: I.77, E.98, P.102, W.105, H.108, K.123, E.127, R.130, R.131, K.142, R.184 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:E.98 Hydrogen bonds: B:K.123, B:K.142 Water bridges: B:E.127, B:R.130, B:R.131, B:R.131, B:R.184, B:R.184 Salt bridges: B:R.130, B:R.131, B:R.184 PLP.3: 11 residues within 4Å: Chain C: I.77, E.98, P.102, W.105, H.108, K.123, E.127, R.130, R.131, K.142, R.184 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:E.98 Hydrogen bonds: C:K.123, C:K.142 Water bridges: C:H.108, C:E.127, C:R.130, C:R.131, C:R.184, C:R.184 Salt bridges: C:H.108, C:R.130, C:R.131, C:R.184 PLP.4: 10 residues within 4Å: Chain D: I.77, E.98, W.105, H.108, K.123, E.127, R.130, R.131, K.142, R.184 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.77, D:E.98 Hydrogen bonds: D:K.123, D:K.142 Water bridges: D:E.127, D:R.130, D:R.184, D:R.184, D:R.184, D:R.184, D:R.184 Salt bridges: D:R.130, D:R.131, D:R.184 pi-Cation interactions: D:H.108 PLP.5: 11 residues within 4Å: Chain E: I.77, E.98, P.102, W.105, H.108, K.123, E.127, R.130, R.131, K.142, R.184 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:E.98 Hydrogen bonds: E:K.123, E:K.142 Water bridges: E:E.127, E:E.127, E:R.131, E:R.131, E:R.184, E:R.184 Salt bridges: E:R.130, E:R.131, E:R.184 PLP.6: 11 residues within 4Å: Chain F: I.77, E.98, P.102, W.105, H.108, K.123, E.127, R.130, R.131, K.142, R.184 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:E.98 Hydrogen bonds: F:K.123, F:K.142 Water bridges: F:H.108, F:E.127, F:R.130, F:R.131, F:R.184, F:R.184 Salt bridges: F:H.108, F:R.130, F:R.131, F:R.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1. Biochem.J. (2010)

Release Date

2010-11-24

Peptides

Pyridoxine biosynthesis protein SNZ1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Pyridoxine biosynthesis protein SNZ1

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