SMTL ID : 3o07.1

Crystal structure of yeast pyridoxal 5-phosphate synthase Snz1 complexed with substrate G3P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x G3H: GLYCERALDEHYDE-3-PHOSPHATE(Non-covalent)

G3H.1: 3 residues within 4Å: Chain A: F.80, E.110 Chain B: R.158 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.158 Water bridges: B:R.158, B:Q.220, A:H.108 Salt bridges: B:R.158, A:H.107 G3H.2: 4 residues within 4Å: Chain B: F.80, H.107, E.110 Chain C: R.158 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Water bridges: B:H.108, C:R.158, C:Q.220 Salt bridges: B:H.107, C:R.158 G3H.3: 5 residues within 4Å: Chain C: F.80, H.107, E.110 Chain D: R.158, L.221 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.158, D:Q.220, C:E.110 Water bridges: D:R.158, C:E.110 Salt bridges: D:R.158, C:H.107 G3H.4: 3 residues within 4Å: Chain D: F.80, E.110 Chain E: R.158 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:R.158 Water bridges: E:R.158, E:Q.220, D:H.108, D:E.110 Salt bridges: E:R.158, D:H.107 G3H.5: 4 residues within 4Å: Chain E: F.80, H.107, E.110 Chain F: R.158 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Water bridges: F:R.158, F:Q.220, E:H.108 Salt bridges: F:R.158, E:H.107 G3H.6: 5 residues within 4Å: Chain A: R.158, L.221 Chain F: F.80, H.107, E.110 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:R.158, A:Q.220, F:E.110 Water bridges: A:R.158, F:E.110 Salt bridges: A:R.158, F:H.107

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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