SMTL ID : 4fir.1

Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-hexamer

Ligands

6 x R5P: RIBOSE-5-PHOSPHATE(Post Translational Modification)(Non-covalent)

R5P.1: 14 residues within 4Å: Chain A: D.30, P.55, K.87, D.108, S.110, V.112, R.153, A.158, G.159, G.256, G.257, V.258, G.278, S.279 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:K.87, A:V.112 Hydrogen bonds: A:D.30, A:D.108, A:G.159, A:G.256, A:G.257, A:V.258, A:V.258, A:G.278, A:S.279, A:G.280 R5P.2: 15 residues within 4Å: Chain B: D.30, P.55, K.87, D.108, S.110, V.112, R.153, A.158, G.159, G.256, G.257, V.258, V.277, G.278, S.279 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:K.87, B:V.112 Hydrogen bonds: B:D.30, B:D.108, B:G.159, B:G.256, B:G.257, B:V.258, B:G.278, B:S.279 R5P.3: 15 residues within 4Å: Chain C: D.30, P.55, K.87, D.108, S.110, V.112, R.153, A.158, G.159, G.256, G.257, V.258, V.277, G.278, S.279 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:K.87 Hydrogen bonds: C:D.30, C:D.108, C:G.159, C:G.256, C:G.257, C:V.258, C:F.276, C:G.278, C:S.279 R5P.4: 15 residues within 4Å: Chain D: D.30, P.55, K.87, D.108, S.110, V.112, R.153, A.158, G.159, G.256, G.257, F.276, V.277, G.278, S.279 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:K.87 Hydrogen bonds: D:D.30, D:K.87, D:S.110, D:S.110, D:R.153, D:R.153, D:G.159, D:G.257, D:V.258, D:G.278, D:S.279 R5P.5: 15 residues within 4Å: Chain E: D.30, P.55, K.87, D.108, S.110, V.112, R.153, A.158, G.159, G.256, G.257, F.276, V.277, G.278, S.279 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:K.87 Hydrogen bonds: E:D.30, E:K.87, E:S.110, E:S.110, E:G.159, E:G.257, E:V.258, E:G.278, E:S.279, E:S.279 R5P.6: 16 residues within 4Å: Chain F: D.30, P.55, K.87, V.112, R.153, K.155, A.158, G.159, A.255, G.256, G.257, V.258, F.276, V.277, G.278, S.279 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:F.276 Hydrogen bonds: F:D.30, F:K.87, F:K.87, F:R.153, F:R.153, F:G.159, F:G.256, F:G.257, F:V.258, F:G.278, F:S.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuura, A. et al., Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii. Mol.Cells (2012)

Release Date

2012-11-14

Peptides

Pyridoxal biosynthesis lyase pdxS: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Pyridoxal biosynthesis lyase pdxS

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