SMTL ID : 3f4n.5 (4 other biounits)

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-octamer

Ligands

8 x PXP: PYRIDOXINE-5'-PHOSPHATE(Non-covalent)

PXP.1: 13 residues within 4Å: Chain A: N.12, D.14, E.75, V.97, F.136, E.156, H.196, G.197, N.216, I.217, G.218, H.219 Chain B: R.23 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.97, A:F.136 Hydrogen bonds: A:N.12, A:D.14, A:D.14, A:H.196, A:G.197, A:G.218, A:H.219 Water bridges: A:H.15, A:R.50, A:E.75, A:L.198, A:L.198, A:H.219, A:A.220, B:R.23 Salt bridges: A:H.196, B:R.23 PXP.2: 14 residues within 4Å: Chain A: R.23 Chain B: N.12, D.14, E.75, C.95, V.97, F.136, E.156, H.196, G.197, N.216, I.217, G.218, H.219 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.97, B:F.136 Hydrogen bonds: B:D.14, B:G.197, B:G.218, B:H.219 Water bridges: B:H.196, B:L.198, B:A.220, A:R.23, A:R.23 Salt bridges: B:H.196, A:R.23 PXP.3: 14 residues within 4Å: Chain C: N.12, D.14, E.75, V.97, F.136, E.156, G.195, H.196, G.197, N.216, I.217, G.218, H.219 Chain D: R.23 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.97, C:F.136 Hydrogen bonds: C:N.12, C:H.196, C:G.197, C:G.218, C:H.219, D:R.23 Water bridges: C:E.75, C:L.198, C:L.198, C:A.220, C:A.220 Salt bridges: C:H.196, D:R.23 PXP.5: 14 residues within 4Å: Chain C: R.23 Chain D: N.12, D.14, E.75, C.95, V.97, F.136, E.156, H.196, G.197, N.216, I.217, G.218, H.219 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.97, D:F.136 Hydrogen bonds: D:N.12, D:D.14, D:H.196, D:G.197, D:G.218, D:H.219 Water bridges: D:H.15, D:L.198, D:L.198, C:R.23 Salt bridges: D:H.196, C:R.23 PXP.6: 13 residues within 4Å: Chain E: N.12, D.14, E.75, C.95, F.136, E.156, H.196, G.197, N.216, I.217, G.218, H.219 Chain F: R.23 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:F.136 Hydrogen bonds: E:D.14, E:G.197, E:G.218, E:H.219, F:R.23 Water bridges: E:N.12, E:L.198, E:L.198 Salt bridges: E:H.196, F:R.23 PXP.9: 13 residues within 4Å: Chain E: R.23 Chain F: N.12, E.75, V.97, F.136, E.156, H.196, G.197, N.216, I.217, G.218, H.219 Ligands: SO4.7 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:V.97, F:F.136 Hydrogen bonds: F:G.197, F:G.218, F:H.219, E:R.23 Water bridges: F:H.15, F:H.196, F:H.196, F:A.220 Salt bridges: F:H.196, E:R.23 PXP.10: 12 residues within 4Å: Chain G: E.75, V.97, F.136, E.156, G.195, H.196, G.197, N.216, I.217, G.218, H.219 Chain H: R.23 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:V.97, G:F.136 Hydrogen bonds: G:G.197, G:G.218, G:H.219, H:R.23 Water bridges: G:N.12, G:N.12, G:H.196, G:L.198 Salt bridges: G:H.196, H:R.23 PXP.11: 12 residues within 4Å: Chain G: R.23 Chain H: E.75, V.97, F.136, E.156, G.195, H.196, G.197, N.216, I.217, G.218, H.219 13 PLIP interactions: 12 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:V.97, H:F.136 Hydrogen bonds: H:H.196, H:G.197, H:G.218, H:H.219 Water bridges: H:N.12, H:L.198, H:L.198, H:A.220, H:A.220 Salt bridges: H:H.196, G:R.23

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

SO4.4: 5 residues within 4Å: Chain C: H.15, R.50, R.54, H.55 Chain D: R.23 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Water bridges: C:R.54, D:R.23, D:R.23 Salt bridges: C:H.15, C:R.50, C:R.54, C:H.55, D:R.23 SO4.7: 4 residues within 4Å: Chain E: R.23 Chain F: H.15, H.55 Ligands: PXP.9 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Water bridges: F:H.15, F:R.54, E:R.23 Salt bridges: F:H.15, E:R.23 SO4.8: 5 residues within 4Å: Chain E: H.15, R.50, R.54, H.55 Chain F: R.23 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Salt bridges: E:H.15, E:R.50, E:H.55, F:R.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis. To be Published (2008)

Release Date

2008-11-25

Peptides

Pyridoxine 5'-phosphate synthase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Pyridoxine 5'-phosphate synthase

Related Entries With Identical Sequence