SMTL ID : 1m5w.1 (4 other biounits)

1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-octamer

Ligands

6 x DXP: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE(Non-covalent)

DXP.1: 14 residues within 4Å: Chain A: N.9, D.11, H.12, H.45, R.47, H.52, E.72, T.102, T.103, F.133, E.153, H.193 Chain E: R.20 Ligands: PO4.2 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:N.9, A:H.45, A:T.102, A:T.102, A:T.103, A:H.193, A:H.193 Salt bridges: A:H.12, A:R.47, A:H.52, E:R.20 Water bridges: E:R.20, E:R.20 DXP.3: 11 residues within 4Å: Chain B: N.9, D.11, H.12, H.45, R.47, H.52, E.72, H.193, G.194, G.215, H.216 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.9, B:D.11, B:H.216 Water bridges: B:E.72, B:N.213 Salt bridges: B:H.12, B:H.45, B:H.52 DXP.4: 13 residues within 4Å: Chain C: N.9, D.11, H.12, H.45, H.52, E.72, T.102, T.103, F.133, E.153, H.193 Chain F: R.20 Ligands: PO4.5 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:N.9, C:D.11, C:H.45, C:T.102, C:T.102, C:T.103, C:T.103, C:H.193 Salt bridges: C:H.12, C:H.52, F:R.20 Water bridges: F:R.20, F:R.20, F:R.20 DXP.6: 11 residues within 4Å: Chain A: R.20 Chain E: N.9, D.11, H.12, H.45, H.52, E.72, K.97, H.193, G.215, H.216 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:D.11, E:E.72, E:H.216, A:R.20 Water bridges: E:N.9, E:N.9 Salt bridges: E:H.12, E:H.45, E:H.52, E:K.97, A:R.20 DXP.7: 12 residues within 4Å: Chain C: R.20 Chain F: N.9, D.11, H.12, H.45, R.47, H.52, E.72, H.193, G.194, G.215, H.216 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:D.11, F:E.72, F:H.216 Water bridges: F:N.9, F:N.9 Salt bridges: F:H.12, F:H.45, F:R.47, F:H.52 DXP.8: 12 residues within 4Å: Chain B: R.20 Chain G: N.9, D.11, H.12, H.45, R.51, H.52, E.72, H.193, G.194, G.215, H.216 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain B Hydrogen bonds: G:N.9, G:D.11, G:D.11, G:H.216, B:R.20 Water bridges: G:G.194, G:G.215 Salt bridges: G:H.12, G:H.45, G:R.51, G:H.52

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: H.193, G.194, I.214, G.215, H.216 Chain E: R.20 Ligands: DXP.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:G.194, A:G.215, A:H.216 Water bridges: A:N.9, A:L.195, A:L.195, A:A.217, E:R.20 Salt bridges: A:H.193, E:R.20 PO4.5: 8 residues within 4Å: Chain C: H.193, G.194, N.213, I.214, G.215, H.216 Chain F: R.20 Ligands: DXP.4 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:H.193, C:G.194, C:G.215, C:H.216 Water bridges: C:L.195, C:L.195, C:A.217 Salt bridges: F:R.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeh, J.I. et al., Multistate Binding in Pyridoxine 5'-Phosphate Synthase: 1.96 A Crystal Structure in Complex with 1-deoxy-D-xylulose phosphate. Biochemistry (2002)

Release Date

2003-07-15

Peptides

Pyridoxal phosphate biosynthetic protein pdxJ: 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

Pyridoxal phosphate biosynthetic protein pdxJ

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