SMTL ID : 1m5w.3 (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-dimer

Ligands

2 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 B: R.20 Ligands: PO4.2 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Water bridges: B:R.20, B:R.20 Salt bridges: B:R.20, A:H.12, A:R.47, A:H.52 Hydrogen bonds: A:N.9, A:H.45, A:T.102, A:T.102, A:T.103, A:H.193, A:H.193 DXP.3: 11 residues within 4Å: Chain A: R.20 Chain B: 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 B, 2 interactions with chain A Hydrogen bonds: B:D.11, B:E.72, B:H.216, A:R.20 Water bridges: B:N.9, B:N.9 Salt bridges: B:H.12, B:H.45, B:H.52, B:K.97, A:R.20

1 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 B: R.20 Ligands: DXP.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B 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, B:R.20 Salt bridges: A:H.193, B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Pyridoxal phosphate biosynthetic protein pdxJ

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