SMTL ID : 3nkl.1

Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: G.13, S.14, A.15, P.74, S.75 Chain B: G.13, S.14 Ligands: GOL.2, GOL.6 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.14, A:S.14, A:A.15, A:S.75 Water bridges: B:A.15, A:G.13, A:G.16 SO4.3: 4 residues within 4Å: Chain A: H.42, K.43, K.55, Y.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.56 Salt bridges: A:H.42, A:K.43, A:K.55 SO4.5: 3 residues within 4Å: Chain A: R.53, P.54, K.55 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.55 Water bridges: A:D.37, A:R.53, A:K.55 Salt bridges: A:R.53 SO4.8: 4 residues within 4Å: Chain B: H.42, K.43, R.53, Y.56 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.55 Salt bridges: B:H.42, B:K.43, B:R.53 SO4.9: 3 residues within 4Å: Chain B: R.53, P.54, K.55 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.55 Water bridges: B:R.39, B:R.53 Salt bridges: B:R.53

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: G.11, A.12, D.36, V.73, P.74, S.75, A.76 Ligands: SO4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.12, A:D.36, A:S.75, A:S.75, A:A.76 Water bridges: A:D.38 GOL.6: 4 residues within 4Å: Chain A: K.41 Chain B: S.75 Ligands: SO4.1, CL.7 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.36, A:K.41, A:K.41 Water bridges: B:D.37, A:D.38

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 5 residues within 4Å: Chain A: V.93, E.94, V.95, E.116, V.117 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.117 Hydrogen bonds: A:V.95, A:E.116

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: S.14 Chain B: V.73, P.74, S.75 Ligands: GOL.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri. To be Published (2010)

Release Date

2010-08-18

Peptides

UDP-D-quinovosamine 4-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-D-quinovosamine 4-dehydrogenase