SMTL ID : 4rgk.1

Crystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Protein YbiU from Yersinia pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.221, H.222 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.221, A:E.237 Salt bridges: A:R.221, A:H.222 SO4.6: 5 residues within 4Å: Chain A: H.202, D.204, Q.258, H.342 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.202, A:H.342 SO4.7: 3 residues within 4Å: Chain B: R.221, H.222 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.221, B:E.237 Salt bridges: B:R.221, B:H.222 SO4.12: 5 residues within 4Å: Chain B: H.202, D.204, Q.258, H.342 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.202, B:H.342

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.221, H.222, S.225, Q.227 Ligands: SO4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.221, A:H.222, A:S.225, A:Q.227 Water bridges: A:R.221 GOL.8: 5 residues within 4Å: Chain B: R.221, H.222, S.225, Q.227 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.221, B:H.222, B:S.225 Water bridges: B:R.221

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: W.165, Q.166, T.167, E.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.165, A:T.167, A:E.168, A:E.168 EDO.4: 6 residues within 4Å: Chain A: I.136, R.188, G.198, L.199, H.202 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.188, A:H.202 EDO.5: 7 residues within 4Å: Chain A: Y.183, P.248, A.249, V.250, R.255, D.387, F.388 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.183, A:V.250, A:R.255 Water bridges: A:D.185, A:D.185, A:V.250, A:R.255 EDO.9: 4 residues within 4Å: Chain B: W.165, Q.166, T.167, E.168 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.165, B:T.167, B:E.168, B:E.168 EDO.10: 6 residues within 4Å: Chain B: I.136, R.188, G.198, L.199, H.202 Ligands: SO4.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.188, B:H.202 EDO.11: 7 residues within 4Å: Chain B: Y.183, P.248, A.249, V.250, R.255, D.387, F.388 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.250, B:R.255 Water bridges: B:D.185, B:D.185, B:V.250, B:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Protein YbiU from Yersinia pestis. To be Published

Release Date

2014-12-31

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Uncharacterized protein

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