SMTL ID : 3r11.1

Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Mg and Fumarate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.28, N.29, H.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.29, A:N.29 Water bridges: A:T.28 Salt bridges: A:H.30 SO4.2: 3 residues within 4Å: Chain A: K.9, T.10, R.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.10, A:T.10 Water bridges: A:R.69 Salt bridges: A:R.69 SO4.5: 5 residues within 4Å: Chain B: Y.47, K.115, G.354, F.355, N.356 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:F.355, B:N.356, B:N.356 Water bridges: B:K.115, B:K.115, B:K.115, B:K.351, B:G.354, B:L.357, B:L.357, B:A.358 Salt bridges: B:K.115 SO4.6: 3 residues within 4Å: Chain B: T.28, N.29, H.30 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:N.29, B:N.29 Salt bridges: B:H.30 SO4.7: 4 residues within 4Å: Chain A: K.94 Chain B: V.25, R.26, S.27 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.27 Water bridges: A:K.94 Salt bridges: A:K.94 SO4.8: 3 residues within 4Å: Chain B: K.18, A.329, K.330 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.330 Salt bridges: B:K.18

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.192, E.220, D.245, K.269 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.192, A:E.220, A:D.245, H2O.1, H2O.2, H2O.9

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: F.97, F.249, D.250, K.252, D.253 Chain B: F.97, Y.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.252, A:K.252 Water bridges: A:E.246 GOL.9: 7 residues within 4Å: Chain A: F.97, Y.225 Chain B: F.97, F.249, D.250, K.252, D.253 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.252, B:K.252, A:Y.225, A:Y.225 Water bridges: B:E.246

1 x FUM: FUMARIC ACID(Non-covalent)

FUM.10: 12 residues within 4Å: Chain B: F.21, R.26, T.53, I.56, K.164, D.192, N.194, D.245, K.269, C.297, M.298, M.299 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.21, B:I.56 Hydrogen bonds: B:T.53, B:N.194 Water bridges: B:K.164, B:K.164, B:D.245, B:E.246 Salt bridges: B:R.26, B:K.162, B:K.164, B:K.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lukk, T. et al., Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2011-04-20

Peptides

Enzyme of enolase superfamily: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Enzyme of enolase superfamily

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