SMTL ID : 3r1z.1

Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Complex with L-Ala-L-Glu and L-Ala-D-Glu

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ALA: ALANINE(Non-covalent)

ALA.1: 10 residues within 4Å: Chain A: F.21, S.137, K.164, C.297, M.298, M.299, D.321, D.323, P.324 Ligands: GLU.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.324 Hydrogen bonds: A:S.137, A:K.164, A:D.323 ALA.7: 9 residues within 4Å: Chain B: F.21, S.137, K.164, C.297, M.298, M.299, D.321, D.323 Ligands: DGL.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.137, B:K.164, B:D.323

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 13 residues within 4Å: Chain A: F.21, R.26, T.53, I.56, K.164, D.192, N.194, D.245, K.269, C.297, M.298, M.299 Ligands: ALA.1 16 PLIP interactions: 14 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.21, A:I.56 Hydrogen bonds: A:T.53, A:N.194, A:K.269, A:C.297 Water bridges: A:R.26, A:E.220, A:D.321, A:D.321, E.2, E.2 Salt bridges: A:R.26, A:K.162, A:K.164, A:K.269

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

SO4.3: 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:I.8 Salt bridges: A:R.69 SO4.4: 3 residues within 4Å: Chain A: T.28, N.29, H.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29, A:N.29 Salt bridges: A:H.30 SO4.9: 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 SO4.10: 5 residues within 4Å: Chain B: Y.47, K.115, G.354, F.355, N.356 11 PLIP interactions: 11 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:A.358 Salt bridges: B:K.115 SO4.11: 4 residues within 4Å: Chain B: K.18, V.328, A.329, K.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.330 Water bridges: B:D.331 Salt bridges: B:K.18 SO4.12: 3 residues within 4Å: Chain A: K.94 Chain B: R.26, S.27 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.94 Hydrogen bonds: B:S.27

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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:D.253 Water bridges: A:E.246 GOL.6: 3 residues within 4Å: Chain A: K.18, A.329, K.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.18 GOL.13: 6 residues within 4Å: Chain A: F.97, Y.225 Chain B: F.97, F.249, K.252, D.253 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.252, B:D.253, A:Y.225, A:Y.225 Water bridges: B:E.246 GOL.14: 9 residues within 4Å: Chain B: I.13, I.15, S.301, P.302, A.303, L.332, Y.336, F.355, L.357 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.301, B:S.301, B:A.303, B:L.332

1 x DGL: D-GLUTAMIC ACID(Non-covalent)

DGL.8: 16 residues within 4Å: Chain B: F.21, R.26, T.53, I.56, K.162, K.164, D.192, N.194, E.220, D.245, K.269, C.297, M.298, M.299, D.321 Ligands: ALA.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.21, B:I.56 Hydrogen bonds: B:T.53, B:N.194, B:K.269, B:C.297, B:D.321 Water bridges: B:K.162, B:E.220, B:N.267 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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