SMTL ID : 3nev.1

Crystal structure of YagE, a prophage protein from E. coli K12 in complex with KDGal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 10 residues within 4Å: Chain A: L.43, F.49, R.57, G.77, T.78, G.79, V.102, V.103, I.104, Y.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.43, A:T.78, A:G.79, A:V.102, A:I.104 EDO.2: 3 residues within 4Å: Chain A: N.115, R.118 Chain B: S.278 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.278 Water bridges: B:S.278, B:P.279, B:P.279, B:D.281 EDO.4: 12 residues within 4Å: Chain B: F.41, L.43, G.44, F.49, R.57, G.77, T.78, G.79, V.102, V.103, I.104, Y.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.43, B:T.78, B:G.79, B:I.104 EDO.5: 8 residues within 4Å: Chain A: P.275, P.276, A.277, S.278 Chain B: N.115, R.118, Y.119, Q.122 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.115, B:R.118, B:R.118, B:Q.122 EDO.7: 11 residues within 4Å: Chain C: L.43, G.44, F.49, R.57, G.77, T.78, G.79, V.102, V.103, I.104, Y.134 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.43, C:T.78, C:G.79, C:I.104 EDO.8: 7 residues within 4Å: Chain C: H.272, V.273, P.275, A.277, S.278, P.279 Chain D: R.118 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.272 Water bridges: C:V.273 EDO.10: 12 residues within 4Å: Chain D: F.41, L.43, G.44, F.49, R.57, G.77, T.78, G.79, V.102, V.103, I.104, Y.134 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.43, D:T.78, D:G.79, D:I.104 EDO.11: 5 residues within 4Å: Chain C: A.114 Chain D: D.251, L.280, D.281, R.284 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.281, D:D.281, D:R.284 Water bridges: D:N.256, D:S.278, D:S.278, C:S.112

4 x RSH: 3-DEOXY-D-LYXO-HEXONIC ACID(Covalent)

RSH.3: 14 residues within 4Å: Chain A: P.9, F.41, G.44, S.45, G.46, Y.134, F.136, K.163, T.165, G.191, Y.192, I.208, S.209, A.210 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.9, A:K.163 Hydrogen bonds: A:S.45, A:G.46, A:Y.134, A:K.163, A:K.163, A:A.210 Water bridges: A:D.193, A:D.193 Salt bridges: A:K.163 RSH.6: 15 residues within 4Å: Chain B: P.9, F.41, G.44, S.45, G.46, Y.134, F.136, K.163, T.165, G.191, Y.192, I.208, S.209, A.210, F.254 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.9, B:P.9 Hydrogen bonds: B:S.45, B:G.46, B:Y.134, B:K.163, B:T.165, B:A.210 Water bridges: B:D.193, B:D.193 Salt bridges: B:K.163 RSH.9: 15 residues within 4Å: Chain C: P.9, F.41, G.44, S.45, G.46, Y.134, F.136, K.163, T.165, G.191, Y.192, I.208, S.209, A.210, F.254 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:P.9 Hydrogen bonds: C:S.45, C:G.46, C:Y.134, C:K.163, C:T.165, C:A.210 Water bridges: C:D.193, C:D.193 Salt bridges: C:K.163 RSH.12: 14 residues within 4Å: Chain D: P.9, F.41, G.44, S.45, G.46, Y.134, F.136, K.163, T.165, G.191, Y.192, I.208, S.209, A.210 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:P.9, D:P.9 Hydrogen bonds: D:S.45, D:G.46, D:Y.134, D:K.163, D:A.210 Salt bridges: D:K.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhaskar, V. et al., Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis. Proteins (2011)

Release Date

2011-04-13

Peptides

Uncharacterized protein yagE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Uncharacterized protein yagE

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