SMTL ID : 2vws.1

Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-hexamer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: T.27, T.28, A.29, D.56, H.59 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.29, A:D.56, A:D.56, A:D.56 Water bridges: A:D.56, B:Q.55, B:Q.55 Salt bridges: A:H.59 PO4.2: 5 residues within 4Å: Chain A: L.4, L.5, S.6, Q.92, R.131 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.6, A:S.6, A:S.6, A:Q.92 Water bridges: A:R.131, A:R.131 Salt bridges: A:R.131 PO4.3: 6 residues within 4Å: Chain B: T.27, T.28, A.29, D.56, H.59, Q.60 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.29, B:D.56, B:D.56 Salt bridges: B:H.59 Water bridges: C:Q.55 PO4.4: 6 residues within 4Å: Chain C: T.27, T.28, A.29, D.56, H.59, Q.60 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Water bridges: A:Q.55, A:Q.55, C:H.59 Hydrogen bonds: C:A.29, C:D.56, C:D.56 Salt bridges: C:H.59 PO4.7: 5 residues within 4Å: Chain D: T.27, T.28, A.29, D.56, H.59 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:A.29, D:D.56, D:D.56 Water bridges: D:D.56, E:Q.55, E:Q.55 Salt bridges: D:H.59 PO4.8: 5 residues within 4Å: Chain D: L.4, L.5, S.6, Q.92, R.131 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.6, D:S.6, D:S.6, D:Q.92 Water bridges: D:R.131, D:R.131 Salt bridges: D:R.131 PO4.9: 6 residues within 4Å: Chain E: T.27, T.28, A.29, D.56, H.59, Q.60 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:A.29, E:D.56, E:D.56, E:D.56 Salt bridges: E:H.59 Water bridges: F:Q.55, F:Q.55 PO4.10: 6 residues within 4Å: Chain F: T.27, T.28, A.29, D.56, H.59, Q.60 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:A.29, F:D.56, F:D.56, F:D.56 Salt bridges: F:H.59 Water bridges: D:Q.55, D:Q.55

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain C: E.77, G.78, S.79, P.97, M.98, Q.104 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.78, C:P.97 Water bridges: C:Q.104, C:Q.104 GOL.6: 6 residues within 4Å: Chain A: V.122 Chain C: W.23, R.74, Q.151, D.179, L.216 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.74, C:R.74, C:Q.151 GOL.11: 6 residues within 4Å: Chain F: E.77, G.78, S.79, P.97, M.98, Q.104 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.78, F:P.97 Water bridges: F:Q.104 GOL.12: 6 residues within 4Å: Chain D: V.122 Chain F: W.23, R.74, Q.151, D.179, L.216 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.74, F:R.74, F:Q.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rea, D. et al., Crystal Structure and Functional Assignment of Yfau, a Metal Ion Dependent Class II Aldolase from Escherichia Coli K12. Biochemistry (2008)

Release Date

2008-09-09

Peptides

YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE

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