SMTL ID : 1pt8.1

Crystal structure of the yfdW gene product of E. coli, in complex with oxalate and acetyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x OXL: OXALATE ION(Non-covalent)

OXL.1: 5 residues within 4Å: Chain A: G.270, Q.271, P.272 Chain B: Q.69, L.70 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.69, B:L.70, A:E.247 Hydrogen bonds: A:Q.271 OXL.6: 5 residues within 4Å: Chain A: Q.69, L.70 Chain B: G.270, Q.271, P.272 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.271 Water bridges: A:L.70

2 x ACO: ACETYL COENZYME *A(Covalent)(Non-covalent)

ACO.2: 22 residues within 4Å: Chain A: V.37, Q.38, S.39, R.59, Y.80, L.93, N.94, T.95, K.96, N.117, F.118, H.119, A.122, I.145, K.158, A.159, Y.160, E.161, D.190, M.221 Chain B: Q.294, Q.296 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.37, A:Q.38, A:K.158, A:Y.160 Hydrogen bonds: A:S.39, A:S.39, A:L.93, A:T.95, A:N.117, A:N.117, A:H.119, A:A.159, B:Q.296 Salt bridges: A:K.96, A:H.119, A:H.119, A:K.158 ACO.7: 24 residues within 4Å: Chain A: G.269, G.270, Q.294 Chain B: V.37, S.39, R.59, Y.80, L.93, N.94, T.95, K.96, N.117, F.118, H.119, A.122, I.145, K.146, G.147, K.158, A.159, Y.160, E.161, D.190, M.221 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.37, B:K.158, B:Y.160, B:Y.160 Hydrogen bonds: B:S.39, B:L.93, B:T.95, B:N.117, B:N.117, B:H.119, B:A.159, B:A.159, B:E.161, A:Q.294 Water bridges: B:R.59 Salt bridges: B:K.96, B:H.119, B:H.119, B:K.158 pi-Cation interactions: B:R.59

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: T.24, W.49, P.402, D.403 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.49, A:D.403 Water bridges: A:A.48, A:N.87, A:K.405 GOL.4: 7 residues within 4Å: Chain A: E.116, I.123, D.124, F.142, S.144, K.146, R.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.124, A:S.144, A:R.216 GOL.5: 6 residues within 4Å: Chain A: R.71, D.72, I.73, P.74 Chain B: L.242, Y.244 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.244 Water bridges: A:R.71 GOL.8: 4 residues within 4Å: Chain A: F.176 Chain B: F.176, G.179, P.180 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:F.176 Hydrogen bonds: B:D.178 GOL.9: 6 residues within 4Å: Chain B: T.24, A.48, W.49, N.87, P.402, D.403 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.403, B:D.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gruez, A. et al., The crystal structure of the Escherichia coli yfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases. J.Biol.Chem. (2003)

Release Date

2003-09-09

Peptides

Hypothetical protein yfdW: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hypothetical protein yfdW

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