SMTL ID : 1pt7.1

Crystal structure of the apo-form of the yfdW gene product of E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: Y.80, Y.160, E.161, D.190 Chain B: G.267, G.269 Ligands: PO4.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.161, B:G.267 Water bridges: A:Q.38, A:Y.80, A:D.190, B:G.269 PO4.2: 10 residues within 4Å: Chain A: V.37, V.65, Q.69, Y.80, Y.160 Chain B: G.269, G.270, Q.271 Ligands: PO4.1, PO4.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.69, A:Y.80, A:Y.80, A:Y.80, B:G.270, B:Q.271 PO4.3: 7 residues within 4Å: Chain A: V.37, V.65, Q.69, Y.160 Chain B: Q.271, Q.294 Ligands: PO4.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.160, A:Y.160, B:Q.271 PO4.4: 5 residues within 4Å: Chain A: H.343, L.360, E.364, D.368 Chain B: Y.154 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.364, A:D.368, A:D.368, B:Y.154, B:Y.154 Salt bridges: A:H.343 PO4.6: 10 residues within 4Å: Chain A: G.269, G.270, Q.271 Chain B: V.37, V.65, Q.69, Y.80, Y.160 Ligands: PO4.7, PO4.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.270, A:Q.271, B:Q.69, B:Y.80 PO4.7: 7 residues within 4Å: Chain A: G.267, G.269 Chain B: Y.80, Y.160, E.161, D.190 Ligands: PO4.6 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.80, B:Y.80, B:E.161 Water bridges: B:Q.38, B:D.190, B:D.190, A:G.269, A:Q.271 PO4.8: 6 residues within 4Å: Chain A: Q.271, Q.294 Chain B: V.37, Q.69, Y.160 Ligands: PO4.6 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.271, A:Q.294, B:Q.69, B:Y.160 PO4.9: 5 residues within 4Å: Chain A: Y.154 Chain B: H.343, L.360, E.364, D.368 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.364, B:D.368, B:D.368 Salt bridges: B:H.343

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: A.48, W.49, G.51, N.87, P.402, D.403 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.403, A:D.403 Water bridges: A:T.24, A:A.48 GOL.10: 5 residues within 4Å: Chain B: A.48, W.49, G.51, P.402, D.403 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.49, B:D.403 Water bridges: B:A.48, B:N.87, B:K.405

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

Related Entries With Identical Sequence