SMTL ID : 3ca8.1 (1 other biounit)

Crystal structure of Escherichia coli YdcF, an S-adenosyl-L-methionine utilizing enzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.92, R.96, T.100 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.92, A:R.96 SO4.2: 5 residues within 4Å: Chain A: H.73, N.125, C.126, M.155, R.158 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:C.126 Water bridges: A:H.73, A:S.74, A:G.127, A:R.158, A:R.218, A:R.218 Salt bridges: A:H.73, A:R.158 SO4.3: 2 residues within 4Å: Chain A: R.220, K.251 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.247 Salt bridges: A:R.220, A:K.251 SO4.4: 4 residues within 4Å: Chain A: D.221, D.222, S.223, R.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.223 Salt bridges: A:R.229

7 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 4 residues within 4Å: Chain A: P.49, D.52, A.53, G.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.49, A:G.181 MPD.6: 9 residues within 4Å: Chain A: A.46, V.47, F.77, S.80, A.81, Q.84, W.203, P.204, R.207 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.47, A:W.203 MPD.7: 4 residues within 4Å: Chain A: R.131, I.134, N.138, M.166 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.166 Hydrogen bonds: A:R.131 MPD.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPD.9: 4 residues within 4Å: Chain A: H.87, Y.88, F.109, W.110 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.87, A:Y.88, A:F.109, A:W.110 MPD.10: 8 residues within 4Å: Chain A: L.137, N.138, V.144, H.145, A.147, T.167, R.175, W.176 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.137, A:V.144, A:A.147, A:T.167, A:W.176 Hydrogen bonds: A:R.175 MPD.11: 2 residues within 4Å: Chain A: F.132, A.135 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.132, A:A.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chao, K.L. et al., The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes. Proteins (2008)

Release Date

2008-05-06

Peptides

Protein ydcF: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein ydcF

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