SMTL ID : 6slb.1

Crystal structure of isomerase PaaG with trans-3,4-didehydroadipyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-trimer

Ligands

3 x T3D: (~{E})-6-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-6-oxidanylidene-hex-3-enoic acid(Non-covalent)

T3D.1: 19 residues within 4Å: Chain A: L.24, R.58, A.62, G.63, Q.64, D.65, L.66, Y.76, H.79, Y.83, V.104, G.107, A.108, A.130, F.131, I.134, D.139 Chain B: F.246, K.249 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.62, A:Q.64, A:Y.76, A:V.104, A:F.131 Hydrogen bonds: A:A.62, A:Q.64, A:Q.64, A:D.65, A:L.66, A:A.108, B:K.249, B:K.249 Water bridges: A:R.58, A:R.58 Salt bridges: A:R.58, A:H.79 pi-Stacking: B:F.246, B:F.246 T3D.2: 19 residues within 4Å: Chain B: L.24, R.58, A.62, G.63, Q.64, D.65, L.66, Y.76, H.79, Y.83, V.104, G.107, A.108, A.130, F.131, I.134, D.139 Chain C: F.246, K.249 18 PLIP interactions: 4 interactions with chain C, 14 interactions with chain B Hydrogen bonds: C:K.249, C:K.249, B:A.62, B:Q.64, B:Q.64, B:L.66, B:A.108 pi-Stacking: C:F.246, C:F.246 Hydrophobic interactions: B:A.62, B:Q.64, B:Y.76, B:V.104, B:F.131 Water bridges: B:R.58, B:R.58 Salt bridges: B:R.58, B:H.79 T3D.3: 19 residues within 4Å: Chain A: F.246, K.249 Chain C: L.24, R.58, A.62, G.63, Q.64, D.65, L.66, Y.76, H.79, Y.83, V.104, G.107, A.108, A.130, F.131, I.134, D.139 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:A.62, C:Q.64, C:Y.76, C:V.104, C:F.131 Hydrogen bonds: C:A.62, C:Q.64, C:Q.64, C:L.66, C:A.108, A:K.249, A:K.249 Water bridges: C:R.58, C:R.58 Salt bridges: C:R.58, C:H.79 pi-Stacking: A:F.246, A:F.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spieker, M. et al., Structural and Mechanistic Basis of an Oxepin-CoA Forming Isomerase in Bacterial Primary and Secondary Metabolism. Acs Chem.Biol. (2019)

Release Date

2019-12-11

Peptides

Enoyl-CoA hydratase/carnithine racemase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

C
AAA

Enoyl-CoA hydratase/carnithine racemase