SMTL ID : 5gxd.1

Structure of acryloyl-CoA lyase PrpE from Dinoroseobacter shibae DFL 12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 16 residues within 4Å: Chain A: V.285, G.365, E.366, R.367, D.386, H.387, W.388, W.389, Q.390, T.391, D.478, I.490, R.493, N.499, R.504 Ligands: AKR.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:T.239, A:G.365, A:H.387, A:H.387, A:W.389, A:Q.390, A:T.391, A:T.391, A:T.391, A:T.391, A:D.478, A:R.493, A:N.499 Water bridges: A:V.285, A:A.368, A:A.368, A:D.478 Salt bridges: A:R.504 pi-Stacking: A:W.388, A:W.388

1 x AKR: ACRYLIC ACID(Non-covalent)

AKR.2: 8 residues within 4Å: Chain A: W.284, V.285, V.286, G.502, H.503, R.504 Ligands: AMP.1, COA.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.284, A:V.285, A:V.286 Hydrogen bonds: A:R.504

1 x COA: COENZYME A(Non-covalent)

COA.3: 24 residues within 4Å: Chain A: F.140, G.141, G.142, E.168, R.171, V.173, S.280, D.281, W.284, V.286, K.308, P.309, A.333, T.335, A.339, A.364, A.501, H.503, K.533, R.563, P.568, V.569, K.573 Ligands: AKR.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.335, A:A.339, A:A.501 Hydrogen bonds: A:E.168, A:E.168, A:R.171, A:D.281, A:K.308 Water bridges: A:Y.175, A:H.503, A:R.563, A:P.568, A:V.569 Salt bridges: A:R.171, A:K.308, A:H.503, A:K.533, A:K.533, A:R.563, A:K.573

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: R.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.69 Water bridges: A:N.66, A:V.70 GOL.5: 8 residues within 4Å: Chain A: E.147, V.150, Y.238, T.239, G.241, T.242, P.246, K.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.147, A:R.151, A:T.239, A:K.247 GOL.6: 2 residues within 4Å: Chain A: R.171, R.563 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.171, A:R.563 Water bridges: A:R.171 GOL.7: 4 residues within 4Å: Chain A: Q.23, A.24, D.26, R.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.26, A:R.60 Water bridges: A:Q.23 GOL.8: 3 residues within 4Å: Chain A: I.135, H.232, P.233 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y.Z. et al., Structure of acryloyl-CoA lyase PrpE from Dinoroseobacter shibae DFL 12. To Be Published

Release Date

2017-09-20

Peptides

AMP-dependent synthetase and ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

AMP-dependent synthetase and ligase