SMTL ID : 6eqo.1

Tri-functional propionyl-CoA synthase of Erythrobacter sp. NAP1 with bound NADP+ and phosphomethylphosphonic acid adenylate ester

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.1: 20 residues within 4Å: Chain A: T.440, W.485, I.486, T.487, C.564, A.565, E.566, P.567, N.586, S.587, Y.588, W.589, A.590, T.591, D.722, L.734, R.737, N.743, G.746, R.748 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.440, A:I.486, A:T.487, A:S.587, A:W.589, A:T.591, A:T.591, A:Q.720, A:D.722, A:R.737 Salt bridges: A:R.748 pi-Stacking: A:Y.588 ACP.3: 14 residues within 4Å: Chain B: C.564, A.565, E.566, P.567, N.586, S.587, Y.588, W.589, A.590, T.591, D.722, L.734, R.737, R.748 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.586, B:S.587, B:S.587, B:W.589, B:T.591, B:T.591, B:D.722, B:R.737, B:R.748 pi-Stacking: B:Y.588, B:Y.588

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 25 residues within 4Å: Chain A: F.1300, W.1304, L.1414, N.1415, T.1418, G.1439, T.1442, G.1443, T.1444, L.1462, V.1463, S.1464, R.1468, R.1483, H.1531, A.1532, A.1536, Y.1553, S.1556, S.1557, W.1752, H.1769, L.1770, N.1811, H.1813 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.1414, A:T.1418, A:T.1444 Hydrogen bonds: A:W.1304, A:T.1418, A:T.1442, A:T.1444, A:S.1464, A:S.1464, A:R.1468, A:H.1531, A:Y.1553, A:S.1556, A:S.1557, A:L.1770, A:N.1811, A:N.1811 Water bridges: A:F.1300, A:F.1300, A:G.1439 Salt bridges: A:R.1468, A:R.1483, A:H.1813 pi-Stacking: A:Y.1553 pi-Cation interactions: A:R.1483, A:R.1483 NAP.4: 25 residues within 4Å: Chain B: F.1300, W.1304, L.1414, N.1415, T.1418, G.1439, T.1442, G.1443, T.1444, L.1462, V.1463, S.1464, R.1468, R.1483, H.1531, A.1532, A.1536, Y.1553, S.1556, S.1557, W.1752, H.1769, L.1770, N.1811, H.1813 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:L.1414, B:T.1418, B:T.1444 Hydrogen bonds: B:W.1304, B:N.1415, B:T.1442, B:T.1442, B:T.1444, B:L.1462, B:S.1464, B:R.1468, B:H.1531, B:Y.1553, B:S.1556, B:S.1557, B:L.1770, B:N.1811 Water bridges: B:F.1300, B:F.1300 Salt bridges: B:R.1468, B:R.1483, B:H.1813 pi-Stacking: B:Y.1553 pi-Cation interactions: B:R.1483, B:R.1483

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bernhardsgrutter, I. et al., The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite. Nat. Chem. Biol. (2018)

Release Date

2018-10-24

Peptides

Acetyl-coenzyme A synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetyl-coenzyme A synthetase