SMTL ID : 2dcf.1 (1 other biounit)

Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N mutant with substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: A.124, D.127, E.128, K.246, R.293, V.294 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.127, A:E.128, A:V.294 Water bridges: A:K.246 Salt bridges: A:K.246 SO4.2: 2 residues within 4Å: Chain A: R.99, G.101 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.99, A:R.99 Salt bridges: A:R.99

2 x ACA: 6-AMINOHEXANOIC ACID(Non-covalent)

ACA.3: 7 residues within 4Å: Chain A: A.112, Y.170, Y.215, W.331, I.343, I.345 Ligands: ACA.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.215, A:W.331, A:I.345 Hydrogen bonds: A:Y.170, A:I.345 ACA.4: 11 residues within 4Å: Chain A: M.111, A.112, Y.170, V.177, D.181, S.217, F.264, N.266, G.344, I.345 Ligands: ACA.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.112, A:Y.170, A:I.345 Hydrogen bonds: A:A.112, A:D.181, A:I.345 Water bridges: A:S.217

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 6 residues within 4Å: Chain A: Q.69, L.70, P.71, D.72, R.76, D.384 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.72 Water bridges: A:R.387 Salt bridges: A:R.76, A:D.384

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: G.316, F.317, H.375, N.379 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.316, A:N.379, A:N.379 GOL.7: 6 residues within 4Å: Chain A: D.159, R.302, G.306, G.307, T.327, R.328 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.159, A:R.302, A:T.327, A:T.327, A:R.328 GOL.8: 4 residues within 4Å: Chain A: G.211, E.212, E.310, A.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.310 GOL.9: 3 residues within 4Å: Chain A: D.106, R.107, R.251 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.107, A:R.107, A:R.107, A:R.251, A:R.251 Water bridges: A:R.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Negoro, S. et al., Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase. J.Mol.Biol. (2007)

Release Date

2007-01-09

Peptides

6-aminohexanoate-dimer hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

6-aminohexanoate-dimer hydrolase

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