SMTL ID : 2dcf.2 (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

homo-dimer

Ligands

4 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: 4 residues within 4Å: Chain A: R.99, G.101 Chain B: W.34, H.38 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:R.99, A:R.99 Salt bridges: A:R.99, B:H.38 SO4.10: 6 residues within 4Å: Chain B: A.124, D.127, E.128, K.246, R.293, V.294 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.294 Water bridges: B:K.246 Salt bridges: B:K.246 SO4.11: 4 residues within 4Å: Chain A: W.34, H.38 Chain B: R.99, G.101 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:H.38, B:R.99 Water bridges: B:R.99, B:R.99

4 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 ACA.12: 7 residues within 4Å: Chain B: A.112, Y.170, Y.215, W.331, I.343, I.345 Ligands: ACA.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.215, B:W.331, B:I.345 Hydrogen bonds: B:Y.170, B:Y.215, B:I.345 ACA.13: 11 residues within 4Å: Chain B: M.111, A.112, Y.170, V.177, D.181, S.217, F.264, N.266, G.344, I.345 Ligands: ACA.12 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.112, B:Y.170, B:I.345 Hydrogen bonds: B:A.112, B:D.181, B:I.345 Water bridges: B:S.217

2 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 MES.14: 6 residues within 4Å: Chain B: Q.69, L.70, P.71, D.72, R.76, D.384 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.72, B:D.72 Water bridges: B:R.387 Salt bridges: B:R.76, B:D.384

8 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: 4 residues within 4Å: Chain A: D.106, R.107, R.251 Chain B: A.37 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 GOL.15: 4 residues within 4Å: Chain B: G.316, F.317, H.375, N.379 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.316, B:H.375, B:N.379, B:N.379 GOL.16: 6 residues within 4Å: Chain B: D.159, R.302, G.306, G.307, T.327, R.328 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.159, B:R.302, B:T.327, B:T.327, B:R.328 Water bridges: B:D.159 GOL.17: 4 residues within 4Å: Chain B: G.211, E.212, E.310, A.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.310 GOL.18: 4 residues within 4Å: Chain A: A.37 Chain B: D.106, R.107, R.251 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.106, B:R.107, B:R.107, B:R.107, B:R.251, B:R.251 Water bridges: B:R.107, A:D.252

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

6-aminohexanoate-dimer hydrolase

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