SMTL ID : 3vwq.1

6-aminohexanoate-dimer hydrolase S112A/G181D/R187A/H266N/D370Y mutant complexd with 6-aminohexanoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ACA.1: 12 residues within 4Å: Chain A: M.111, A.112, K.115, D.181, W.186, Y.215, S.217, F.264, N.266, G.344, I.345 Ligands: GOL.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.112, A:W.186 Hydrogen bonds: A:A.112, A:D.181, A:I.345 Water bridges: A:S.217 Salt bridges: A:K.115 ACA.9: 12 residues within 4Å: Chain B: M.111, A.112, K.115, D.181, W.186, Y.215, S.217, F.264, N.266, G.344, I.345 Ligands: GOL.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.112, B:W.186 Hydrogen bonds: B:A.112, B:D.181, B:Y.215, B:I.345 Water bridges: B:S.217 Salt bridges: B:K.115

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: D.159, Q.161, G.306, G.307, S.308, T.327, R.328 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.159, A:Q.161, A:S.308, A:T.327, A:R.328, A:R.328 GOL.3: 3 residues within 4Å: Chain A: Q.79, Y.81, W.374 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.79 GOL.4: 6 residues within 4Å: Chain A: A.47, D.106, R.107, R.251 Chain B: A.37, D.252 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.107, A:R.107, A:R.107, A:R.251, A:R.251, B:D.252 GOL.5: 8 residues within 4Å: Chain A: A.112, Y.215, W.331, I.343, G.344, I.345 Ligands: ACA.1, GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.343 Water bridges: A:Y.215 GOL.6: 8 residues within 4Å: Chain A: D.314, G.316, F.317, W.331, I.343, Y.370, H.375 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.316, A:Y.370 GOL.10: 7 residues within 4Å: Chain B: D.159, Q.161, G.306, G.307, S.308, T.327, R.328 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.159, B:Q.161, B:S.308, B:T.327, B:R.328, B:R.328 GOL.11: 3 residues within 4Å: Chain B: Q.79, Y.81, W.374 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.79 GOL.12: 6 residues within 4Å: Chain A: A.37, D.252 Chain B: A.47, D.106, R.107, R.251 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.107, B:R.107, B:R.107, B:R.251, B:R.251, A:D.252, A:D.252 GOL.13: 8 residues within 4Å: Chain B: A.112, Y.215, W.331, I.343, G.344, I.345 Ligands: ACA.9, GOL.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.215, B:I.343 GOL.14: 8 residues within 4Å: Chain B: D.314, G.316, F.317, W.331, I.343, Y.370, H.375 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.316

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

MES.7: 7 residues within 4Å: Chain A: Y.13, P.30, R.33, W.34, H.38 Chain B: R.99, G.101 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.99, A:H.38 MES.8: 6 residues within 4Å: Chain A: Q.69, L.70, P.71, D.72, R.76, D.384 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.72 Salt bridges: A:R.76, A:D.384 MES.15: 7 residues within 4Å: Chain A: R.99, G.101 Chain B: Y.13, P.30, R.33, W.34, H.38 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.99, B:H.38 MES.16: 6 residues within 4Å: Chain B: Q.69, L.70, P.71, D.72, R.76, D.384 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.72, B:D.72 Salt bridges: B:R.76, B:D.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Negoro, S. et al., Structural, kinetic and theoretical analyses of hydrolase mutants altering in the directionality and equilibrium point of reversible amide-synthetic/hydrolytic reaction. to be published

Release Date

2013-10-16

Peptides

6-aminohexanoate-dimer hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

6-aminohexanoate-dimer hydrolase