SMTL ID : 3vwm.1

Crystal structure of 6-aminohexanoate-dimer hydrolase G181D/R187A/H266N/D370Y mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: L.155, D.159, Q.161, G.306, G.307, S.308, T.327, R.328 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.161, A:G.306, A:S.308, A:T.327, A:R.328 Water bridges: A:R.328, A:R.328 GOL.2: 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.3: 5 residues within 4Å: Chain A: A.47, D.106, R.107, R.251 Chain B: A.37 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.106, A:R.107, A:R.107 Water bridges: A:R.107, A:R.251, B:A.37 GOL.4: 10 residues within 4Å: Chain A: M.111, S.112, D.181, W.186, S.217, F.264, N.266, G.267, I.345 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.112, A:S.217 Water bridges: A:S.112, A:H.180, A:D.181 GOL.5: 8 residues within 4Å: Chain A: Y.166, E.168, Y.215, C.216, S.217, I.345 Ligands: GOL.4, MES.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.217, A:S.217 Water bridges: A:S.112, A:H.180 GOL.11: 8 residues within 4Å: Chain B: L.155, D.159, Q.161, G.306, G.307, S.308, T.327, R.328 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.161, B:G.306, B:S.308, B:T.327, B:R.328 Water bridges: B:R.328, B:R.328 GOL.12: 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.13: 5 residues within 4Å: Chain A: A.37 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:D.106, B:D.106, B:R.107, B:R.107 Water bridges: B:R.107, A:A.37, A:D.252 GOL.14: 10 residues within 4Å: Chain B: M.111, S.112, D.181, W.186, S.217, F.264, N.266, G.267, I.345 Ligands: GOL.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.112, B:S.217 Water bridges: B:S.112, B:H.180, B:D.181 GOL.15: 8 residues within 4Å: Chain B: Y.166, E.168, Y.215, C.216, S.217, I.345 Ligands: GOL.14, MES.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.217, B:S.217 Water bridges: B:S.112, B:H.180

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

MES.6: 11 residues within 4Å: Chain A: S.112, Y.215, G.316, F.317, W.331, I.343, G.344, I.345, Y.370, H.375 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.112, A:Y.215, A:I.345 Water bridges: A:S.112, A:I.343, A:Q.348 MES.7: 7 residues within 4Å: Chain A: Y.13, P.30, R.33, W.34, H.38 Chain B: R.99, G.101 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:W.34, B:R.99, B:R.99 Salt bridges: A:H.38, B:R.99 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.16: 11 residues within 4Å: Chain B: S.112, Y.215, G.316, F.317, W.331, I.343, G.344, I.345, Y.370, H.375 Ligands: GOL.15 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.112, B:Y.215, B:Y.215, B:I.345 Water bridges: B:S.112, B:I.343, B:Q.348, B:H.375 MES.17: 7 residues within 4Å: Chain A: R.99, G.101 Chain B: Y.13, P.30, R.33, W.34, H.38 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:W.34, A:R.99, A:R.99 Salt bridges: B:H.38, A:R.99 MES.18: 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

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

SO4.9: 5 residues within 4Å: Chain A: R.107, R.251, D.252 Chain B: R.251 Ligands: SO4.19 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Water bridges: B:R.107, B:R.107, B:R.251, B:R.251 Salt bridges: B:R.251, A:R.107, A:R.251 Hydrogen bonds: A:D.252, A:D.252 SO4.10: 1 residues within 4Å: Chain A: R.293 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.293 SO4.19: 5 residues within 4Å: Chain A: R.251 Chain B: R.107, R.251, D.252 Ligands: SO4.9 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.252, B:D.252 Salt bridges: B:R.107, B:R.251, A:R.251 Water bridges: A:R.107, A:R.107, A:R.251, A:R.251 SO4.20: 1 residues within 4Å: Chain B: R.293 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.293

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