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

Crystal Structure of 6-Aminohexanoate-dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 1 residues within 4Å: Chain A: R.205 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.205 Salt bridges: A:R.205 SO4.2: 5 residues within 4Å: Chain A: R.107, R.251, D.252 Chain B: R.251 Ligands: SO4.15 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:R.50, A:D.252 Salt bridges: B:R.251, A:R.107, A:R.251 Hydrogen bonds: A:D.252, A:D.252 SO4.3: 6 residues within 4Å: Chain A: A.124, D.127, E.128, K.246, R.293, V.294 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.127, A:E.128, A:V.294 Water bridges: A:K.246, A:K.246 Salt bridges: A:K.246 SO4.4: 1 residues within 4Å: Chain A: R.293 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.293 SO4.5: 4 residues within 4Å: Chain A: L.70, P.71, D.72, R.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.72, A:D.72 Salt bridges: A:R.76 SO4.14: 1 residues within 4Å: Chain B: R.205 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.205 Salt bridges: B:R.205 SO4.15: 5 residues within 4Å: Chain A: R.251 Chain B: R.107, R.251, D.252 Ligands: SO4.2 7 PLIP interactions: 4 interactions with chain B, 3 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.50, A:R.251 SO4.16: 6 residues within 4Å: Chain B: A.124, D.127, E.128, K.246, R.293, V.294 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.294 Water bridges: B:K.246, B:K.246 Salt bridges: B:K.246 SO4.17: 1 residues within 4Å: Chain B: R.293 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.293 SO4.18: 4 residues within 4Å: Chain B: L.70, P.71, D.72, R.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.72, B:D.72 Salt bridges: B:R.76

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

ACA.6: 11 residues within 4Å: Chain A: A.112, Y.170, Y.215, F.317, W.331, I.343, I.345, Y.370, H.375 Ligands: ACA.7, GOL.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.331, A:I.343 Hydrogen bonds: A:Y.170, A:I.345, A:Y.370 Salt bridges: A:H.375 ACA.7: 11 residues within 4Å: Chain A: M.111, A.112, Y.170, D.181, Y.215, S.217, F.264, N.266, G.344, I.345 Ligands: ACA.6 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.19: 11 residues within 4Å: Chain B: A.112, Y.170, Y.215, F.317, W.331, I.343, I.345, Y.370, H.375 Ligands: ACA.20, GOL.22 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.331, B:I.343 Hydrogen bonds: B:Y.170, B:Y.215, B:I.345 Salt bridges: B:H.375 ACA.20: 11 residues within 4Å: Chain B: M.111, A.112, Y.170, D.181, Y.215, S.217, F.264, N.266, G.344, I.345 Ligands: ACA.19 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.8: 7 residues within 4Å: Chain A: R.99, G.101 Chain B: Y.13, P.30, R.33, 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 MES.21: 7 residues within 4Å: Chain A: Y.13, P.30, R.33, 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

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: E.168, Y.170, Y.215, D.314, W.331 Ligands: ACA.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.170 GOL.10: 8 residues within 4Å: Chain A: L.155, D.159, Q.161, G.306, G.307, S.308, T.327, R.328 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.161, A:G.306, A:S.308, A:T.327, A:R.328, A:R.328 Water bridges: A:Q.161, A:S.308 GOL.11: 3 residues within 4Å: Chain A: T.91, V.93, R.274 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.91, A:R.274 Water bridges: A:V.93, A:R.278 GOL.12: 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.13: 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.22: 6 residues within 4Å: Chain B: E.168, Y.170, Y.215, D.314, W.331 Ligands: ACA.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.170, B:Y.170 Water bridges: B:D.314 GOL.23: 8 residues within 4Å: Chain B: L.155, D.159, Q.161, G.306, G.307, S.308, T.327, R.328 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.161, B:G.306, B:S.308, B:T.327, B:R.328, B:R.328 Water bridges: B:Q.161, B:S.308 GOL.24: 3 residues within 4Å: Chain B: T.91, V.93, R.274 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.91, B:R.274 Water bridges: B:V.93, B:R.278 GOL.25: 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.26: 4 residues within 4Å: Chain A: A.37 Chain B: D.106, R.107, R.251 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.107, B:R.107, B:R.107, B:R.251, B:R.251 Water bridges: B:R.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawashima, Y. et al., Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold. Febs J. (2009)

Release Date

2009-04-07

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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