SMTL ID : 2e8i.2 (1 other biounit)

Structure of 6-aminohexanoate-dimer hydrolase, D1 mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.107, R.251, D.252 Chain B: R.251 Ligands: SO4.10 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.252, A:D.252 Salt bridges: A:R.107, A:R.251, B:R.251 Water bridges: B:R.107, B:R.107, B:R.251, B:R.251 SO4.2: 1 residues within 4Å: Chain A: R.293 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.293 SO4.10: 5 residues within 4Å: Chain A: R.251 Chain B: R.107, R.251, D.252 Ligands: SO4.1 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Water bridges: A:R.107, A:R.107, A:R.251, A:R.251 Salt bridges: A:R.251, B:R.107, B:R.251 Hydrogen bonds: B:D.252, B:D.252 SO4.11: 1 residues within 4Å: Chain B: R.293 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.293

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

MES.3: 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.4: 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: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:R.99, B:R.99 Salt bridges: B:R.99, A:H.38 Hydrogen bonds: A:R.33 MES.12: 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 MES.13: 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 Hydrogen bonds: B:R.33 Salt bridges: B:H.38, A:R.99 Water bridges: A:R.99, A:R.99

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: Y.166, E.168, V.177, Y.215, C.216, S.217, I.345 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.168, A:S.217 Water bridges: A:E.168, A:S.217, A:S.217 GOL.6: 9 residues within 4Å: Chain A: M.111, S.112, K.115, D.181, W.186, H.266, G.267, I.345 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.181, A:H.266 Water bridges: A:S.112, A:S.112, A:S.217 GOL.7: 6 residues within 4Å: Chain A: D.314, G.316, F.317, W.331, D.370, H.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.314 Water bridges: A:G.316, A:D.370, A:H.375 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: P.322, N.335, E.336 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.323, A:E.336, A:E.336 Water bridges: A:T.320, A:N.335 GOL.14: 8 residues within 4Å: Chain B: Y.166, E.168, V.177, Y.215, C.216, S.217, I.345 Ligands: GOL.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.168, B:S.217 Water bridges: B:Y.166, B:S.217 GOL.15: 9 residues within 4Å: Chain B: M.111, S.112, K.115, D.181, W.186, H.266, G.267, I.345 Ligands: GOL.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.181, B:H.266 Water bridges: B:S.112, B:S.112, B:S.217 GOL.16: 6 residues within 4Å: Chain B: D.314, G.316, F.317, W.331, D.370, H.375 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.314 Water bridges: B:G.316, B:D.370 GOL.17: 4 residues within 4Å: Chain B: G.211, E.212, E.310, A.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.310 Water bridges: B:E.212 GOL.18: 3 residues within 4Å: Chain B: P.322, N.335, E.336 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.336 Water bridges: B:T.320, B:N.335

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

2008-01-15

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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