SMTL ID : 8vb3.1

Dienelactone hydrolase from Solimonas fluminis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

7 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 10 residues within 4Å: Chain A: E.23, H.28, V.75, D.76, I.77, W.104, R.107, A.111, F.133, C.137 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.75, A:A.111, A:F.133 Hydrogen bonds: A:E.23, A:R.107, A:R.107 MPD.2: 4 residues within 4Å: Chain A: R.61, R.64, D.235, W.239 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.64, A:R.64 Hydrogen bonds: A:R.61, A:D.235 MPD.3: 6 residues within 4Å: Chain A: T.22, G.25, Q.26, R.27 Chain B: E.113, L.114 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.22, B:E.113 Hydrogen bonds: A:T.22 Water bridges: B:A.110 MPD.7: 10 residues within 4Å: Chain B: E.23, H.28, V.75, D.76, L.97, W.104, R.107, A.111, F.133, C.137 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.75, B:L.97, B:A.111, B:F.133 Hydrogen bonds: B:E.23, B:R.107, B:R.107 Water bridges: B:A.111 MPD.8: 5 residues within 4Å: Chain B: R.61, R.64, D.235, R.236, W.239 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.64, B:W.239 MPD.11: 5 residues within 4Å: Chain A: N.24 Chain B: E.23, N.24, A.106, R.107 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.23, B:A.106, B:R.107, A:N.24 Hydrogen bonds: B:E.23, B:A.106 MPD.12: 7 residues within 4Å: Chain B: P.43, L.68, G.69, Y.70, R.125, A.247, F.250 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.70, B:A.247 Hydrogen bonds: B:R.125

5 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: F.84, Q.85, D.86, Q.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.85, A:D.86, A:D.86 NA.5: 4 residues within 4Å: Chain A: R.116, A.117, Q.118, V.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.118 Water bridges: A:A.123 NA.6: 2 residues within 4Å: Chain A: S.144, K.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.144 NA.9: 1 residues within 4Å: Chain B: S.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.144 NA.10: 4 residues within 4Å: Chain B: R.116, A.117, Q.118, V.121 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.116, B:V.121 Water bridges: B:A.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schnettler Fernandez, J.D.F. et al., Metal-independent organophosphate hydrolysis in a protein family possessing a catalytic triad. To Be Published

Release Date

2024-12-18

Peptides

Dienelactone hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dienelactone hydrolase