SMTL ID : 6c4r.1

Staphylopine dehydrogenase (SaODH) - Apo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: Q.119, Q.120, L.121, S.122, L.123, L.126, F.148, F.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.119, A:Q.119 GOL.2: 9 residues within 4Å: Chain A: A.245, G.249, T.250, V.252, P.253, V.254, P.358, F.359, Q.361 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.250, A:V.254, A:V.254, A:F.359, A:Q.361 Water bridges: A:T.250, A:T.250 GOL.7: 8 residues within 4Å: Chain B: Q.119, Q.120, L.121, S.122, L.123, L.126, F.148, F.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.119, B:Q.119 GOL.8: 9 residues within 4Å: Chain B: A.245, G.249, T.250, V.252, P.253, V.254, P.358, F.359, Q.361 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.250, B:V.254, B:V.254, B:F.359, B:Q.361 Water bridges: B:T.250, B:T.250

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

SO4.3: 6 residues within 4Å: Chain A: H.131, E.157, H.194, S.197, T.198, M.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.194, A:T.198 SO4.4: 9 residues within 4Å: Chain A: Y.380, A.384, Q.387, L.404, E.408, N.430, L.431, F.432, K.436 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.380, A:E.408 Salt bridges: A:K.436 SO4.5: 8 residues within 4Å: Chain A: N.239, F.241, F.260, P.264, T.266, T.268, L.269 Chain B: E.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.239, A:T.266, A:T.266 Water bridges: A:D.240 SO4.6: 6 residues within 4Å: Chain A: S.228, V.232, M.298, N.302, R.333, Y.334 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.228, A:S.228, A:N.302, A:Y.334 Salt bridges: A:R.333 SO4.9: 6 residues within 4Å: Chain B: H.131, E.157, H.194, S.197, T.198, M.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.194, B:T.198 SO4.10: 9 residues within 4Å: Chain B: Y.380, A.384, Q.387, L.404, E.408, N.430, L.431, F.432, K.436 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.380, B:E.408 Salt bridges: B:K.436 SO4.11: 8 residues within 4Å: Chain A: E.308 Chain B: N.239, F.241, F.260, P.264, T.266, T.268, L.269 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.239, B:T.266, B:T.266 Water bridges: B:D.240 SO4.12: 6 residues within 4Å: Chain B: S.228, V.232, M.298, N.302, R.333, Y.334 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.228, B:S.228, B:N.302, B:Y.334 Salt bridges: B:R.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McFarlane, J.S. et al., Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase. J. Biol. Chem. (2018)

Release Date

2018-04-11

Peptides

Staphylopine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Staphylopine dehydrogenase

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