SMTL ID : 5gjo.1

Crystal structure of SrLDC mutant (A225C/T302C) in complex with PLP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.144, L.186, S.187, T.188, A.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.188, A:A.189 Water bridges: A:K.144 Salt bridges: A:K.144 SO4.2: 5 residues within 4Å: Chain A: T.151, G.154 Chain B: K.276, R.278, W.283 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:T.151, A:G.154, B:R.278 Salt bridges: B:R.278 SO4.3: 2 residues within 4Å: Chain A: R.6, H.307 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.6, A:R.6, A:C.308 Salt bridges: A:R.6, A:H.307 SO4.4: 2 residues within 4Å: Chain A: S.8, E.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.9 Water bridges: A:R.6, A:S.8, A:K.10 SO4.10: 4 residues within 4Å: Chain B: K.144, S.187, T.188, A.189 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.187, B:T.188, B:A.189 Water bridges: B:T.188, B:T.188 Salt bridges: B:K.144 SO4.11: 3 residues within 4Å: Chain B: L.7, S.8, E.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.9 Water bridges: B:K.10

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: T.359, R.360, F.361 Chain B: S.355, V.356, A.358 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.356, A:R.360 Water bridges: B:S.355, A:G.363 GOL.12: 6 residues within 4Å: Chain A: S.355, V.356, A.358 Chain B: T.359, R.360, F.361 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.360 Water bridges: B:A.358, A:S.355

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.6: 15 residues within 4Å: Chain A: A.50, K.52, D.71, A.94, L.149, H.180, S.183, G.219, G.220, E.256, P.257, G.258, R.259, Y.353 Chain B: C.324 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.50, A:K.52 Hydrogen bonds: A:Q.184, A:G.220, A:E.256, A:G.258, A:R.259, A:Y.353 Water bridges: A:R.137, A:Y.260, B:C.324 Salt bridges: A:H.180 pi-Stacking: A:H.180 PLP.13: 16 residues within 4Å: Chain A: C.324 Chain B: A.50, K.52, D.71, A.94, R.137, L.149, H.180, S.183, G.219, G.220, E.256, P.257, G.258, R.259, Y.353 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.50, B:K.52 Hydrogen bonds: B:K.52, B:S.183, B:G.220, B:E.256, B:G.258, B:R.259 Water bridges: B:R.137, B:Q.184, B:F.221, B:Y.260, A:C.324 Salt bridges: B:H.180 pi-Stacking: B:H.180

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

NA.7: 3 residues within 4Å: Chain A: V.157, E.158, R.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.157, A:R.200, A:R.200 NA.8: 6 residues within 4Å: Chain A: Y.299 Chain B: S.295, Y.299, S.357, T.359 Ligands: NA.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.357 NA.9: 2 residues within 4Å: Chain A: R.200, D.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.203, A:D.203 NA.14: 6 residues within 4Å: Chain A: S.295, Y.299, S.357, T.359 Chain B: Y.299 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sagong, H.-Y. et al., Lysine Decarboxylase with an Enhanced Affinity for Pyridoxal 5-Phosphate by Disulfide Bond-Mediated Spatial Reconstitution. PLoS ONE (2017)

Release Date

2017-05-10

Peptides

Lysine/ornithine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine/ornithine decarboxylase