SMTL ID : 6jy1.1

Crystal Structure of a Group II pyridoxal dependent decarboxylase, LLP-bound form from Methanocaldococcus jannaschii at 1.72 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: N.335, K.398, R.399 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.335, A:N.335, A:R.399, A:R.399 Water bridges: A:K.398, A:K.398 SO4.2: 2 residues within 4Å: Chain A: D.183, D.187 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.183, A:D.183 SO4.3: 2 residues within 4Å: Chain A: I.352, E.353 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.353 SO4.4: 3 residues within 4Å: Chain A: K.241, K.242, K.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.243 Water bridges: A:K.242, A:K.242 Salt bridges: A:K.242 SO4.5: 1 residues within 4Å: Chain A: Y.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.188 SO4.9: 3 residues within 4Å: Chain B: N.335, K.398, R.399 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.335, B:N.335, B:R.399, B:R.399 Water bridges: B:K.398, B:K.398 SO4.10: 2 residues within 4Å: Chain B: D.183, D.187 No protein-ligand interaction detected (PLIP) SO4.11: 2 residues within 4Å: Chain B: I.352, E.353 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.353 SO4.12: 3 residues within 4Å: Chain B: K.241, K.242, K.243 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.243 Water bridges: B:K.242, B:K.242 Salt bridges: B:K.242 SO4.13: 1 residues within 4Å: Chain B: Y.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.188

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: I.127, D.279, G.281, Y.282, Y.285 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.279 GOL.7: 8 residues within 4Å: Chain A: W.128, K.131, L.136, S.137, N.139, D.189, V.190, D.191 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.131, A:S.137, A:S.137, A:N.139 Water bridges: A:V.190, A:V.190, A:V.190, A:N.219 GOL.8: 7 residues within 4Å: Chain A: I.127, N.219, I.220, Y.221, D.256, Y.282 Ligands: GOL.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.219, A:Y.221, A:D.256, A:Y.282 Water bridges: A:K.131, A:K.131, A:N.219 GOL.14: 6 residues within 4Å: Chain B: I.127, D.279, G.281, Y.282, Y.285 Ligands: GOL.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.279 GOL.15: 8 residues within 4Å: Chain B: W.128, K.131, L.136, S.137, N.139, D.189, V.190, D.191 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.131, B:S.137, B:S.137, B:N.139 Water bridges: B:V.190, B:V.190, B:V.190, B:N.219 GOL.16: 7 residues within 4Å: Chain B: I.127, N.219, I.220, Y.221, D.256, Y.282 Ligands: GOL.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.219, B:Y.221, B:D.256, B:Y.282 Water bridges: B:K.131, B:K.131, B:N.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chellam Gayathri, S. et al., Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase. J.Struct.Biol. (2019)

Release Date

2019-10-30

Peptides

L-tyrosine/L-aspartate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

L-tyrosine/L-aspartate decarboxylase