SMTL ID : 6m4y.1

Structure of a R371A mutant of a Group II PLP dependent decarboxylase from Methanocaldococcus jannaschii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: N.335, K.398, R.399 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.335, A:R.399 Water bridges: A:E.400 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: 3 residues within 4Å: Chain A: Y.319 Chain B: S.29, E.30 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.30, A:Y.319, A:Y.319 SO4.4: 2 residues within 4Å: Chain A: I.352, E.353 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.353 Water bridges: A:E.353 SO4.7: 3 residues within 4Å: Chain B: N.335, K.398, R.399 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.335, B:R.399 Water bridges: B:E.400 SO4.8: 2 residues within 4Å: Chain B: D.183, D.187 No protein-ligand interaction detected (PLIP) SO4.9: 3 residues within 4Å: Chain A: S.29, E.30 Chain B: Y.319 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.319, B:Y.319, A:E.30, A:E.30 SO4.10: 2 residues within 4Å: Chain B: I.352, E.353 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.353 Water bridges: B:E.353, B:E.353, B:E.353

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: N.59, V.60, L.61, P.62, H.267, I.328, P.395 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.59, A:V.60 Water bridges: A:N.59, A:H.267 GOL.6: 8 residues within 4Å: Chain A: W.128, K.131, S.137, N.139, D.189, V.190, D.191, I.220 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.131, A:S.137, A:S.137, A:N.139, A:V.190, A:V.190 GOL.11: 7 residues within 4Å: Chain B: N.59, V.60, L.61, P.62, H.267, I.328, P.395 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.59, B:V.60 Water bridges: B:N.59, B:H.267 GOL.12: 8 residues within 4Å: Chain B: W.128, K.131, S.137, N.139, D.189, V.190, D.191, I.220 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.131, B:S.137, B:S.137, B:N.139, B:V.190, B:V.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gayathri, S.C. et al., Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases. J.Mol.Biol. (2020)

Release Date

2020-12-02

Peptides

L-tyrosine/L-aspartate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

L-tyrosine/L-aspartate decarboxylase