SMTL ID : 6ldt.1

K245A mutant of L-tyrosine decarboxylase from Methanocaldococcus jannaschii complexed with a post-decarboxylation quinonoid-like intermediate formed with L-tyrosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: I.127, D.279, G.281, Y.282, Y.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.281 GOL.2: 4 residues within 4Å: Chain A: K.125, W.128, R.129 Chain B: D.162 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:D.162, B:D.162 Hydrogen bonds: A:R.129 GOL.3: 7 residues within 4Å: Chain A: W.128, K.131, S.137, N.139, D.189, V.190, D.191 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.131, A:K.131, A:N.139, A:V.190, A:D.191 Water bridges: A:D.189 GOL.6: 5 residues within 4Å: Chain B: I.127, D.279, G.281, Y.282, Y.285 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.281 GOL.7: 4 residues within 4Å: Chain A: D.162 Chain B: K.125, W.128, R.129 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.129 Water bridges: A:D.162 GOL.8: 7 residues within 4Å: Chain B: W.128, K.131, S.137, N.139, D.189, V.190, D.191 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.131, B:K.131, B:N.139, B:D.189, B:V.190, B:D.191 Water bridges: B:D.189

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

SO4.4: 3 residues within 4Å: Chain A: N.335, K.398, R.399 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.335, A:N.335, A:R.399 Water bridges: A:R.399 Salt bridges: A:R.399 SO4.9: 3 residues within 4Å: Chain B: N.335, K.398, R.399 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.335, B:N.335, B:R.399 Water bridges: B:R.399 Salt bridges: B:R.399

2 x EBR: [(4Z)-4-[[(Z)-2-(4-hydroxyphenyl)ethylideneamino]methylidene]-6-methyl-5-oxidanyl-1H-pyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

EBR.5: 18 residues within 4Å: Chain A: S.55, M.56, C.57, G.112, G.113, T.114, N.117, H.151, G.198, T.200, D.225, A.227, D.261, H.263 Chain B: N.75, D.78, L.81, T.304 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:M.56, B:D.78 Hydrogen bonds: A:S.55, A:G.113, A:T.114, A:T.114, A:N.117, A:T.200, A:D.225, B:N.75, B:T.304, B:T.304, B:T.304 Water bridges: A:S.55, A:S.111, A:G.112, A:T.114, A:H.151, B:G.303 Salt bridges: A:H.263 pi-Stacking: A:H.151 EBR.10: 18 residues within 4Å: Chain A: N.75, D.78, L.81, T.304 Chain B: S.55, M.56, C.57, G.112, G.113, T.114, N.117, H.151, G.198, T.200, D.225, A.227, D.261, H.263 23 PLIP interactions: 16 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:M.56, A:D.78 Hydrogen bonds: B:S.55, B:G.113, B:T.114, B:N.117, B:T.200, B:D.225, A:N.75, A:D.78, A:T.304, A:T.304, A:T.304 Water bridges: B:S.55, B:S.111, B:G.112, B:T.114, B:T.114, B:T.114, B:H.151, A:G.303 Salt bridges: B:H.263 pi-Stacking: B:H.151

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

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

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