SMTL ID : 6lds.1

Structure of a K245A mutant of L-tyrosine decarboxylase from Methanocaldococcus jannaschii complexed with L-Tyr: External aldimine form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.335, K.398, R.399, E.400 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.335, A:N.335, A:R.399 Water bridges: A:K.398, A:K.398 Salt bridges: A:R.399 SO4.2: 2 residues within 4Å: Chain A: I.352, E.353 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.353 SO4.8: 4 residues within 4Å: Chain B: N.335, K.398, R.399, E.400 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.335, B:N.335, B:R.399 Water bridges: B:K.398, B:K.398 Salt bridges: B:R.399 SO4.9: 2 residues within 4Å: Chain B: I.352, E.353 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.353

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: K.125, W.128, R.129 Chain B: D.162 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.129, B:D.162 Water bridges: A:K.125, B:D.162, B:D.162 GOL.4: 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, A:V.190, A:V.190 Water bridges: A:V.190, A:N.219 GOL.5: 8 residues within 4Å: Chain A: I.127, K.131, N.219, I.220, Y.221, D.256, Y.282 Ligands: GOL.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.221, A:Y.282, A:Y.282 Water bridges: A:K.131, A:K.131, A:N.219, A:N.219 GOL.6: 6 residues within 4Å: Chain A: I.127, D.279, G.281, Y.282, Y.285 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.282 GOL.10: 4 residues within 4Å: Chain A: D.162 Chain B: K.125, W.128, R.129 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.129, A:D.162 Water bridges: B:K.125, A:D.162 GOL.11: 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, B:V.190, B:V.190 Water bridges: B:V.190, B:N.219 GOL.12: 8 residues within 4Å: Chain B: I.127, K.131, N.219, I.220, Y.221, D.256, Y.282 Ligands: GOL.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.221, B:Y.282, B:Y.282 Water bridges: B:K.131, B:K.131, B:N.219, B:N.219 GOL.13: 6 residues within 4Å: Chain B: I.127, D.279, G.281, Y.282, Y.285 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.282

2 x 0PR: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tyrosine(Non-covalent)

0PR.7: 26 residues within 4Å: Chain A: S.55, M.56, C.57, G.112, G.113, T.114, N.117, H.151, S.153, F.154, I.196, G.198, T.199, T.200, D.225, A.227, F.228, T.259, D.261, H.263, R.390 Chain B: N.75, D.78, L.81, G.303, T.304 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.55, A:G.113, A:T.114, A:T.114, A:N.117, A:H.151, A:T.200, A:D.225, A:D.261, B:N.75, B:T.304, B:T.304 Water bridges: A:S.111, A:G.112, A:T.114, A:H.263, A:R.390, B:G.303 Salt bridges: A:H.151, A:H.263, A:R.390 pi-Stacking: A:H.151 Hydrophobic interactions: B:D.78 0PR.14: 26 residues within 4Å: Chain A: N.75, D.78, L.81, G.303, T.304 Chain B: S.55, M.56, C.57, G.112, G.113, T.114, N.117, H.151, S.153, F.154, I.196, G.198, T.199, T.200, D.225, A.227, F.228, T.259, D.261, H.263, R.390 24 PLIP interactions: 6 interactions with chain A, 18 interactions with chain B Hydrophobic interactions: A:D.78 Hydrogen bonds: A:N.75, A:D.78, A:T.304, A:T.304, B:S.55, B:G.113, B:T.114, B:T.114, B:N.117, B:H.151, B:T.200, B:D.225, B:D.261 Water bridges: A:G.303, B:S.111, B:G.112, B:T.114, B:H.263, B:R.390 Salt bridges: B:H.151, B:H.263, B:R.390 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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