SMTL ID : 6ldr.1

Structure of a K245A mutant of a Group II PLP dependent decarboxylase from Methanocaldococcus jannaschii, in complex with PLP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 19 residues within 4Å: Chain A: M.56, G.112, G.113, T.114, N.117, H.151, S.153, I.196, G.198, T.199, T.200, D.225, A.227, F.228, T.259, D.261, H.263 Chain B: G.303, T.304 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:T.304, B:T.304, A:G.113, A:T.114, A:T.114, A:T.114, A:N.117, A:T.200 Water bridges: B:G.303, B:G.303, A:E.115, A:H.263, A:H.263 Salt bridges: A:H.263 pi-Stacking: A:H.151 PLP.6: 19 residues within 4Å: Chain A: G.303, T.304 Chain B: M.56, G.112, G.113, T.114, N.117, H.151, S.153, I.196, G.198, T.199, T.200, D.225, A.227, F.228, T.259, D.261, H.263 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.113, B:T.114, B:T.114, B:T.114, B:N.117, B:T.200, A:T.304, A:T.304 Water bridges: B:E.115, B:H.263, B:H.263, A:G.303, A:G.303 Salt bridges: B:H.263 pi-Stacking: B:H.151

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.2: 7 residues within 4Å: Chain A: G.54, S.55, M.56, C.57 Chain B: N.75, D.78, L.81 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.55, B:N.75 Water bridges: A:S.55 NH4.7: 7 residues within 4Å: Chain A: N.75, D.78, L.81 Chain B: G.54, S.55, M.56, C.57 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.55, A:N.75, A:D.78 Water bridges: B:S.55

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: I.127, D.279, G.281, Y.282, Y.285 No protein-ligand interaction detected (PLIP) 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.8: 5 residues within 4Å: Chain B: I.127, D.279, G.281, Y.282, Y.285 No protein-ligand interaction detected (PLIP) GOL.9: 8 residues within 4Å: Chain B: W.128, K.131, L.136, S.137, N.139, D.189, V.190, D.191 9 PLIP interactions: 9 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:D.189, B:V.190, B:N.219

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

SO4.5: 4 residues within 4Å: Chain A: N.335, K.398, R.399, E.400 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.335, A:N.335, A:R.399 Water bridges: A:K.398, A:K.398, A:K.398, A:R.399 Salt bridges: A:R.399 SO4.10: 4 residues within 4Å: Chain B: N.335, K.398, R.399, E.400 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.335, B:N.335, B:R.399 Water bridges: B:K.398, B:K.398, B:K.398, B:R.399 Salt bridges: B:R.399

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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