SMTL ID : 1dge.2 (1 other biounit)

AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

4 x RB: RUBIDIUM ION(Non-covalent)

RB.1: 5 residues within 4Å: Chain A: A.94, T.97, P.98, P.99, L.101 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:A.94, A:T.97, A:P.98, A:L.101 RB.2: 5 residues within 4Å: Chain A: L.77, S.79, T.302, V.304, D.306 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:L.77, A:S.79, A:T.302, A:V.304, A:D.306 RB.5: 5 residues within 4Å: Chain B: A.94, T.97, P.98, P.99, L.101 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:A.94, B:T.97, B:P.98, B:L.101 RB.6: 5 residues within 4Å: Chain B: L.77, S.79, T.302, V.304, D.306 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:L.77, B:S.79, B:T.302, B:V.304, B:D.306

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.3: 14 residues within 4Å: Chain A: T.109, G.110, A.111, N.114, W.137, H.138, E.209, D.242, A.244, Q.245, K.271 Chain B: T.301, T.302 Ligands: MES.4 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.209, A:K.271 Hydrogen bonds: A:T.109, A:T.109, A:G.110, A:A.111, A:N.114, A:Q.245, B:T.302, B:T.302, B:T.302 Water bridges: A:W.137, A:T.141, A:E.209, B:H.303 Salt bridges: A:K.271 pi-Stacking: A:W.137 PLP.7: 14 residues within 4Å: Chain A: T.301, T.302 Chain B: T.109, G.110, A.111, N.114, W.137, H.138, E.209, D.242, A.244, Q.245, K.271 Ligands: MES.8 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:E.209, B:K.271 Hydrogen bonds: B:T.109, B:G.110, B:A.111, B:N.114, B:Q.245, B:K.271, A:T.302, A:T.302, A:T.302 Water bridges: B:T.109, B:W.137, B:T.141, B:E.209, A:T.301, A:H.303 Salt bridges: B:K.271 pi-Stacking: B:W.137

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 8 residues within 4Å: Chain A: Q.51, W.137, S.214, Q.245, K.271, R.405 Chain B: Y.300 Ligands: PLP.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.51, A:S.214, A:Q.245 Water bridges: A:S.214, A:R.405, B:Y.300 Salt bridges: A:K.271, A:R.405 pi-Cation interactions: A:W.137 MES.8: 8 residues within 4Å: Chain A: Y.300 Chain B: Q.51, W.137, S.214, Q.245, K.271, R.405 Ligands: PLP.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.51, B:S.214, B:Q.245 Water bridges: B:S.214, B:R.405, A:Y.300 Salt bridges: B:K.271, B:R.405 pi-Cation interactions: B:W.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hohenester, E. et al., An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase. Biochemistry (1994)

Release Date

1994-09-30

Peptides

DIALKYLGLYCINE DECARBOXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DIALKYLGLYCINE DECARBOXYLASE

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