SMTL ID : 1dge.1 (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-tetramer

Ligands

8 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 RB.9: 5 residues within 4Å: Chain C: A.94, T.97, P.98, P.99, L.101 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:A.94, C:T.97, C:P.98, C:L.101 RB.10: 5 residues within 4Å: Chain C: L.77, S.79, T.302, V.304, D.306 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:L.77, C:S.79, C:T.302, C:V.304, C:D.306 RB.13: 5 residues within 4Å: Chain D: A.94, T.97, P.98, P.99, L.101 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:A.94, D:T.97, D:P.98, D:L.101 RB.14: 5 residues within 4Å: Chain D: L.77, S.79, T.302, V.304, D.306 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:L.77, D:S.79, D:T.302, D:V.304, D:D.306

4 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 C: T.301, T.302 Ligands: MES.4 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain C 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, C:T.302, C:T.302, C:T.302 Water bridges: A:W.137, A:T.141, A:E.209, C:H.303 Salt bridges: A:K.271 pi-Stacking: A:W.137 PLP.7: 14 residues within 4Å: Chain B: T.109, G.110, A.111, N.114, W.137, H.138, E.209, D.242, A.244, Q.245, K.271 Chain D: T.301, T.302 Ligands: MES.8 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:E.209, B:K.271 Hydrogen bonds: B:T.109, B:T.109, B:G.110, B:A.111, B:N.114, B:Q.245, D:T.302, D:T.302, D:T.302 Water bridges: B:W.137, B:T.141, B:E.209, D:H.303 Salt bridges: B:K.271 pi-Stacking: B:W.137 PLP.11: 14 residues within 4Å: Chain A: T.301, T.302 Chain C: T.109, G.110, A.111, N.114, W.137, H.138, E.209, D.242, A.244, Q.245, K.271 Ligands: MES.12 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain C Hydrogen bonds: A:T.302, A:T.302, A:T.302, C:T.109, C:G.110, C:A.111, C:N.114, C:Q.245, C:K.271 Water bridges: A:T.301, A:H.303, C:T.109, C:W.137, C:T.141, C:E.209 Hydrophobic interactions: C:E.209, C:K.271 Salt bridges: C:K.271 pi-Stacking: C:W.137 PLP.15: 14 residues within 4Å: Chain B: T.301, T.302 Chain D: T.109, G.110, A.111, N.114, W.137, H.138, E.209, D.242, A.244, Q.245, K.271 Ligands: MES.16 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:E.209, D:K.271 Hydrogen bonds: D:T.109, D:G.110, D:A.111, D:N.114, D:Q.245, D:K.271, B:T.302, B:T.302, B:T.302 Water bridges: D:T.109, D:W.137, D:T.141, D:E.209, B:T.301, B:H.303 Salt bridges: D:K.271 pi-Stacking: D:W.137

4 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 C: Y.300 Ligands: PLP.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.51, A:S.214, A:Q.245 Water bridges: A:S.214, A:R.405, C:Y.300 Salt bridges: A:K.271, A:R.405 pi-Cation interactions: A:W.137 MES.8: 8 residues within 4Å: Chain B: Q.51, W.137, S.214, Q.245, K.271, R.405 Chain D: Y.300 Ligands: PLP.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.51, B:S.214, B:Q.245 Water bridges: B:S.214, B:R.405, D:Y.300 Salt bridges: B:K.271, B:R.405 pi-Cation interactions: B:W.137 MES.12: 8 residues within 4Å: Chain A: Y.300 Chain C: Q.51, W.137, S.214, Q.245, K.271, R.405 Ligands: PLP.11 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.51, C:S.214, C:Q.245 Water bridges: C:S.214, C:R.405, A:Y.300 Salt bridges: C:K.271, C:R.405 pi-Cation interactions: C:W.137 MES.16: 8 residues within 4Å: Chain B: Y.300 Chain D: Q.51, W.137, S.214, Q.245, K.271, R.405 Ligands: PLP.15 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.51, D:S.214, D:Q.245 Water bridges: D:S.214, D:R.405, B:Y.300 Salt bridges: D:K.271, D:R.405 pi-Cation interactions: D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

DIALKYLGLYCINE DECARBOXYLASE

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