SMTL ID : 1dka.1

DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: A.95, T.98, P.99, P.100, L.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.98, A:T.98, A:L.102, A:L.102 NA.5: 5 residues within 4Å: Chain B: A.95, T.98, P.99, P.100, L.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.98, B:L.102, B:L.102 NA.9: 5 residues within 4Å: Chain C: A.95, T.98, P.99, P.100, L.102 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.95, C:T.98, C:L.102 NA.13: 5 residues within 4Å: Chain D: A.95, T.98, P.99, P.100, L.102 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.98, D:T.98, D:T.98, D:L.102

4 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: L.78, S.80, T.303, V.305, D.307 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.80, A:T.303, A:V.305, A:D.307, H2O.2 K.6: 5 residues within 4Å: Chain B: L.78, S.80, T.303, V.305, D.307 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.80, B:T.303, B:V.305, B:D.307, H2O.7 K.10: 5 residues within 4Å: Chain C: L.78, S.80, T.303, V.305, D.307 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.80, C:T.303, C:V.305, C:D.307, H2O.13 K.14: 5 residues within 4Å: Chain D: L.78, S.80, T.303, V.305, D.307 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.80, D:T.303, D:V.305, D:D.307, H2O.18

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

PLP.3: 14 residues within 4Å: Chain A: T.110, G.111, A.112, N.115, W.138, H.139, E.210, D.243, A.245, Q.246, K.272 Chain B: T.302, T.303 Ligands: MES.4 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:E.210, A:A.245, A:K.272 Hydrogen bonds: A:T.110, A:G.111, A:A.112, A:N.115, A:Q.246, B:T.303, B:T.303 Water bridges: A:W.138, A:E.210, B:T.303, B:T.303, B:H.304 Salt bridges: A:K.272 pi-Stacking: A:W.138 PLP.7: 14 residues within 4Å: Chain A: T.302, T.303 Chain B: T.110, G.111, A.112, N.115, W.138, H.139, E.210, D.243, A.245, Q.246, K.272 Ligands: MES.8 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:E.210, B:A.245, B:K.272 Hydrogen bonds: B:G.111, B:A.112, B:N.115, B:Q.246, A:T.303, A:T.303, A:T.303 Water bridges: B:T.110, B:W.138, B:E.210, A:T.302, A:H.304 Salt bridges: B:K.272 pi-Stacking: B:W.138 PLP.11: 14 residues within 4Å: Chain C: T.110, G.111, A.112, N.115, W.138, H.139, E.210, D.243, A.245, Q.246, K.272 Chain D: T.302, T.303 Ligands: MES.12 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:E.210, C:A.245, C:K.272 Hydrogen bonds: C:G.111, C:A.112, C:N.115, C:Q.246, D:T.303, D:T.303, D:T.303 Water bridges: C:T.110, C:W.138, C:E.210, D:T.302, D:H.304 Salt bridges: C:K.272 pi-Stacking: C:W.138 PLP.15: 14 residues within 4Å: Chain C: T.302, T.303 Chain D: T.110, G.111, A.112, N.115, W.138, H.139, E.210, D.243, A.245, Q.246, K.272 Ligands: MES.16 17 PLIP interactions: 12 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:E.210, D:A.245, D:K.272 Hydrogen bonds: D:T.110, D:G.111, D:A.112, D:N.115, D:Q.246, C:T.303, C:T.303 Water bridges: D:W.138, D:E.210, C:T.303, C:T.303, C:H.304 Salt bridges: D:K.272 pi-Stacking: D:W.138

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

MES.4: 8 residues within 4Å: Chain A: Q.52, W.138, S.215, Q.246, K.272, R.406 Chain B: Y.301 Ligands: PLP.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.52, A:S.215, A:Q.246 Water bridges: A:S.215, A:R.406, B:Y.301 Salt bridges: A:K.272, A:R.406 pi-Cation interactions: A:W.138 MES.8: 8 residues within 4Å: Chain A: Y.301 Chain B: Q.52, W.138, S.215, Q.246, K.272, R.406 Ligands: PLP.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.52, B:S.215, B:Q.246 Water bridges: B:S.215, B:R.406, A:Y.301 Salt bridges: B:K.272, B:R.406 pi-Cation interactions: B:W.138 MES.12: 8 residues within 4Å: Chain C: Q.52, W.138, S.215, Q.246, K.272, R.406 Chain D: Y.301 Ligands: PLP.11 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.52, C:S.215, C:Q.246 Water bridges: C:S.215, C:R.406, D:Y.301 Salt bridges: C:K.272, C:R.406 pi-Cation interactions: C:W.138 MES.16: 8 residues within 4Å: Chain C: Y.301 Chain D: Q.52, W.138, S.215, Q.246, K.272, R.406 Ligands: PLP.15 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.52, D:S.215, D:Q.246 Water bridges: D:S.215, D:R.406, C:Y.301 Salt bridges: D:K.272, D:R.406 pi-Cation interactions: D:W.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toney, M.D. et al., Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites. Science (1993)

Release Date

1994-10-15

Peptides

2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)

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