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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: A.95, T.98, P.99, 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.2: 5 residues within 4Å: Chain A: L.78, S.80, V.305, S.306, D.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.78, A:D.307 NA.5: 4 residues within 4Å: Chain B: A.95, T.98, P.99, L.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.98, B:T.98, B:L.102 NA.6: 5 residues within 4Å: Chain B: L.78, S.80, V.305, S.306, D.307 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.78, B:V.305

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

PLP.3: 15 residues within 4Å: Chain A: T.110, G.111, A.112, N.115, W.138, H.139, G.140, E.210, D.243, A.245, Q.246, K.272 Chain B: T.302, T.303 Ligands: MES.4 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.210, A:A.245, A:K.272 Hydrogen bonds: A:G.111, A:A.112, A:N.115, A:Q.246, B:T.303, B:T.303 Water bridges: A:W.138, A:M.141, A:T.142, B:T.303, B:H.304 Salt bridges: A:K.272 pi-Stacking: A:W.138 PLP.7: 15 residues within 4Å: Chain A: T.302, T.303 Chain B: T.110, G.111, A.112, N.115, W.138, H.139, G.140, E.210, D.243, A.245, Q.246, K.272 Ligands: MES.8 19 PLIP interactions: 14 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, B:K.272, A:T.303, A:T.303, A:T.303 Water bridges: B:T.110, B:W.138, B:M.141, B:T.142, A:E.113, A:H.304 Salt bridges: B:K.272 pi-Stacking: B:W.138

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

MES.4: 9 residues within 4Å: Chain A: Q.52, W.138, A.152, S.215, Q.246, K.272, R.406 Chain B: Y.301 Ligands: PLP.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.52, A:S.215, A:Q.246 Water bridges: A:Q.52, A:W.138, A:S.215, A:K.272, A:R.406 Salt bridges: A:K.272, A:R.406 MES.8: 9 residues within 4Å: Chain A: Y.301 Chain B: Q.52, W.138, A.152, S.215, Q.246, K.272, R.406 Ligands: PLP.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.52, B:S.215, B:Q.246 Water bridges: B:Q.52, B:W.138, B:S.215, B:K.272, B:R.406 Salt bridges: B:K.272, B:R.406

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): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)

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