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

Crystal structure of dialkylglycine decarboxylase bound with cesium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x CS: CESIUM ION(Non-covalent)

CS.1: 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 CS.5: 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.10 CS.9: 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.17 CS.13: 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.24

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

NA.2: 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.6: 4 residues within 4Å: Chain B: A.95, T.98, P.99, L.102 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.98, B:T.98, B:T.98, B:L.102 NA.10: 4 residues within 4Å: Chain C: A.95, T.98, P.99, L.102 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.98, C:L.102, C:L.102 NA.14: 4 residues within 4Å: Chain D: A.95, T.98, P.99, L.102 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.95, D:T.98, D:L.102

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

MES.3: 9 residues within 4Å: Chain A: Q.52, W.138, A.152, S.215, Q.246, K.272, V.396, R.406 Ligands: PLP.4 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.52, A:S.215, A:Q.246 Water bridges: A:S.215, A:K.272, C:Y.301 Salt bridges: A:K.272, A:R.406 MES.7: 9 residues within 4Å: Chain B: Q.52, W.138, A.152, S.215, Q.246, K.272, V.396, R.406 Ligands: PLP.8 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.52, B:S.215, B:Q.246 Water bridges: B:S.215, B:K.272, D:Y.301 Salt bridges: B:K.272, B:R.406 MES.11: 9 residues within 4Å: Chain C: Q.52, W.138, A.152, S.215, Q.246, K.272, V.396, R.406 Ligands: PLP.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.52, C:S.215, C:Q.246 Water bridges: C:S.215, C:R.406 Salt bridges: C:K.272, C:R.406 MES.15: 9 residues within 4Å: Chain D: Q.52, W.138, A.152, S.215, Q.246, K.272, V.396, R.406 Ligands: PLP.16 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.52, D:S.215, D:Q.246 Water bridges: D:S.215, D:R.406 Salt bridges: D:K.272, D:R.406

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

PLP.4: 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 C: T.302, T.303 Ligands: MES.3 16 PLIP interactions: 3 interactions with chain C, 13 interactions with chain A Hydrogen bonds: C:T.303, C:T.303, A:T.110, A:T.110, A:G.111, A:A.112, A:N.115, A:Q.246 Water bridges: C:H.304, A:W.138, A:E.210, A:K.272 Hydrophobic interactions: A:E.210, A:K.272 Salt bridges: A:K.272 pi-Stacking: A:W.138 PLP.8: 15 residues within 4Å: 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 Chain D: T.302, T.303 Ligands: MES.7 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:E.210, B:K.272 Hydrogen bonds: B:T.110, B:T.110, B:G.111, B:A.112, B:N.115, B:Q.246, D:T.303, D:T.303 Water bridges: B:W.138, B:E.210, B:K.272, D:H.304 Salt bridges: B:K.272 pi-Stacking: B:W.138 PLP.12: 15 residues within 4Å: Chain A: T.302, T.303 Chain C: 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.11 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:E.210, C:K.272 Hydrogen bonds: C:T.110, C:G.111, C:A.112, C:N.115, C:Q.246, A:T.303, A:T.303, A:T.303 Water bridges: C:T.110, C:W.138, C:E.210, A:H.304 Salt bridges: C:K.272 pi-Stacking: C:W.138 PLP.16: 15 residues within 4Å: Chain B: T.302, T.303 Chain D: 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.15 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:E.210, D:K.272 Hydrogen bonds: D:T.110, D:G.111, D:A.112, D:N.115, D:Q.246, B:T.303, B:T.303, B:T.303 Water bridges: D:T.110, D:W.138, D:E.210, B:H.304 Salt bridges: D:K.272 pi-Stacking: D:W.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., Crystal structures of dialkylglycine decarboxylase bound with cesium ion and calcium ion. To be Published

Release Date

2006-08-08

Peptides

2,2-dialkylglycine decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

2,2-dialkylglycine decarboxylase

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