SMTL ID : 3k5p.1

Crystal structure of amino acid-binding ACT: D-isomer specific 2-hydroxyacid dehydrogenase catalytic domain from Brucella melitensis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: R.152, D.210, K.235, K.236, G.237, A.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.152, A:R.152, A:D.210, A:G.237 EDO.5: 6 residues within 4Å: Chain B: R.152, D.210, K.235, K.236, G.237, A.238 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.152, B:R.152, B:D.210, B:G.237 EDO.9: 6 residues within 4Å: Chain C: R.152, D.210, K.235, K.236, G.237, A.238 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.152, C:R.152, C:G.237 EDO.13: 6 residues within 4Å: Chain D: R.152, D.210, K.235, K.236, G.237, A.238 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.152, D:R.152, D:G.237

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: V.162, Y.185, D.186, T.187, V.216, P.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.187 GOL.3: 8 residues within 4Å: Chain A: F.111, S.112, N.113, T.114, R.115, Q.170, R.308 Chain C: R.155 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:F.111, A:R.115, A:Q.170, A:R.308, C:R.155, C:R.155 GOL.4: 9 residues within 4Å: Chain A: P.339, R.340, P.341, T.342, G.343, T.344, R.345, E.388, Y.416 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.340, A:E.388 Water bridges: A:A.389 GOL.6: 6 residues within 4Å: Chain B: V.162, Y.185, D.186, T.187, V.216, P.217 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.187 GOL.7: 8 residues within 4Å: Chain B: F.111, S.112, N.113, T.114, R.115, Q.170, R.308 Chain D: R.155 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:R.155, D:R.155, B:F.111, B:R.115, B:Q.170, B:R.308 GOL.8: 9 residues within 4Å: Chain B: P.339, R.340, P.341, T.342, G.343, T.344, R.345, E.388, Y.416 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.340, B:E.388 Water bridges: B:A.389 GOL.10: 6 residues within 4Å: Chain C: V.162, Y.185, D.186, T.187, V.216, P.217 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.187 GOL.11: 8 residues within 4Å: Chain A: R.155 Chain C: F.111, S.112, N.113, T.114, R.115, Q.170, R.308 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:F.111, C:R.115, C:Q.170, C:R.308, A:R.155, A:R.155 GOL.12: 9 residues within 4Å: Chain C: P.339, R.340, P.341, T.342, G.343, T.344, R.345, E.388, Y.416 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.340, C:E.388 Water bridges: C:A.389, C:Y.416 GOL.14: 6 residues within 4Å: Chain D: V.162, Y.185, D.186, T.187, V.216, P.217 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.187 GOL.15: 8 residues within 4Å: Chain B: R.155 Chain D: F.111, S.112, N.113, T.114, R.115, Q.170, R.308 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:R.155, B:R.155, D:F.111, D:R.115, D:Q.170, D:R.308 GOL.16: 9 residues within 4Å: Chain D: P.339, R.340, P.341, T.342, G.343, T.344, R.345, E.388, Y.416 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.340, D:E.388 Water bridges: D:A.389, D:Y.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, T.E. et al., Crystal structure of amino acid-binding ACT: D-isomer specific 2-hydroxyacid dehydrogenase catalytic domain from Brucella melitensis. To be Published

Release Date

2009-11-03

Peptides

D-3-phosphoglycerate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

D-3-phosphoglycerate dehydrogenase