SMTL ID : 2vbg.1

The complex structure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis with 2R-1-hydroxyethyl-deazaThDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.452, I.477, N.479, G.481 Ligands: R1T.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.452, A:G.481, H2O.15 MG.3: 4 residues within 4Å: Chain B: D.452, N.479, G.481 Ligands: R1T.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.452, B:G.481, H2O.33

2 x R1T: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

R1T.2: 23 residues within 4Å: Chain A: G.401, T.402, G.425, S.426, I.427, G.451, D.452, G.453, S.454, L.457, N.479, G.481, Y.482, T.483, V.484, E.485, I.488 Chain B: P.47, G.48, E.72, V.97, H.136 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.427, A:L.457, A:Y.482, A:V.484, A:I.488 Hydrogen bonds: A:T.402, A:G.425, A:G.425, A:I.427, A:G.451, A:G.453, A:S.454, A:N.479, A:T.483, A:V.484 Water bridges: A:S.403, A:D.452, A:S.454, A:S.454, A:N.479 R1T.4: 22 residues within 4Å: Chain A: P.47, G.48, E.72, V.97, H.136 Chain B: G.401, T.402, G.425, S.426, I.427, G.451, D.452, G.453, S.454, L.457, N.479, G.481, Y.482, T.483, V.484, E.485 Ligands: MG.3 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.427, B:L.457, B:Y.482, B:V.484 Hydrogen bonds: B:T.402, B:G.425, B:G.425, B:I.427, B:G.451, B:G.453, B:S.454, B:N.479, B:T.483, B:T.483, B:V.484 Water bridges: B:S.403, B:D.452, B:S.454, B:S.454, B:N.479, A:E.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berthold, C.L. et al., Crystal Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) from Lactococcus Lactis Provides Insights Into the Structural Basis for the Chemo- and Enantioselective Carboligation Reaction. Acta Crystallogr.,Sect.D (2007)

Release Date

2007-11-27

Peptides

BRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

BRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE

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